Sample records for dynamics simulation reactivator
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Ultrafast impact dynamics of reactive materials (Dlott)
2013-04-16
Kalia, A. Nakano, B. E. Hohman, and K. L. McNesby, Multimillion atom reactive simulations of nanostructured energetic materials, J. Propul. Power 23...34Materials for Energy Applications - Experiment, Modeling and Simulations ", Mar. 2011, Los Angeles, CA. 7. (invited) Studium Conference on in situ...intermetallics. 7,20-24 The dynamics of conventional reactive materials containing micron to millimeter particles are usually viewed within a
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NASA Astrophysics Data System (ADS)
Macedo-Filho, A.; Alves, G. A.; Costa Filho, R. N.; Alves, T. F. A.
2018-04-01
We investigated the susceptible-infected-susceptible model on a square lattice in the presence of a conjugated field based on recently proposed reactivating dynamics. Reactivating dynamics consists of reactivating the infection by adding one infected site, chosen randomly when the infection dies out, avoiding the dynamics being trapped in the absorbing state. We show that the reactivating dynamics can be interpreted as the usual dynamics performed in the presence of an effective conjugated field, named the reactivating field. The reactivating field scales as the inverse of the lattice number of vertices n, which vanishes at the thermodynamic limit and does not affect any scaling properties including ones related to the conjugated field.
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Adaptive accelerated ReaxFF reactive dynamics with validation from simulating hydrogen combustion.
Cheng, Tao; Jaramillo-Botero, Andrés; Goddard, William A; Sun, Huai
2014-07-02
We develop here the methodology for dramatically accelerating the ReaxFF reactive force field based reactive molecular dynamics (RMD) simulations through use of the bond boost concept (BB), which we validate here for describing hydrogen combustion. The bond order, undercoordination, and overcoordination concepts of ReaxFF ensure that the BB correctly adapts to the instantaneous configurations in the reactive system to automatically identify the reactions appropriate to receive the bond boost. We refer to this as adaptive Accelerated ReaxFF Reactive Dynamics or aARRDyn. To validate the aARRDyn methodology, we determined the detailed sequence of reactions for hydrogen combustion with and without the BB. We validate that the kinetics and reaction mechanisms (that is the detailed sequences of reactive intermediates and their subsequent transformation to others) for H2 oxidation obtained from aARRDyn agrees well with the brute force reactive molecular dynamics (BF-RMD) at 2498 K. Using aARRDyn, we then extend our simulations to the whole range of combustion temperatures from ignition (798 K) to flame temperature (2998K), and demonstrate that, over this full temperature range, the reaction rates predicted by aARRDyn agree well with the BF-RMD values, extrapolated to lower temperatures. For the aARRDyn simulation at 798 K we find that the time period for half the H2 to form H2O product is ∼538 s, whereas the computational cost was just 1289 ps, a speed increase of ∼0.42 trillion (10(12)) over BF-RMD. In carrying out these RMD simulations we found that the ReaxFF-COH2008 version of the ReaxFF force field was not accurate for such intermediates as H3O. Consequently we reoptimized the fit to a quantum mechanics (QM) level, leading to the ReaxFF-OH2014 force field that was used in the simulations.
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NASA Astrophysics Data System (ADS)
Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.
2018-05-01
Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.
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Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai
2018-06-13
An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.
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The Reactivation of Motion influences Size Categorization in a Visuo-Haptic Illusion.
Rey, Amandine E; Dabic, Stephanie; Versace, Remy; Navarro, Jordan
2016-09-01
People simulate themselves moving when they view a picture, read a sentence, or simulate a situation that involves motion. The simulation of motion has often been studied in conceptual tasks such as language comprehension. However, most of these studies investigated the direct influence of motion simulation on tasks inducing motion. This article investigates whether a mo- tion induced by the reactivation of a dynamic picture can influence a task that did not require motion processing. In a first phase, a dynamic picture and a static picture were systematically presented with a vibrotactile stimulus (high or low frequency). The second phase of the experiment used a priming paradigm in which a vibrotactile stimulus was presented alone and followed by pictures of objects. Participants had to categorize objects as large or small relative to their typical size (simulated size). Results showed that when the target object was preceded by the vibrotactile stimulus previously associated with the dynamic picture, participants perceived all the objects as larger and categorized them more quickly when the objects were typically "large" and more slowly when the objects were typically "small." In light of embodied cognition theories, this bias in participants' perception is assumed to be caused by an induced forward motion. generated by the reactivated dynamic picture, which affects simulation of the size of the objects.
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Ashraf, Chowdhury; Jain, Abhishek; Xuan, Yuan; van Duin, Adri C T
2017-02-15
In this paper, we present the first atomistic-scale based method for calculating ignition front propagation speed and hypothesize that this quantity is related to laminar flame speed. This method is based on atomistic-level molecular dynamics (MD) simulations with the ReaxFF reactive force field. Results reported in this study are for supercritical (P = 55 MPa and T u = 1800 K) combustion of hydrocarbons as elevated pressure and temperature are required to accelerate the dynamics for reactive MD simulations. These simulations are performed for different types of hydrocarbons, including alkyne, alkane, and aromatic, and are able to successfully reproduce the experimental trend of reactivity of these hydrocarbons. Moreover, our results indicate that the ignition front propagation speed under supercritical conditions has a strong dependence on equivalence ratio, similar to experimentally measured flame speeds at lower temperatures and pressures which supports our hypothesis that ignition front speed is a related quantity to laminar flame speed. In addition, comparisons between results obtained from ReaxFF simulation and continuum simulations performed under similar conditions show good qualitative, and reasonable quantitative agreement. This demonstrates that ReaxFF based MD-simulations are a promising tool to study flame speed/ignition front speed in supercritical hydrocarbon combustion.
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NASA Astrophysics Data System (ADS)
Shan, Tzu-Ray; Wixom, Ryan R.; Thompson, Aidan P.
2016-08-01
In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed by coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. The formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.
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Diffusional correlations among multiple active sites in a single enzyme.
Echeverria, Carlos; Kapral, Raymond
2014-04-07
Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.
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NASA Astrophysics Data System (ADS)
Marcolongo, Juan P.; Zeida, Ari; Semelak, Jonathan A.; Foglia, Nicolás O.; Morzan, Uriel N.; Estrin, Dario A.; González Lebrero, Mariano C.; Scherlis, Damián A.
2018-03-01
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
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NASA Astrophysics Data System (ADS)
Tejada, I. G.; Brochard, L.; Stoltz, G.; Legoll, F.; Lelièvre, T.; Cancès, E.
2015-01-01
Molecular dynamics is a simulation technique that can be used to study failure in solids, provided the inter-atomic potential energy is able to account for the complex mechanisms at failure. Reactive potentials fitted on ab initio results or on experimental values have the ability to adapt to any complex atomic arrangement and, therefore, are suited to simulate failure. But the complexity of these potentials, together with the size of the systems considered, make simulations computationally expensive. In order to improve the efficiency of numerical simulations, simpler harmonic potentials can be used instead of complex reactive potentials in the regions where the system is close to its ground state and a harmonic approximation reasonably fits the actual reactive potential. However the validity and precision of such an approach has not been investigated in detail yet. We present here a methodology for constructing a reduced potential and combining it with the reactive one. We also report some important features of crack propagation that may be affected by the coupling of reactive and reduced potentials. As an illustrative case, we model a crystalline two-dimensional material (graphene) with a reactive empirical bond-order potential (REBO) or with harmonic potentials made of bond and angle springs that are designed to reproduce the second order approximation of REBO in the ground state. We analyze the consistency of this approximation by comparing the mechanical behavior and the phonon spectra of systems modeled with these potentials. These tests reveal when the anharmonicity effects appear. As anharmonic effects originate from strain, stress or temperature, the latter quantities are the basis for establishing coupling criteria for on the fly substitution in large simulations.
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Hu, Xiao Liang; Ciaglia, Riccardo; Pietrucci, Fabio; Gallet, Grégoire A; Andreoni, Wanda
2014-06-19
We introduce a new ab initio derived reactive potential for the simulation of CdTe within density functional theory (DFT) and apply it to calculate both static and dynamical properties of a number of systems (bulk solid, defective structures, liquid, surfaces) at finite temperature. In particular, we also consider cases with low sulfur concentration (CdTe:S). The analysis of DFT and classical molecular dynamics (MD) simulations performed with the same protocol leads to stringent performance tests and to a detailed comparison of the two schemes. Metadynamics techniques are used to empower both Car-Parrinello and classical molecular dynamics for the simulation of activated processes. For the latter, we consider surface reconstruction and sulfur diffusion in the bulk. The same procedures are applied using previously proposed force fields for CdTe and CdTeS materials, thus allowing for a detailed comparison of the various schemes.
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Shan, Tzu -Ray; Wixom, Ryan R.; Thompson, Aidan P.
2016-08-01
In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed bymore » coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. Furthermore, the formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Shan, Tzu -Ray; Wixom, Ryan R.; Thompson, Aidan P.
In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed bymore » coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. Furthermore, the formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.« less
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Mogo, César; Brandão, João
2014-06-30
READY (REActive DYnamics) is a program for studying reactive dynamic systems using a global potential energy surface (PES) built from previously existing PESs corresponding to each of the most important elementary reactions present in the system. We present an application to the combustion dynamics of a mixture of hydrogen and oxygen using accurate PESs for all the systems involving up to four oxygen and hydrogen atoms. Results at the temperature of 4000 K and pressure of 2 atm are presented and compared with model based on rate constants. Drawbacks and advantages of this approach are discussed and future directions of research are pointed out. Copyright © 2014 Wiley Periodicals, Inc.
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NASA Astrophysics Data System (ADS)
Olney, Karl L.
The dynamic behavior of granular/porous and laminate reactive materials is of interest due to their practical applications; reactive structural components, reactive fragments, etc. The mesostructural properties control meso- and macro-scale dynamic behavior of these heterogeneous composites including the behavior during the post-critical stage of deformation. They heavily influence mechanisms of fragment generation and the in situ development of local hot spots, which act as sites of ignition in these materials. This dissertation concentrates on understanding the mechanisms of plastic strain accommodation in two representative reactive material systems with different heterogeneous mesostructrues: Aluminum-Tungsten granular/porous and Nickel-Aluminum laminate composites. The main focus is on the interpretation of results of the following dynamic experiments conducted at different strain and strain rates: drop weight tests, explosively expanded ring experiments, and explosively collapsed thick walled cylinder experiments. Due to the natural limitations in the evaluation of the mesoscale behavior of these materials experimentally and the large variation in the size scales between the mesostructural level and the sample, it is extremely difficult, if not impossible, to examine the mesoscale behavior in situ. Therefore, numerical simulations of the corresponding experiments are used as the main tool to explore material behavior at the mesoscale. Numerical models were developed to elucidate the mechanisms of plastic strain accommodation and post critical behavior in these heterogeneous composites subjected to dynamic loading. These simulations were able to reproduce the qualitative and quantitative features that were observable in the experiments and provided insight into the evolution of the mechanisms of plastic strain accommodation and post critical behavior in these materials with complex mesotructure. Additionally, these simulations provided a framework to examine the influence of various mesoscale properties such as the bonding of interfaces, the role of material properties, and the influence of mesoscale geometry. The results of this research are helpful in the design of material mesotructures conducive to the desirable behavior under dynamic loading.
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Lattice Boltzmann simulation of CO2 reactive transport in network fractured media
NASA Astrophysics Data System (ADS)
Tian, Zhiwei; Wang, Junye
2017-08-01
Carbon dioxide (CO2) geological sequestration plays an important role in mitigating CO2 emissions for climate change. Understanding interactions of the injected CO2 with network fractures and hydrocarbons is key for optimizing and controlling CO2 geological sequestration and evaluating its risks to ground water. However, there is a well-known, difficult process in simulating the dynamic interaction of fracture-matrix, such as dynamic change of matrix porosity, unsaturated processes in rock matrix, and effect of rock mineral properties. In this paper, we develop an explicit model of the fracture-matrix interactions using multilayer bounce-back treatment as a first attempt to simulate CO2 reactive transport in network fractured media through coupling the Dardis's LBM porous model for a new interface treatment. Two kinds of typical fracture networks in porous media are simulated: straight cross network fractures and interleaving network fractures. The reaction rate and porosity distribution are illustrated and well-matched patterns are found. The species concentration distribution and evolution with time steps are also analyzed and compared with different transport properties. The results demonstrate the capability of this model to investigate the complex processes of CO2 geological injection and reactive transport in network fractured media, such as dynamic change of matrix porosity.
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The ReaxFF reactive force-field: Development, applications, and future directions
Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; ...
2016-03-04
The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFFmore » method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less
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NASA Astrophysics Data System (ADS)
Sellers, Michael S.; Lísal, Martin; Schweigert, Igor; Larentzos, James P.; Brennan, John K.
2017-01-01
In discrete particle simulations, when an atomistic model is coarse-grained, a tradeoff is made: a boost in computational speed for a reduction in accuracy. The Dissipative Particle Dynamics (DPD) methods help to recover lost accuracy of the viscous and thermal properties, while giving back a relatively small amount of computational speed. Since its initial development for polymers, one of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. In 2007, Maillet, Soulard, and Stoltz introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We present an extended and generalized version of the DPD-RX method, and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Demonstration simulations of reacting RDX are performed under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its transition to hot product gases within DPD-RX is presented. Additionally, we discuss several examples of the effect of shock speed and microstructure on the corresponding material chemistry.
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Guo, Feng; Cheng, Xin-lu; Zhang, Hong
2012-04-12
Which is the first step in the decomposition process of nitromethane is a controversial issue, proton dissociation or C-N bond scission. We applied reactive force field (ReaxFF) molecular dynamics to probe the initial decomposition mechanisms of nitromethane. By comparing the impact on (010) surfaces and without impact (only heating) for nitromethane simulations, we found that proton dissociation is the first step of the pyrolysis of nitromethane, and the C-N bond decomposes in the same time scale as in impact simulations, but in the nonimpact simulation, C-N bond dissociation takes place at a later time. At the end of these simulations, a large number of clusters are formed. By analyzing the trajectories, we discussed the role of the hydrogen bond in the initial process of nitromethane decompositions, the intermediates observed in the early time of the simulations, and the formation of clusters that consisted of C-N-C-N chain/ring structures.
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NASA Astrophysics Data System (ADS)
Zhao, T.; Shi, L.; Zhang, Y. T.; Zou, L.; Zhang, L.
2017-10-01
Atmospheric pressure non-equilibrium plasmas have attracted significant attention and have been widely used to inactivate pathogens, yet the mechanisms underlying the interactions between plasma-generated species and bio-organisms have not been elucidated clearly. In this paper, reactive molecular dynamics simulations are employed to investigate the mechanisms of interactions between reactive oxygen plasma species (O, OH, and O2) and β-1,6-glucan (a model for the C. albicans cell wall) from a microscopic point of view. Our simulations show that O and OH species can break structurally important C-C and C-O bonds, while O2 molecules exhibit only weak, non-bonded interactions with β-1,6-glucan. Hydrogen abstraction from hydroxyl or CH groups occurs first in all bond cleavage mechanisms. This is followed by a cascade of bond cleavage and double bond formation events. These lead to the destruction of the fungal cell wall. O and OH have similar effects related to their bond cleavage mechanisms. Our simulation results provide fundamental insights into the mechanisms underlying the interactions between reactive oxygen plasma species and the fungal cell wall of C. albicans at the atomic level.
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Gooseff, M.N.; Bencala, K.E.; Scott, D.T.; Runkel, R.L.; McKnight, Diane M.
2005-01-01
The transient storage model (TSM) has been widely used in studies of stream solute transport and fate, with an increasing emphasis on reactive solute transport. In this study we perform sensitivity analyses of a conservative TSM and two different reactive solute transport models (RSTM), one that includes first-order decay in the stream and the storage zone, and a second that considers sorption of a reactive solute on streambed sediments. Two previously analyzed data sets are examined with a focus on the reliability of these RSTMs in characterizing stream and storage zone solute reactions. Sensitivities of simulations to parameters within and among reaches, parameter coefficients of variation, and correlation coefficients are computed and analyzed. Our results indicate that (1) simulated values have the greatest sensitivity to parameters within the same reach, (2) simulated values are also sensitive to parameters in reaches immediately upstream and downstream (inter-reach sensitivity), (3) simulated values have decreasing sensitivity to parameters in reaches farther downstream, and (4) in-stream reactive solute data provide adequate data to resolve effective storage zone reaction parameters, given the model formulations. Simulations of reactive solutes are shown to be equally sensitive to transport parameters and effective reaction parameters of the model, evidence of the control of physical transport on reactive solute dynamics. Similar to conservative transport analysis, reactive solute simulations appear to be most sensitive to data collected during the rising and falling limb of the concentration breakthrough curve. ?? 2005 Elsevier Ltd. All rights reserved.
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Dynamical footprint of cross-reactivity in a human autoimmune T-cell receptor
NASA Astrophysics Data System (ADS)
Kumar, Amit; Delogu, Francesco
2017-02-01
The present work focuses on the dynamical aspects of cross-reactivity between myelin based protein (MBP) self-peptide and two microbial peptides (UL15, PMM) for Hy.1B11 T-cell receptor (TCR). This same TCR was isolated from a patient suffering from multiple sclerosis (MS). The study aims at highlighting the chemical interactions underlying recognition mechanisms between TCR and the peptides presented by Major Histocompatibility Complex (MHC) proteins, which form a crucial component in adaptive immune response against foreign antigens. Since the ability of a TCR to recognize different peptide antigens presented by MHC depends on its cross-reactivity, we used molecular dynamics methods to obtain atomistic detail on TCR-peptide-MHC complexes. Our results show how the dynamical basis of Hy.1B11 TCR’s cross-reactivity is rooted in a similar bridging interaction pattern across the TCR-peptide-MHC interface. Our simulations confirm the importance of TCR CDR3α E98 residue interaction with MHC and a predominant role of P6 peptide residue in MHC binding affinity. Altogether, our study provides energetic and dynamical insights into factors governing peptide recognition by the cross-reactive Hy.1B11 TCR, found in MS patient.
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Reactive multi-particle collision dynamics with reactive boundary conditions
NASA Astrophysics Data System (ADS)
Sayyidmousavi, Alireza; Rohlf, Katrin
2018-07-01
In the present study, an off-lattice particle-based method called the reactive multi-particle collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian Dynamics. The main advantages of the RMPC compared to other molecular based methods are less computational cost as well as conservation of mass, energy and momentum in the collision and free streaming steps. The proposed approach is tested on three reaction-diffusion systems and very good agreement with the solutions to their corresponding partial differential equations is observed.
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Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José
2016-11-03
The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.
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NASA Astrophysics Data System (ADS)
Sellers, Michael; Lisal, Martin; Schweigert, Igor; Larentzos, James; Brennan, John
2015-06-01
In discrete particle simulations, when an atomistic model is coarse-grained, a trade-off is made: a boost in computational speed for a reduction in accuracy. Dissipative Particle Dynamics (DPD) methods help to recover accuracy in viscous and thermal properties, while giving back a small amount of computational speed. One of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. Today, pairing the current evolution of DPD-RX with a coarse-grained potential and its chemical decomposition reactions allows for the simulation of the shock behavior of energetic materials at a timescale faster than an atomistic counterpart. In 2007, Maillet et al. introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We have recently extended the DPD-RX method and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its tranition to hot product gases within DPD-RX will be presented. Additionally, examples of the effect of microstructure on shock behavior will be shown. Approved for public release. Distribution is unlimited.
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Early Stage of Oxidation on Titanium Surface by Reactive Molecular Dynamics Simulation
Yang, Liang; Wang, C. Z.; Lin, Shiwei; ...
2018-01-01
Understanding of metal oxidation is very critical to corrosion control, catalysis synthesis, and advanced materials engineering. Metal oxidation is a very complex phenomenon, with many different processes which are coupled and involved from the onset of reaction. In this work, the initial stage of oxidation on titanium surface was investigated in atomic scale by molecular dynamics (MD) simulations using a reactive force field (ReaxFF). We show that oxygen transport is the dominant process during the initial oxidation. Our simulation also demonstrate that a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Titaniummore » (0001) surface and further prevented oxidation in the deeper layers. As a result, the mechanism of initial oxidation observed in this work can be also applicable to other self-limiting oxidation.« less
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Microscopic approaches to liquid nitromethane detonation properties.
Hervouët, Anaïs; Desbiens, Nicolas; Bourasseau, Emeric; Maillet, Jean-Bernard
2008-04-24
In this paper, thermodynamic and chemical properties of nitromethane are investigated using microscopic simulations. The Hugoniot curve of the inert explosive is computed using Monte Carlo simulations with a modified version of the adaptative Erpenbeck equation of state and a recently developed intermolecular potential. Molecular dynamic simulations of nitromethane decomposition have been performed using a reactive potential, allowing the calculation of kinetic rate constants and activation energies. Finally, the Crussard curve of detonation products as well as thermodynamic properties at the Chapman-Jouguet (CJ) point are computed using reactive ensemble Monte Carlo simulations. Results are in good agreement with both thermochemical calculations and experimental measurements.
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Atomistic Simulations of Chemical Reactivity of TATB Under Thermal and Shock Conditions
DOE Office of Scientific and Technical Information (OSTI.GOV)
Manaa, M R; Reed, E J; Fried, L E
2009-09-23
The study of chemical transformations that occur at the reactive shock front of energetic materials provides important information for the development of predictive models at the grain-and continuum scales. A major shortcoming of current high explosives models is the lack of chemical kinetics data of the reacting explosive in the high pressure and temperature regimes. In the absence of experimental data, long-time scale atomistic molecular dynamics simulations with reactive chemistry become a viable recourse to provide an insight into the decomposition mechanism of explosives, and to obtain effective reaction rate laws. These rates can then be incorporated into thermo-chemical-hydro codesmore » (such as Cheetah linked to ALE3D) for accurate description of the grain and macro scales dynamics of reacting explosives. In this talk, I will present quantum simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) crystals under thermal decomposition (high density and temperature) and shock compression conditions. This is the first time that condensed phase quantum methods have been used to study the chemistry of insensitive high explosives. We used the quantum-based, self-consistent charge density functional tight binding method (SCC{_}DFTB) to calculate the interatomic forces for reliable predictions of chemical reactions, and to examine electronic properties at detonation conditions for a relatively long time-scale on the order of several hundreds of picoseconds. For thermal decomposition of TATB, we conducted constant volume-temperature simulations, ranging from 0.35 to 2 nanoseconds, at {rho} = 2.87 g/cm{sup 3} at T = 3500, 3000, 2500, and 1500 K, and {rho} = 2.9 g/cm{sup 3} and 2.72 g/cm{sup 3}, at T = 3000 K. We also simulated crystal TATB's reactivity under steady overdriven shock compression using the multi-scale shock technique. We conducted shock simulations with specified shock speeds of 8, 9, and 10 km/s for up to 0.43 ns duration, enabling us to track the reactivity of TATB well into the formation of several stable gas products, such as H{sub 2}O, N{sub 2}, and CO{sub 2}. Although complex chemical transformations are occurring continuously in the dynamical, high temperature, reactive environment of our simulations, a simple overall scheme for the decomposition of TATB emerges: Water is the earliest decomposition products to form, followed by a polymerization (or condensation) process in which several TATB remaining fragments are joined together, initiating the early step in the formation of high-nitrogen clusters, along with stable products such as N{sub 2} and CO{sub 2}. Remarkably, these clusters with high concentration of carbon and nitrogen (and little oxygen) remain dynamically stable for the remaining period of the simulations. Our simulations, thus, reveal a hitherto unidentified region of high concentrations of nitrogen-rich heterocyclic clusters in reacting TATB, whose persistence impede further reactivity towards final products of fluid N{sub 2} and solid carbon. These simulations also predict significant populations of charged species such as NCO{sup -}, H{sup +}, OH{sup -}, H{sub 3}O{sup +}, and O{sup -2}, the first such observation in a reacting explosive. Finally, A reduced four steps, global reaction mechanism with Arrhenius kinetic rates for the decomposition of TATB, along with comparative Cheetah decomposition kinetics at various temperatures has been constructed and will be discussed.« less
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Guo, Dezhou; Zybin, Sergey V; An, Qi; Goddard, William A; Huang, Fenglei
2016-01-21
The combustion or detonation of reacting materials at high temperature and pressure can be characterized by the Chapman-Jouguet (CJ) state that describes the chemical equilibrium of the products at the end of the reaction zone of the detonation wave for sustained detonation. This provides the critical properties and product kinetics for input to macroscale continuum simulations of energetic materials. We propose the ReaxFF Reactive Dynamics to CJ point protocol (Rx2CJ) for predicting the CJ state parameters, providing the means to predict the performance of new materials prior to synthesis and characterization, allowing the simulation based design to be done in silico. Our Rx2CJ method is based on atomistic reactive molecular dynamics (RMD) using the QM-derived ReaxFF force field. We validate this method here by predicting the CJ point and detonation products for three typical energetic materials. We find good agreement between the predicted and experimental detonation velocities, indicating that this method can reliably predict the CJ state using modest levels of computation.
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NASA Astrophysics Data System (ADS)
Thallmair, Sebastian; Roos, Matthias K.; de Vivie-Riedle, Regina
2016-06-01
Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstrated for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.
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Thallmair, Sebastian; Roos, Matthias K; de Vivie-Riedle, Regina
2016-06-21
Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstrated for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.
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2012-08-01
Molecular Dynamics Simulations Coarse-Grain Particle Dynamics Simulations Local structure; Force field parameterization Extended structure...K) C8H18 C12H26 C16H34 Adhesive forces can cause local density gradients and defects " Pronounced layering of polymer near interfaces...reactive end groups (CnH2n+1S) on Cu Gap SubPc on C60 Pentacene on a-SiO2 Cyclopentene on Au Crystalline CuPc on Al Polyimide on Si
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NASA Astrophysics Data System (ADS)
Kozlova, S. A.; Gubin, S. A.; Maklashova, I. V.; Selezenev, A. A.
2017-11-01
Molecular dynamic simulations of isothermal compression parameters are performed for a hexanitrohexaazaisowurtzitane single crystal (C6H6O12N12) using a modified ReaxFF-log reactive force field. It is shown that the pressure-compression ratio curve for a single C6H6O12N12 crystal at constant temperature T = 300 K in pressure range P = 0.05-40 GPa is in satisfactory agreement with experimental compression isotherms obtained for a single C6H6O12N12 crystal. Hugoniot molecular-dynamic simulations of the shock-wave hydrostatic compression of a single C6H6O12N12 crystal are performed. Along with Hugoniot temperature-pressure curves, calculated shock-wave pressure-compression ratios for a single C6H6O12N12 crystal are obtained for a wide pressure range of P = 1-40 GPa. It is established that the percussive adiabat obtained for a single C6H6O12N12 crystal is in a good agreement with the experimental data. All calculations are performed using a LAMMPS molecular dynamics simulation software package that provides a ReaxFF-lg reactive force field to support the approach.
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Computationally Efficient Multiconfigurational Reactive Molecular Dynamics
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.
2012-01-01
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924
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NASA Astrophysics Data System (ADS)
Brandt, Erik G.; Agosta, Lorenzo; Lyubartsev, Alexander P.
2016-07-01
Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and coordination numbers); radial distribution functions for all O-Ti pairs over the entire data domain; comparison of coordination number distributions for dry and wet nanoparticles; dynamics of water reactivity; high-resolution electron density for the rutile NP. A movie of the simulation trajectory for the rutile (TiO2)24.30H2O system. See DOI: 10.1039/C6NR02791A
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Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX
NASA Astrophysics Data System (ADS)
Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek
2017-01-01
We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Thallmair, Sebastian; Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 München; Roos, Matthias K.
Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstratedmore » for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.« less
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Nanostructures nucleation in carbon-metal gaseous phase: A molecular dynamics study
NASA Astrophysics Data System (ADS)
Galiullina, G. M.; Orekhov, N. D.; Stegailov, V. V.
2018-01-01
We perform nonequilibrium molecular dynamics simulation of carbon nanoclusters nucleation and early stages of growth from the gaseous phase. We analyze the catalytic effect of iron atoms on the nucleation kinetics and structure of the resultant nanoparticles. Reactive Force Field (ReaxFF) is used in the simulations for the description of bond formation and dissociation during the nucleation process at the nanoscale. The catalytic effect of iron reveals itself even on nanosecond simulation times: iron atoms accelerate the process of clustering but result in less graphitized carbon structures.
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NASA Astrophysics Data System (ADS)
Islam, Md Mahbubul; Strachan, Alejandro
A detailed atomistic-level understanding of the ultrafast chemistry of detonation processes of high energy materials is crucial to understand their performance and safety. Recent advances in laser shocks and ultra-fast spectroscopy is yielding the first direct experimental evidence of chemistry at extreme conditions. At the same time, reactive molecular dynamics (MD) in current high-performance computing platforms enable an atomic description of shock-induced chemistry with length and timescales approaching those of experiments. We use MD simulations with the reactive force field ReaxFF to investigate the shock-induced chemical decomposition mechanisms of polyvinyl nitrate (PVN) and nitromethane (NM). The effect of shock pressure on chemical reaction mechanisms and kinetics of both the materials are investigated. For direct comparison of our simulation results with experimentally derived IR absorption data, we performed spectral analysis using atomistic velocity at various shock conditions. The combination of reactive MD simulations and ultrafast spectroscopy enables both the validation of ReaxFF at extreme conditions and contributes to the interpretation of the experimental data relating changes in spectral features to atomic processes. Office of Naval Research MURI program.
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ReaxFF Study of the Oxidation of Softwood Lignin in View of Carbon Fiber Production
Beste, Ariana
2014-10-06
We investigate the oxidative, thermal conversion of softwood lignin by performing molecular dynamics simulations based on a reactive force field (ReaxFF). The lignin samples are constructed from coniferyl alcohol units, which are connected through linkages that are randomly selected from a natural distribution of linkages in softwood. The goal of this work is to simulate the oxidative stabilization step during carbon fiber production from lignin precursor. We find that at simulation conditions where stabilization reactions occur, the lignin fragments have already undergone extensive degradation. The 5-5 linkage shows the highest reactivity towards cyclization and dehydrogenation.
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NASA Astrophysics Data System (ADS)
Juromskiy, V. M.
2016-09-01
It is developed a mathematical model for an electric drive of high-speed separation device in terms of the modeling dynamic systems Simulink, MATLAB. The model is focused on the study of the automatic control systems of the power factor (Cosφ) of an actuator by compensating the reactive component of the total power by switching a capacitor bank in series with the actuator. The model is based on the methodology of the structural modeling of dynamic processes.
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Reactive power and voltage control strategy based on dynamic and adaptive segment for DG inverter
NASA Astrophysics Data System (ADS)
Zhai, Jianwei; Lin, Xiaoming; Zhang, Yongjun
2018-03-01
The inverter of distributed generation (DG) can support reactive power to help solve the problem of out-of-limit voltage in active distribution network (ADN). Therefore, a reactive voltage control strategy based on dynamic and adaptive segment for DG inverter is put forward to actively control voltage in this paper. The proposed strategy adjusts the segmented voltage threshold of Q(U) droop curve dynamically and adaptively according to the voltage of grid-connected point and the power direction of adjacent downstream line. And then the reactive power reference of DG inverter can be got through modified Q(U) control strategy. The reactive power of inverter is controlled to trace the reference value. The proposed control strategy can not only control the local voltage of grid-connected point but also help to maintain voltage within qualified range considering the terminal voltage of distribution feeder and the reactive support for adjacent downstream DG. The scheme using the proposed strategy is compared with the scheme without the reactive support of DG inverter and the scheme using the Q(U) control strategy with constant segmented voltage threshold. The simulation results suggest that the proposed method has a significant improvement on solving the problem of out-of-limit voltage, restraining voltage variation and improving voltage quality.
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Hajilar, Shahin; Shafei, Behrouz; Cheng, Tao; Jaramillo-Botero, Andres
2017-06-22
Understanding the structural, thermal, and mechanical properties of thaumasite is of great interest to the cement industry, mainly because it is the phase responsible for the aging and deterioration of civil infrastructures made of cementitious materials attacked by external sources of sulfate. Despite the importance, effects of temperature and strain rate on the mechanical response of thaumasite had remained unexplored prior to the current study, in which the mechanical properties of thaumasite are fully characterized using the reactive molecular dynamics (RMD) method. With employing a first-principles based reactive force field, the RMD simulations enable the description of bond dissociation and formation under realistic conditions. From the stress-strain curves of thaumasite generated in the x, y, and z directions, the tensile strength, Young's modulus, and fracture strain are determined for the three orthogonal directions. During the course of each simulation, the chemical bonds undergoing tensile deformations are monitored to reveal the bonds responsible for the mechanical strength of thaumasite. The temperature increase is found to accelerate the bond breaking rate and consequently the degradation of mechanical properties of thaumasite, while the strain rate only leads to a slight enhancement of them for the ranges considered in this study.
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Dynamic Response Testing in an Electrically Heated Reactor Test Facility
NASA Astrophysics Data System (ADS)
Bragg-Sitton, Shannon M.; Morton, T. J.
2006-01-01
Non-nuclear testing can be a valuable tool in the development of a space nuclear power or propulsion system. In a non-nuclear test bed, electric heaters are used to simulate the heat from nuclear fuel. Standard testing allows one to fully assess thermal, heat transfer, and stress related attributes of a given system, but fails to demonstrate the dynamic response that would be present in an integrated, fueled reactor system. The integration of thermal hydraulic hardware tests with simulated neutronic response provides a bridge between electrically heated testing and fueled nuclear testing. By implementing a neutronic response model to simulate the dynamic response that would be expected in a fueled reactor system, one can better understand system integration issues, characterize integrated system response times and response characteristics, and assess potential design improvements at a relatively small fiscal investment. Initial system dynamic response testing was demonstrated on the integrated SAFE-100a heat pipe (HP) cooled, electrically heated reactor and heat exchanger hardware, utilizing a one-group solution to the point kinetics equations to simulate the expected neutronic response of the system. Reactivity feedback calculations were then based on a bulk reactivity feedback coefficient and measured average core temperature. This paper presents preliminary results from similar dynamic testing of a direct drive gas cooled reactor system (DDG), demonstrating the applicability of the testing methodology to any reactor type and demonstrating the variation in system response characteristics in different reactor concepts. Although the HP and DDG designs both utilize a fast spectrum reactor, the method of cooling the reactor differs significantly, leading to a variable system response that can be demonstrated and assessed in a non-nuclear test facility. Planned system upgrades to allow implementation of higher fidelity dynamic testing are also discussed. Proposed DDG testing will utilize a higher fidelity point kinetics model to control core power transients, and reactivity feedback will be based on localized feedback coefficients and several independent temperature measurements taken within the core block. This paper presents preliminary test results and discusses the methodology that will be implemented in follow-on DDG testing and the additional instrumentation required to implement high fidelity dynamic testing.
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Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.
Zheng, Mo; Li, Xiaoxia; Guo, Li
2013-04-01
Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. Copyright © 2013 Elsevier Inc. All rights reserved.
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Ab initio molecular dynamics of the reactivity of vitamin C toward hydroxyl and HO₂/O⁻₂ radicals.
Lespade, Laure
2017-11-21
Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and [Formula: see text] radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of [Formula: see text] radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton. Graphical Abstract Reactivity of vitamin C toward hydroxyl and [Formula: see text] radicals.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Borkiewicz, O. J.; Wiaderek, Kamila M.; Chupas, Peter J.
Dynamic properties and multiscale complexities governing electrochemical energy storage in batteries are most ideally interrogated under simulated operating conditions within an electrochemical cell. We assess how electrochemical reactivity can be impacted by experiment design, including the X-ray measurements or by common features or adaptations of electrochemical cells that enable X-ray measurements.
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NASA Astrophysics Data System (ADS)
Tian, Ziqi; Wen, Jin; Ma, Jing
2013-07-01
It is a challenge to simulate the switching process of functional self-assembled monolayers (SAMs) on metal surfaces, since the systems consist of thousands of atoms and the switching is triggered by quantum-mechanical events. Herein a molecular dynamics simulation with a reactive rotation potential of N=N bond is implemented to investigate the dynamic conformational changes and packing effects on the stimuli-responsive isomerization of the terminally thiol functionalized azobiphenyls (AZOs), which are bound on the Au(111) surface. To, respectively, distinguish the time evolutions that start from cis and trans initial configurations, two different functions are established to model the potential energy curves for cis-to-trans and trans-to-cis transitions, instead of the only one cosine function used in the conventional non-reactive force fields. In order to simulate the conformation transitions of the AZO film on surface, a random switching function, depending on the N=N twisting angle, is constructed to consider both forward and backward cis/trans isomerization events and to trigger the reaction by changing the N atom types automatically. The factors that will influence the isomerization process, including the choice of ensembles and thermostat algorithms, the time intervals separating each switching, and the forms of the switching function, are systematically tested. Most AZO molecules switch from the cis to trans configuration with a coverage of 5.76 × 10-6 mol/m2 on a picosecond time scale, and a low coverage might make the switching irreversible, which is in agreement with the experiments.
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Function and dynamics of aptamers: A case study on the malachite green aptamer
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wang, Tianjiao
Aptamers are short single-stranded nucleic acids that can bind to their targets with high specificity and high affinity. To study aptamer function and dynamics, the malachite green aptamer was chosen as a model. Malachite green (MG) bleaching, in which an OH- attacks the central carbon (C1) of MG, was inhibited in the presence of the malachite green aptamer (MGA). The inhibition of MG bleaching by MGA could be reversed by an antisense oligonucleotide (AS) complementary to the MGA binding pocket. Computational cavity analysis of the NMR structure of the MGA-MG complex predicted that the OH - is sterically excluded frommore » the C1 of MG. The prediction was confirmed experimentally using variants of the MGA with changes in the MG binding pocket. This work shows that molecular reactivity can be reversibly regulated by an aptamer-AS pair based on steric hindrance. In addition to demonstrate that aptamers could control molecular reactivity, aptamer dynamics was studied with a strategy combining molecular dynamics (MD) simulation and experimental verification. MD simulation predicted that the MG binding pocket of the MGA is largely pre-organized and that binding of MG involves reorganization of the pocket and a simultaneous twisting of the MGA terminal stems around the pocket. MD simulation also provided a 3D-structure model of unoccupied MGA that has not yet been obtained by biophysical measurements. These predictions were consistent with biochemical and biophysical measurements of the MGA-MG interaction including RNase I footprinting, melting curves, thermodynamic and kinetic constants measurement. This work shows that MD simulation can be used to extend our understanding of the dynamics of aptamer-target interaction which is not evident from static 3D-structures. To conclude, I have developed a novel concept to control molecular reactivity by an aptamer based on steric protection and a strategy to study the dynamics of aptamer-target interaction by combining MD simulation and experimental verification. The former has potential application in controlling metabolic reactions and protein modifications by small reactants and the latter may serve as a general approach to study the dynamics of aptamer-target interaction for new insights into mechanisms of aptamer-target recognition.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Pratihar, Subha; Barnes, George L.; Laskin, Julia
In this Perspective mass spectrometry experiments and chemical dynamics simulations are described which have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated surface-induced dissociation (SID) for which peptide-H+ fragments upon collision with the surface, peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). The simulations include QM+MM and QM/MM direct dynamics. For collisions with self-assembled monolayer (SAM) surfaces there is quite good agreement between experiment and simulation in the efficiency of energy transfer to the peptide-H+ ion’s internal degrees of freedom. Both themore » experiments and simulations show two mechanisms for peptide-H+ fragmentation, i.e. shattering and statistical, RRKM dynamics. Mechanisms for SL are probed in simulations of collisions of protonated dialanine with a perfluorinated SAM surface. RL has been studied experimentally for a number of peptide-H+ + surface systems, and qualitative agreement between simulation and experiment is found for two similar systems.« less
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NASA Astrophysics Data System (ADS)
Venâncio, Mateus F.; Rocha, Willian R.
2015-10-01
Ab initio molecular dynamics simulations were used to investigate the early chemical events involved in the dynamics of nitric oxide (NOrad), nitrosonium cation (NO+) and nitroxide anion (NO-) in aqueous solution. The NO+ ion is very reactive in aqueous solution having a lifetime of ∼4 × 10-13 s, which is shorter than the value of 3 × 10-10 s predicted experimentally. The NO+ reacts generating the nitrous acid as an intermediate and the NO2- ion as the final product. The dynamics of NOrad revealed the reversibly formation of a transient anion radical species HONOrad -.
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Abiotic/biotic coupling in the rhizosphere: a reactive transport modeling analysis
Lawrence, Corey R.; Steefel, Carl; Maher, Kate
2014-01-01
A new generation of models is needed to adequately simulate patterns of soil biogeochemical cycling in response changing global environmental drivers. For example, predicting the influence of climate change on soil organic matter storage and stability requires models capable of addressing complex biotic/abiotic interactions of rhizosphere and weathering processes. Reactive transport modeling provides a powerful framework simulating these interactions and the resulting influence on soil physical and chemical characteristics. Incorporation of organic reactions in an existing reactive transport model framework has yielded novel insights into soil weathering and development but much more work is required to adequately capture root and microbial dynamics in the rhizosphere. This endeavor provides many advantages over traditional soil biogeochemical models but also many challenges.
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Multiscale Reactive Molecular Dynamics
2012-08-15
biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system ...coupling to slower, cooperative motions of the system . These inherently multiscale problems require computationally efficient and accurate methods to...condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus
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Non-equilibrium dynamics due to moving deflagration front at RDX/HTPB interface
NASA Astrophysics Data System (ADS)
Chaudhuri, Santanu; Joshi, Kaushik; Lacevic, Naida
Reactive dissipative particle dynamics (DPD-RX), a promising tool in characterizing the sensitivity and performance of heterogeneous solid propellants like polymer bonded explosives (PSXs), requires further testing for non-equilibrium dynamics. It is important to understand detailed atomistic chemistry for developing coarse grain reactive models needed for the DPD-RX. In order to obtain insights into combustion chemistry of RDX/HTPB binder, we used reactive molecular dynamics (RMD) to obtain energy up-pumping and reaction mechanisms at RDX/HTPB interface when exposed to a self-sustaining deflagration front. Hot spots are ignited near and away from the heterogeneous interface using the thermal pulse. The results show that the hot spot near interface significantly delays the transition from ignition to deflagration. We will present the mechanical response and the combustion chemistry of HTPB when the propagating deflagration front hits the polymer binder. We will discuss our efforts to incorporate this RMD based chemistry into the DPD-RX which will enable us to perform such non-equilibrium dynamics simulations on large-length scale with microstructural heterogeneities. Funding from DTRA Grant Number HDTRA1-15-1-0034 is acknowledged.
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Assess and improve the sustainability of water treatment facility using Computational Fluid Dynamics
NASA Astrophysics Data System (ADS)
Zhang, Jie; Tejada-Martinez, Andres; Lei, Hongxia; Zhang, Qiong
2016-11-01
Fluids problems in water treatment industry are often simplified or omitted since the focus is usually on chemical process only. However hydraulics also plays an important role in determining effluent water quality. Recent studies have demonstrated that computational fluid dynamics (CFD) has the ability to simulate the physical and chemical processes in reactive flows in water treatment facilities, such as in chlorine and ozone disinfection tanks. This study presents the results from CFD simulations of reactive flow in an existing full-scale ozone disinfection tank and in potential designs. Through analysis of the simulation results, we found that baffling factor and CT10 are not optimal indicators of disinfection performance. We also found that the relationship between effluent CT (the product of disinfectant concentration and contact time) obtained from CT transport simulation and baffling factor depends on the location of ozone release. In addition, we analyzed the environmental and economic impacts of ozone disinfection tank designs and developed a composite indicator to quantify the sustainability of ozone disinfection tank in technological, environmental and economic dimensions.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cao, Haining; Kim, Seungchul; Lee, Kwang-Ryeol, E-mail: krlee@kist.re.kr
2016-03-28
Initial stage of oxynitridation process of Si substrate is of crucial importance in fabricating the ultrathin gate dielectric layer of high quality in advanced MOSFET devices. The oxynitridation reaction on a relaxed Si(001) surface is investigated via reactive molecular dynamics (MD) simulation. A total of 1120 events of a single nitric oxide (NO) molecule reaction at temperatures ranging from 300 to 1000 K are statistically analyzed. The observed reaction kinetics are consistent with the previous experimental or calculation results, which show the viability of the reactive MD technique to study the NO dissociation reaction on Si. We suggest the reaction pathwaymore » for NO dissociation that is characterized by the inter-dimer bridge of a NO molecule as the intermediate state prior to NO dissociation. Although the energy of the inter-dimer bridge is higher than that of the intra-dimer one, our suggestion is supported by the ab initio nudged elastic band calculations showing that the energy barrier for the inter-dimer bridge formation is much lower. The growth mechanism of an ultrathin Si oxynitride layer is also investigated via consecutive NO reactions simulation. The simulation reveals the mechanism of self-limiting reaction at low temperature and the time evolution of the depth profile of N and O atoms depending on the process temperature, which would guide to optimize the oxynitridation process condition.« less
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Mlýnský, Vojtěch; Bussi, Giovanni
2018-01-18
The function of RNA molecules usually depends on their overall fold and on the presence of specific structural motifs. Chemical probing methods are routinely used in combination with nearest-neighbor models to determine RNA secondary structure. Among the available methods, SHAPE is relevant due to its capability to probe all RNA nucleotides and the possibility to be used in vivo. However, the structural determinants for SHAPE reactivity and its mechanism of reaction are still unclear. Here molecular dynamics simulations and enhanced sampling techniques are used to predict the accessibility of nucleotide analogs and larger RNA structural motifs to SHAPE reagents. We show that local RNA reconformations are crucial in allowing reagents to reach the 2'-OH group of a particular nucleotide and that sugar pucker is a major structural factor influencing SHAPE reactivity.
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García-Guerrero, Estefanía; Pérez-Simón, José Antonio; Sánchez-Abarca, Luis Ignacio; Díaz-Moreno, Irene; De la Rosa, Miguel A; Díaz-Quintana, Antonio
2016-01-01
Generating the immune response requires the discrimination of peptides presented by the human leukocyte antigen complex (HLA) through the T-cell receptor (TCR). However, how a single amino acid substitution in the antigen bonded to HLA affects the response of T cells remains uncertain. Hence, we used molecular dynamics computations to analyze the molecular interactions between peptides, HLA and TCR. We compared immunologically reactive complexes with non-reactive and weakly reactive complexes. MD trajectories were produced to simulate the behavior of isolated components of the various p-HLA-TCR complexes. Analysis of the fluctuations showed that p-HLA binding barely restrains TCR motions, and mainly affects the CDR3 loops. Conversely, inactive p-HLA complexes displayed significant drop in their dynamics when compared with its free versus ternary forms (p-HLA-TCR). In agreement, the free non-reactive p-HLA complexes showed a lower amount of salt bridges than the responsive ones. This resulted in differences between the electrostatic potentials of reactive and inactive p-HLA species and larger vibrational entropies in non-elicitor complexes. Analysis of the ternary p-HLA-TCR complexes also revealed a larger number of salt bridges in the responsive complexes. To summarize, our computations indicate that the affinity of each p-HLA complex towards TCR is intimately linked to both, the dynamics of its free species and its ability to form specific intermolecular salt-bridges in the ternary complexes. Of outstanding interest is the emerging concept of antigen reactivity involving its interplay with the HLA head sidechain dynamics by rearranging its salt-bridges.
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A model for the catalytic reduction of NO with CO and N desorption
NASA Astrophysics Data System (ADS)
Díaz, J. J.; Buendía, G. M.
2018-02-01
In this work we have investigated by Monte Carlo simulations the dynamical behavior of a modified Yaldram-Khan (YK) model for the catalytic reduction of NO on a surface. Our model is simulated on a square lattice and includes the individual desorption of CO molecules and N atoms, processes associated with temperature effects. When CO desorption is added, strong fluctuations appear, which are associated with the spreading of N checkerboard structures on the surface. These structures take a long time to coalesce, allowing the existence of a unsteady but long lasting reactive state. N desorption also favors the reactivity of the system, this time by diminishing the size of the N structures and impeding their coalescence. The combined desorption of CO and N produces a reactive state as well, where reactive zones among N structures can take place on the surface.
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NASA Technical Reports Server (NTRS)
Bragg-Sitton, Shannon M.; Hervol, David S.; Godfroy, Thomas J.
2009-01-01
A Direct Drive Gas-Cooled (DDG) reactor core simulator has been coupled to a Brayton Power Conversion Unit (BPCU) for integrated system testing at NASA Glenn Research Center (GRC) in Cleveland, OH. This is a closed-cycle system that incorporates an electrically heated reactor core module, turbo alternator, recuperator, and gas cooler. Nuclear fuel elements in the gas-cooled reactor design are replaced with electric resistance heaters to simulate the heat from nuclear fuel in the corresponding fast spectrum nuclear reactor. The thermodynamic transient behavior of the integrated system was the focus of this test series. In order to better mimic the integrated response of the nuclear-fueled system, a simulated reactivity feedback control loop was implemented. Core power was controlled by a point kinetics model in which the reactivity feedback was based on core temperature measurements; the neutron generation time and the temperature feedback coefficient are provided as model inputs. These dynamic system response tests demonstrate the overall capability of a non-nuclear test facility in assessing system integration issues and characterizing integrated system response times and response characteristics.
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NASA Technical Reports Server (NTRS)
Bragg-Sitton, Shannon M.; Hervol, David S.; Godfroy, Thomas J.
2010-01-01
A Direct Drive Gas-Cooled (DDG) reactor core simulator has been coupled to a Brayton Power Conversion Unit (BPCU) for integrated system testing at NASA Glenn Research Center (GRC) in Cleveland, Ohio. This is a closed-cycle system that incorporates an electrically heated reactor core module, turboalternator, recuperator, and gas cooler. Nuclear fuel elements in the gas-cooled reactor design are replaced with electric resistance heaters to simulate the heat from nuclear fuel in the corresponding fast spectrum nuclear reactor. The thermodynamic transient behavior of the integrated system was the focus of this test series. In order to better mimic the integrated response of the nuclear-fueled system, a simulated reactivity feedback control loop was implemented. Core power was controlled by a point kinetics model in which the reactivity feedback was based on core temperature measurements; the neutron generation time and the temperature feedback coefficient are provided as model inputs. These dynamic system response tests demonstrate the overall capability of a non-nuclear test facility in assessing system integration issues and characterizing integrated system response times and response characteristics.
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PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kylasa, S.B., E-mail: skylasa@purdue.edu; Aktulga, H.M., E-mail: hmaktulga@lbl.gov; Grama, A.Y., E-mail: ayg@cs.purdue.edu
2014-09-01
We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques wemore » developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.« less
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Simulation of Initiation in Hexanitrostilbene
NASA Astrophysics Data System (ADS)
Thompson, Aidan; Shan, Tzu-Ray; Yarrington, Cole; Wixom, Ryan
We report on the effect of isolated voids and pairs of nearby voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock loading. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating in HNS crystal along the [010] orientation are performed (up = 1.25 km/s, Us =4.0 km/s, P = 11GPa.) We compare the effect on hot spot formation and growth rate of isolated cylindrical voids up to 0.1 µm in size with that of two 50nm voids set 100nm apart. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lock- heed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.
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An accurate reactive power control study in virtual flux droop control
NASA Astrophysics Data System (ADS)
Wang, Aimeng; Zhang, Jia
2017-12-01
This paper investigates the problem of reactive power sharing based on virtual flux droop method. Firstly, flux droop control method is derived, where complicated multiple feedback loops and parameter regulation are avoided. Then, the reasons for inaccurate reactive power sharing are theoretically analyzed. Further, a novel reactive power control scheme is proposed which consists of three parts: compensation control, voltage recovery control and flux droop control. Finally, the proposed reactive power control strategy is verified in a simplified microgrid model with two parallel DGs. The simulation results show that the proposed control scheme can achieve accurate reactive power sharing and zero deviation of voltage. Meanwhile, it has some advantages of simple control and excellent dynamic and static performance.
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Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R
2011-03-25
The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment. Published by Elsevier B.V.
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Reactive simulation of the chemistry behind the condensed-phase ignition of RDX from hot spots.
Joshi, Kaushik L; Chaudhuri, Santanu
2015-07-28
Chemical events that lead to thermal initiation and spontaneous ignition of the high-pressure phase of RDX are presented using reactive molecular dynamics simulations. In order to initiate the chemistry behind thermal ignition, approximately 5% of RDX crystal is subjected to a constant temperature thermal pulse for various time durations to create a hot spot. After application of the thermal pulse, the ensuing chemical evolution of the system is monitored using reactive molecular dynamics under adiabatic conditions. Thermal pulses lasting longer than certain time durations lead to the spontaneous ignition of RDX after an incubation period. For cases where the ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. Contrary to the widely accepted unimolecular models of initiation chemistry, N-N bond dissociations that produce NO2 species are suppressed in the condensed phase. The gradual temperature and pressure increase in the incubation period is accompanied by the accumulation of short-lived, heavier polyradicals. The polyradicals contain intact triazine rings from the RDX molecules. At certain temperatures and pressures, the polyradicals undergo ring-opening reactions, which fuel a series of rapid exothermic chemical reactions leading to a thermal runaway regime with stable gas-products such as N2, H2O and CO2. The evolution of the RDX crystal throughout the thermal initiation, incubation and thermal runaway phases observed in the reactive simulations contains a rich diversity of condensed-phase chemistry of nitramines under high-temperature/pressure conditions.
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The effect of core configuration on temperature coefficient of reactivity in IRR-1
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bettan, M.; Silverman, I.; Shapira, M.
1997-08-01
Experiments designed to measure the effect of coolant moderator temperature on core reactivity in an HEU swimming pool type reactor were performed. The moderator temperature coefficient of reactivity ({alpha}{sub {omega}}) was obtained and found to be different in two core loadings. The measured {alpha}{sub {omega}} of one core loading was {minus}13 pcm/{degrees}C at the temperature range of 23-30{degrees}C. This value of {alpha}{sub {omega}} is comparable to the data published by the IAEA. The {alpha}{sub {omega}} measured in the second core loading was found to be {minus}8 pcm/{degrees}C at the same temperature range. Another phenomenon considered in this study is coremore » behavior during reactivity insertion transient. The results were compared to a core simulation using the Dynamic Simulator for Nuclear Power Plants. It was found that in the second core loading factors other than the moderator temperature influence the core reactivity more than expected. These effects proved to be extremely dependent on core configuration and may in certain core loadings render the reactor`s reactivity coefficient undesirable.« less
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Towards coupled earthquake dynamic rupture and tsunami simulations: The 2011 Tohoku earthquake.
NASA Astrophysics Data System (ADS)
Galvez, Percy; van Dinther, Ylona
2016-04-01
The 2011 Mw9 Tohoku earthquake has been recorded with a vast GPS and seismic network given an unprecedented chance to seismologists to unveil complex rupture processes in a mega-thrust event. The seismic stations surrounding the Miyagi regions (MYGH013) show two clear distinct waveforms separated by 40 seconds suggesting two rupture fronts, possibly due to slip reactivation caused by frictional melting and thermal fluid pressurization effects. We created a 3D dynamic rupture model to reproduce this rupture reactivation pattern using SPECFEM3D (Galvez et al, 2014) based on a slip-weakening friction with sudden two sequential stress drops (Galvez et al, 2015) . Our model starts like a M7-8 earthquake breaking dimly the trench, then after 40 seconds a second rupture emerges close to the trench producing additional slip capable to fully break the trench and transforming the earthquake into a megathrust event. The seismograms agree roughly with seismic records along the coast of Japan. The resulting sea floor displacements are in agreement with 1Hz GPS displacements (GEONET). The simulated sea floor displacement reaches 8-10 meters of uplift close to the trench, which may be the cause of such a devastating tsunami followed by the Tohoku earthquake. To investigate the impact of such a huge uplift, we ran tsunami simulations with the slip reactivation model and plug the sea floor displacements into GeoClaw (Finite element code for tsunami simulations, George and LeVeque, 2006). Our recent results compare well with the water height at the tsunami DART buoys 21401, 21413, 21418 and 21419 and show the potential using fully dynamic rupture results for tsunami studies for earthquake-tsunami scenarios.
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Fernando L. Dri; Xiawa Wu; Robert J. Moon; Ashlie Martini; Pablo D. Zavattieri
2015-01-01
Molecular dynamics simulation is commonly used to study the properties of nanocellulose-based materials at the atomic scale. It is well known that the accuracy of these simulations strongly depends on the force field that describes energetic interactions. However, since there is no force field developed specifically for cellulose, researchers utilize models...
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NASA Technical Reports Server (NTRS)
Davy, W. C.; Green, M. J.; Lombard, C. K.
1981-01-01
The factored-implicit, gas-dynamic algorithm has been adapted to the numerical simulation of equilibrium reactive flows. Changes required in the perfect gas version of the algorithm are developed, and the method of coupling gas-dynamic and chemistry variables is discussed. A flow-field solution that approximates a Jovian entry case was obtained by this method and compared with the same solution obtained by HYVIS, a computer program much used for the study of planetary entry. Comparison of surface pressure distribution and stagnation line shock-layer profiles indicates that the two solutions agree well.
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Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro
2006-03-02
We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to coexistence of brittle grains and soft amorphous-like grain boundary phases. Simulations predict a crossover from intergranular continuous deformation to intragrain discrete deformation at a critical indentation depth.
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NASA Astrophysics Data System (ADS)
Shekhar, Adarsh
Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in nanoporous silica are different from that of bulk water, and insight into the properties of confined water is important for our understanding of many geological and biological processes. Nanoporous silica has a wide range of technological applications because it is easy to tune the size of pores and their morphologies and to functionalize pore surfaces with a variety of molecular moieties. Nanoporous silica is used in catalysis, chromatography, anticorrosion coatings, desalination membranes, and as drug delivery vehicles. We use reactive molecular dynamics to study the structure and dynamics of nanoconfined water between 100 and 300 K
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Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lee, Kibaek; Stewart, D. Scott, E-mail: santc@illinois.edu, E-mail: dss@illinois.edu; Joshi, Kaushik
2016-05-14
We present a mirrored atomistic and continuum framework that is used to describe the ignition of energetic materials, and a high-pressure phase of RDX in particular. The continuum formulation uses meaningful averages of thermodynamic properties obtained from the atomistic simulation and a simplification of enormously complex reaction kinetics. In particular, components are identified based on molecular weight bin averages and our methodology assumes that both the averaged atomistic and continuum simulations are represented on the same time and length scales. The atomistic simulations of thermally initiated ignition of RDX are performed using reactive molecular dynamics (RMD). The continuum model ismore » based on multi-component thermodynamics and uses a kinetics scheme that describes observed chemical changes of the averaged atomistic simulations. Thus the mirrored continuum simulations mimic the rapid change in pressure, temperature, and average molecular weight of species in the reactive mixture. This mirroring enables a new technique to simplify the chemistry obtained from reactive MD simulations while retaining the observed features and spatial and temporal scales from both the RMD and continuum model. The primary benefit of this approach is a potentially powerful, but familiar way to interpret the atomistic simulations and understand the chemical events and reaction rates. The approach is quite general and thus can provide a way to model chemistry based on atomistic simulations and extend the reach of those simulations.« less
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Mesoscopic simulations of shock-to-detonation transition in reactive liquid high explosive
NASA Astrophysics Data System (ADS)
Maillet, J. B.; Bourasseau, E.; Desbiens, N.; Vallverdu, G.; Stoltz, G.
2011-12-01
An extension of the model described in a previous work (see Maillet J. B. et al., EPL, 78 (2007) 68001) based on Dissipative Particle Dynamics is presented and applied to a liquid high explosive (HE), with thermodynamic properties mimicking those of liquid nitromethane. Large scale nonequilibrium simulations of reacting liquid HE with model kinetic under sustained shock conditions allow a better understanding of the shock-to-detonation transition in homogeneous explosives. Moreover, the propagation of the reactive wave appears discontinuous since ignition points in the shocked material can be activated by the compressive waves emitted from the onset of chemical reactions.
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Glassy Dynamics in the Adaptive Immune Response Prevents Autoimmune Disease
NASA Astrophysics Data System (ADS)
Sun, Jun; Deem, Michael
2006-03-01
The immune system normally protects the human host against death by infection. However, when an immune response is mistakenly directed at self antigens, autoimmune disease can occur. We describe a model of protein evolution to simulate the dynamics of the adaptive immune response to antigens. Computer simulations of the dynamics of antibody evolution show that different evolutionary mechanisms, namely gene segment swapping and point mutation, lead to different evolved antibody binding affinities. Although a combination of gene segment swapping and point mutation can yield a greater affinity to a specific antigen than point mutation alone, the antibodies so evolved are highly cross-reactive and would cause autoimmune disease, and this is not the chosen dynamics of the immune system. We suggest that in the immune system a balance has evolved between binding affinity and specificity in the mechanism for searching the amino acid sequence space of antibodies. Our model predicts that chronic infection may lead to autoimmune disease as well due to cross-reactivity and suggests a broad distribution for the time of onset of autoimmune disease due to chronic exposure. The slow search of antibody sequence space by point mutation leads to the broad of distribution times.
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NASA Astrophysics Data System (ADS)
Chen, Chen; Arntsen, Christopher; Voth, Gregory A.
2017-10-01
Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.
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Detonation initiation in a model of explosive: Comparative atomistic and hydrodynamics simulations
NASA Astrophysics Data System (ADS)
Murzov, S. A.; Sergeev, O. V.; Dyachkov, S. A.; Egorova, M. S.; Parshikov, A. N.; Zhakhovsky, V. V.
2016-11-01
Here we extend consistent simulations to reactive materials by the example of AB model explosive. The kinetic model of chemical reactions observed in a molecular dynamics (MD) simulation of self-sustained detonation wave can be used in hydrodynamic simulation of detonation initiation. Kinetic coefficients are obtained by minimization of difference between profiles of species calculated from the kinetic model and observed in MD simulations of isochoric thermal decomposition with a help of downhill simplex method combined with random walk in multidimensional space of fitting kinetic model parameters.
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Neuro-estimator based GMC control of a batch reactive distillation.
Prakash, K J Jithin; Patle, Dipesh S; Jana, Amiya K
2011-07-01
In this paper, an artificial neural network (ANN)-based nonlinear control algorithm is proposed for a simulated batch reactive distillation (RD) column. In the homogeneously catalyzed reactive process, an esterification reaction takes place for the production of ethyl acetate. The fundamental model has been derived incorporating the reaction term in the model structure of the nonreactive distillation process. The process operation is simulated at the startup phase under total reflux conditions. The open-loop process dynamics is also addressed running the batch process at the production phase under partial reflux conditions. In this study, a neuro-estimator based generic model controller (GMC), which consists of an ANN-based state predictor and the GMC law, has been synthesized. Finally, this proposed control law has been tested on the representative batch reactive distillation comparing with a gain-scheduled proportional integral (GSPI) controller and with its ideal performance (ideal GMC). Copyright © 2011 ISA. Published by Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.
2018-04-01
Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.
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Safe motion planning for mobile agents: A model of reactive planning for multiple mobile agents
DOE Office of Scientific and Technical Information (OSTI.GOV)
Fujimura, Kikuo.
1990-01-01
The problem of motion planning for multiple mobile agents is studied. Each planning agent independently plans its own action based on its map which contains a limited information about the environment. In an environment where more than one mobile agent interacts, the motions of the robots are uncertain and dynamic. A model for reactive agents is described and simulation results are presented to show their behavior patterns. 18 refs., 2 figs.
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Molecular Dynamics Studies of Thermal Induced Chemistry in Tatb
NASA Astrophysics Data System (ADS)
Quenneville, J.; Germann, T. C.; Thompson, A. P.; Kober, E. M.
2007-12-01
A reactive force field (ReaxFF) is used with molecular dynamics to probe the chemistry induced by intense heating (`accelerated cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 32-molecule simulations, we calculate the reaction rate as a function of temperature and compare the Arrhenius-predicted activation energy with experiment. Decomposition product evolution (mainly N2, H2O, CO2 and graphitic carbon clusters) is followed using a 576-molecule larger simulation, which also illustrates the effect of system size on both carbon clustering and reaction rate.
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LES, DNS, and RANS for the Analysis of High-Speed Turbulent Reacting Flows
NASA Technical Reports Server (NTRS)
Colucci, P. J.; Jaberi, F. A.; Givi, P.
1996-01-01
A filtered density function (FDF) method suitable for chemically reactive flows is developed in the context of large eddy simulation. The advantage of the FDF methodology is its inherent ability to resolve subgrid scales (SGS) scalar correlations that otherwise have to be modeled. Because of the lack of robust models to accurately predict these correlations in turbulent reactive flows, simulations involving turbulent combustion are often met with a degree of skepticism. The FDF methodology avoids the closure problem associated with these terms and treats the reaction in an exact manner. The scalar FDF approach is particularly attractive since it can be coupled with existing hydrodynamic computational fluid dynamics (CFD) codes.
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Metascalable molecular dynamics simulation of nano-mechano-chemistry
NASA Astrophysics Data System (ADS)
Shimojo, F.; Kalia, R. K.; Nakano, A.; Nomura, K.; Vashishta, P.
2008-07-01
We have developed a metascalable (or 'design once, scale on new architectures') parallel application-development framework for first-principles based simulations of nano-mechano-chemical processes on emerging petaflops architectures based on spatiotemporal data locality principles. The framework consists of (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms, (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these scalable algorithms onto hardware. The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics (MD) and 17.7-million-atom (1.56 trillion electronic degrees of freedom) quantum mechanical (QM) MD in the framework of the density functional theory (DFT) on adaptive multigrids, in addition to 201-billion-atom nonreactive MD, on 196 608 IBM BlueGene/L processors. We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on demand and tasks were migrated according to unexpected faults. The paper presents the application of the framework to the study of nanoenergetic materials: (1) combustion of an Al/Fe2O3 thermite and (2) shock initiation and reactive nanojets at a void in an energetic crystal.
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Yang, Li; Liu, Xu; Zhang, Jiaxu; Xie, Jing
2017-04-12
Systematic studies of microsolvation in the gas phase have enriched our knowledge of solvent effects. Here, the dynamics of a prototype S N 2 reaction of a hydrated fluoride ion with methyl iodide is uncovered employing direct dynamics simulations that show strikingly distinct features from those determined for an unsolvated system. An indirect scattering is found to prevail, which occurs dominantly by forming hydrated F - (H 2 O)-HCH 2 I and F - (H 2 O)-CH 3 I pre-reaction complexes at low energies, but proceeds through their water-free counterparts at higher energies. This finding is in strong contrast to a general evolution from indirect to direct dynamics with enhancing energy for the unsolvated substitution reactions, and this discrepancy is understood by the substantial steric hindrance introduced by a water molecule. As established in experiments, solvation suppresses the reactivity, whereas we find that this depression is remarkably frustrated upon raising the energy given that collision-induced dehydration essentially diminishes the water block for reactive collisions. The present study sheds light on how solute-solvent interactions affect the underlying dynamics at a deeper atomic level, thereby promoting our understanding of the fundamental solvent effects on chemical reactions in solution.
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NASA Astrophysics Data System (ADS)
Yu, Yingtian; Krishnan, N. M. Anoop; Smedskjaer, Morten M.; Sant, Gaurav; Bauchy, Mathieu
2018-02-01
The surface reactivity and hydrophilicity of silicate materials are key properties for various industrial applications. However, the structural origin of their affinity for water remains unclear. Here, based on reactive molecular dynamics simulations of a series of artificial glassy silica surfaces annealed at various temperatures and subsequently exposed to water, we show that silica exhibits a hydrophilic-to-hydrophobic transition driven by its silanol surface density. By applying topological constraint theory, we show that the surface reactivity and hydrophilic/hydrophobic character of silica are controlled by the atomic topology of its surface. This suggests that novel silicate materials with tailored reactivity and hydrophilicity could be developed through the topological nanoengineering of their surface.
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NASA Astrophysics Data System (ADS)
DePaolo, D. J.; Steefel, C. I.; Bourg, I. C.
2013-12-01
This talk will review recent research relating to pore scale reactive transport effects done in the context of the Department of Energy-sponsored Energy Frontier Research Center led by Lawrence Berkeley National Laboratory with several other laboratory and University partners. This Center, called the Center for Nanoscale Controls on Geologic CO2 (NCGC) has focused effort on the behavior of supercritical CO2 being injected into and/or residing as capillary trapped-bubbles in sandstone and shale, with particular emphasis on the description of nanoscale to pore scale processes that could provide the basis for advanced simulations. In general, simulation of reservoir-scale behavior of CO2 sequestration assumes a number of mostly qualitative relationships that are defensible as nominal first-order descriptions of single-fluid systems, but neglect the many complications that are associated with a two-phase or three-phase reactive system. The contrasts in properties, and the mixing behavior of scCO2 and brine provide unusual conditions for water-rock interaction, and the NCGC has investigated the underlying issues by a combination of approaches including theoretical and experimental studies of mineral nucleation and growth, experimental studies of brine films, mineral wetting properties, dissolution-precipitation rates and infiltration patterns, molecular dynamic simulations and neutron scattering experiments of fluid properties for fluid confined in nanopores, and various approaches to numerical simulation of reactive transport processes. The work to date has placed new constraints on the thickness of brine films, and also on the wetting properties of CO2 versus brine, a property that varies between minerals and with salinity, and may also change with time as a result of the reactivity of CO2-saturated brine. Mineral dissolution is dependent on reactive surface area, which can be shown to vary by a large factor for various minerals, especially when correlated with interconnected pore space. High-resolution numerical simulations of reactive transport can ultimate lead to quantitative descriptions of pore scale chemistry and flow, and examples of recent developments will be presented. However, only a limited description of the processes can realistically be treated in such simulations, and only for chemically simple systems. Whether and when more complete simulations will be achievable is yet to be determined.
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Chattopadhyay, Aditya; Zheng, Min; Waller, Mark Paul; Priyakumar, U Deva
2018-05-23
Knowledge of the structure and dynamics of biomolecules is essential for elucidating the underlying mechanisms of biological processes. Given the stochastic nature of many biological processes, like protein unfolding, it's almost impossible that two independent simulations will generate the exact same sequence of events, which makes direct analysis of simulations difficult. Statistical models like Markov Chains, transition networks etc. help in shedding some light on the mechanistic nature of such processes by predicting long-time dynamics of these systems from short simulations. However, such methods fall short in analyzing trajectories with partial or no temporal information, for example, replica exchange molecular dynamics or Monte Carlo simulations. In this work we propose a probabilistic algorithm, borrowing concepts from graph theory and machine learning, to extract reactive pathways from molecular trajectories in the absence of temporal data. A suitable vector representation was chosen to represent each frame in the macromolecular trajectory (as a series of interaction and conformational energies) and dimensionality reduction was performed using principal component analysis (PCA). The trajectory was then clustered using a density-based clustering algorithm, where each cluster represents a metastable state on the potential energy surface (PES) of the biomolecule under study. A graph was created with these clusters as nodes with the edges learnt using an iterative expectation maximization algorithm. The most reactive path is conceived as the widest path along this graph. We have tested our method on RNA hairpin unfolding trajectory in aqueous urea solution. Our method makes the understanding of the mechanism of unfolding in RNA hairpin molecule more tractable. As this method doesn't rely on temporal data it can be used to analyze trajectories from Monte Carlo sampling techniques and replica exchange molecular dynamics (REMD).
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Atomistic Simulation of Initiation in Hexanitrostilbene
NASA Astrophysics Data System (ADS)
Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan
2015-06-01
We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.
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Rutqvist, Jonny; Cappa, Frederic; Rinaldi, Antonio P.; ...
2014-12-31
We summarize recent modeling studies of injection-induced fault reactivation, seismicity, and its potential impact on surface structures and nuisance to the local human population. We used coupled multiphase fluid flow and geomechanical numerical modeling, dynamic wave propagation modeling, seismology theories, and empirical vibration criteria from mining and construction industries. We first simulated injection-induced fault reactivation, including dynamic fault slip, seismic source, wave propagation, and ground vibrations. From co-seismic average shear displacement and rupture area, we determined the moment magnitude to about M w = 3 for an injection-induced fault reactivation at a depth of about 1000 m. We then analyzedmore » the ground vibration results in terms of peak ground acceleration (PGA), peak ground velocity (PGV), and frequency content, with comparison to the U.S. Bureau of Mines’ vibration criteria for cosmetic damage to buildings, as well as human-perception vibration limits. For the considered synthetic M w = 3 event, our analysis showed that the short duration, high frequency ground motion may not cause any significant damage to surface structures, and would not cause, in this particular case, upward CO 2 leakage, but would certainly be felt by the local population.« less
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Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking
DOE Office of Scientific and Technical Information (OSTI.GOV)
Grama, Ananth
2013-12-18
A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability.more » • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.« less
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Extending atomistic scale chemistry to mesoscale model of condensed-phase deflagration
NASA Astrophysics Data System (ADS)
Joshi, Kaushik; Chaudhuri, Santanu
2017-01-01
Predictive simulations connecting chemistry that follow the shock or thermal initiation of energetic materials to subsequent deflagration or detonation events is currently outside the realm of possibilities. Molecular dynamics and first-principles based dynamics have made progress in understanding reactions in picosecond to nanosecond time scale. Results from thermal ignition of different phases of RDX show a complex reaction network and emergence of a deterministic behavior for critical temperature before ignition and hot spot growth rates. The kinetics observed is dependent on the hot spot temperature, system size and thermal conductivity. For cases where ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. The gradual temperature and pressure increase in the incubation period is accompanied by accumulation of heavier polyradicals. The challenge of connecting such chemistry in mesoscale simulations remain in reducing the complexity of chemistry. The hot spot growth kinetics in RDX grains and interfaces is an important challenge for reactive simulations aiming to fill in the gaps in our knowledge in the nanoseconds to microseconds time scale. The results discussed indicate that the mesoscale chemistry may include large polyradical molecules in dense reactive mix reaching an instability point at certain temperatures and pressures.
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The effect of target materials on the propagation of atmospheric-pressure plasma jets
NASA Astrophysics Data System (ADS)
Ji, Longfei; Yan, Wen; Xia, Yang; Liu, Dongping
2018-05-01
The current study is focused on the effect of target materials (quartz plate, copper sheet, and quartz plate with a grounded copper sheet on the back) on the propagation of atmospheric-pressure helium plasma jets. The dynamics of ionization waves (IWs) and the relative amount of reactive oxygen species (OH and O) in the IW front were compared by using spatial and temporal images and relative optical emission spectroscopy. Our measurements show that the targets can significantly affect the propagation and intensity of the IWs. In addition, strong OH emission lines were detected when the IWs impinged upon the damp surface. Numerical simulations have been carried out to explain the experimental observation. The propagation velocity of IWs predicted by the simulation was in good agreement with the experimental results. Simulation results suggest that the density and velocity of IWs mainly depend on the electric field between the high voltage electrode tip and the target. Analysis indicates that the targets could change the electric field distribution between the high voltage electrode and targets and thus affect the dynamics and the density of the IWs, the generation of reactive oxygen species, and the corresponding sterilization efficiency.
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NASA Technical Reports Server (NTRS)
Bragg-Sitton, S. M.; Webster, K. L.
2007-01-01
Nonnuclear testing can be a valuable tool in the development of an in-space nuclear power or propulsion system. In a nonnuclear test facility, electric heaters are used to simulate heat from nuclear fuel. Standard testing allows one to fully assess thermal, heat transfer, and stress related attributes of a given system but fails to demonstrate the dynamic response that would be present in an integrated, fueled reactor system. The integration of thermal hydraulic hardware tests with simulated neutronic response provides a bridge between electrically heated testing and full nuclear testing. By implementing a neutronic response model to simulate the dynamic response that would be expected in a fueled reactor system, one can better understand system integration issues, characterize integrated system response times and response and response characteristics, and assess potential design improvements with a relatively small fiscal investment. Initial system dynamic response testing was demonstrated on the integrated SAFE 100a heat pipe cooled, electrically heated reactor and heat exchanger hardware. This Technical Memorandum discusses the status of the planned dynamic test methodology for implementation in the direct-drive gas-cooled reactor testing and assesses the additional instrumentation needed to implement high-fidelity dynamic testing.
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NASA Astrophysics Data System (ADS)
Ranjith, P. K.; Al-Abdullah, Ebtehal S.; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Anto, P. L.; Sheena, Mary Y.; Armaković, Stevan; Armaković, Sanja J.; Zitko, Jan; Dolezal, Martin; Van Alsenoy, C.
2017-05-01
The FT-IR and FT-Raman spectra of N-(3-iodo-4-methylphenyl)pyrazine-2-carboxamide were recorded and the experimentally observed wavenumbers are compared with the theoretically obtained wavenumbers. The redshift of the Nsbnd H stretching mode in the IR spectrum from the computed value indicated the weakening of the Nsbnd H bond. The ring breathing modes of the phenyl ring and pyrazine ring are assigned at 819 and 952 cm-1 theoretically. Using natural bond orbital analysis, the stability of the molecule arising from hyperconjugative interaction and charge delocalization has been analyzed. The most reactive sites in the molecule were identified by molecular electrostatic potential map. The calculations of the average local ionization energy (ALIE) were used for visualization and determination of molecule sites possibly prone to electrophilic attacks. Further information on possible reactive centers of title molecule has been obtained by calculations of Fukui functions. Vulnerability of title molecule towards autoxidation mechanism was investigated by calculations of bond dissociation energies (BDE), while vulnerability towards hydrolysis was investigated by calculations of radial distribution functions (RDF) as obtained after molecular dynamics (MD) simulations. Molecular docking studies suggest that the compound might exhibit inhibitory activity against mGluRs.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Guthrie, George Drake Jr.; Pawar, Rajesh J.; Carey, James William
2017-07-28
This report analyzes the dynamics and mechanisms of the interactions of carbonated brine with hydrated Portland cement. The analysis is based on a recent set of comprehensive reactive-transport simulations, and it relies heavily on the synthesis of the body of work on wellbore integrity that we have conducted for the Carbon Storage Program over the past decade.
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NASA Astrophysics Data System (ADS)
Pandey, S.; Rajaram, H.
2015-12-01
This work investigates hydrologic and geochemical interactions in the Critical Zone (CZ) using high-resolution reactive transport modeling. Reactive transport models can be used to predict the response of geochemical weathering and solute fluxes in the CZ to changes in a dynamic environment, such as those pertaining to human activities and climate change in recent years. The scales of hydrology and geochemistry in the CZ range from days to eons in time and centimeters to kilometers in space. Here, we present results of a multi-dimensional, multi-scale hydro-geochemical model to investigate the role of subsurface heterogeneity on the formation of mineral weathering fronts in the CZ, which requires consideration of many of these spatio-temporal scales. The model is implemented using the reactive transport code PFLOTRAN, an open source subsurface flow and reactive transport code that utilizes parallelization over multiple processing nodes and provides a strong framework for simulating weathering in the CZ. The model is set up to simulate weathering dynamics in the mountainous catchments representative of the Colorado Front Range. Model parameters were constrained based on hydrologic, geochemical, and geophysical observations from the Boulder Creek Critical Zone Observatory (BcCZO). Simulations were performed in fractured rock systems and compared with systems of heterogeneous and homogeneous permeability fields. Tracer simulations revealed that the mean residence time of solutes was drastically accelerated as fracture density increased. In simulations that include mineral reactions, distinct signatures of transport limitations on weathering arose when discrete flow paths were included. This transport limitation was related to both advective and diffusive processes in the highly heterogeneous systems (i.e. fractured media and correlated random permeability fields with σlnk > 3). The well-known time-dependence of mineral weathering rates was found to be the most pronounced in the fractured systems, with a departure from the maximum system-averaged dissolution rate occurring after ~100 kyr followed by a gradual decrease in the reaction rate with time that persists beyond 104 kyr.
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Reactive pathways of hydrogen and carbon removal from organosilicate glass low- κ films by F atoms
NASA Astrophysics Data System (ADS)
Voronina, Ekaterina N.; Mankelevich, Yuri A.; Rakhimova, Tatyana V.
2017-07-01
Direct molecular dynamic simulation on the base of the density functional theory (DFT) method is used to study some critical reactions of F atoms with organosilicate glass (OSG) low-κ films. Here static and dynamic DFT-based approaches are applied for a variety of reactive pathways of hydrogen and carbon removal in the form of volatile products (HF, CF2 and CF3 molecules) from initial SiCH3 surface groups. These reactions constitute an important part of the proposed multi-step mechanism of OSG films damage and etching by thermal F atoms. Two models (POSS and TMCTS macromolecules and their modifications) are used to illustrate the peculiarities and dynamics of the successive reactions of F atoms with the initial SiCH3 and appeared SiCHxFy (x + y ≤ 3) surface groups. Contribution to the Topical Issue "Dynamics of Molecular Systems (MOLEC 2016)", edited by Alberto Garcia-Vela, Luis Banares and Maria Luisa Senent.
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Ab Initio Reactive Computer Aided Molecular Design
DOE Office of Scientific and Technical Information (OSTI.GOV)
Martínez, Todd J.
Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This then opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. Here, we arguemore » that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.« less
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Ab Initio Reactive Computer Aided Molecular Design
Martínez, Todd J.
2017-03-21
Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This then opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. Here, we arguemore » that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.« less
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Determination of the plasma impedance of a glow discharge in carbon dioxide
NASA Astrophysics Data System (ADS)
Kiselev, A. S.; Smirnov, E. A.
2017-07-01
In this work an expression for the dynamic resistance of a glow discharge flowing in long tubes is obtained and analyzed. The expression describes the physical processes occurring in the positive column of a glow discharge. The frequency dependences of the active and reactive components as well as the dynamic resistance module for the discharge conditions corresponding to CO2-lasers have been calculated. Based on the simulation results developed a computer program in the C# programming language for modeling the dynamic resistance discharge of glow discharge lasers.
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A micro-macro coupling approach of MD-SPH method for reactive energetic materials
NASA Astrophysics Data System (ADS)
Liu, Gui Rong; Wang, Guang Yu; Peng, Qing; De, Suvranu
2017-01-01
The simulation of reactive energetic materials has long been the interest of researchers because of the extensive applications of explosives. Much research has been done on the subject at macro scale in the past and research at micro scale has been initiated recently. Equation of state (EoS) is the relation between physical quantities (pressure, temperature, energy and volume) describing thermodynamic states of materials under a given set of conditions. It plays a significant role in determining the characteristics of energetic materials, including Chapman-Jouguet point and detonation velocity. Furthermore, EoS is the key to connect microscopic and macroscopic phenomenon when simulating the macro effects of an explosion. For instance, an ignition and growth model for high explosives uses two JWL EoSs, one for solid explosive and the other for gaseous products, which are often obtained from experiments that can be quite expensive and hazardous. Therefore, it is ideal to calculate the EoS of energetic materials through computational means. In this paper, the EoSs for both solid and gaseous products of β-HMX are calculated using molecular dynamics simulation with ReaxFF-d3, a reactive force field obtained from quantum mechanics. The microscopic simulation results are then compared with experiments and the continuum ignition and growth model. Good agreement is observed. Then, the EoSs obtained through micro-scale simulation is applied in a smoothed particle hydrodynamics (SPH) code to simulate the macro effects of explosions. Simulation results are compared with experiments.
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Rahnamoun, A; van Duin, A C T
2014-04-17
Atomic oxygen (AO) is the most abundant element in the low Earth orbit (LEO). It is the result of the dissociation of molecular oxygen by ultraviolet radiation from the sun. In the LEO, it collides with the materials used on spacecraft surfaces and causes degradation of these materials. The degradation of the materials on the surface of spacecrafts at LEO has been a significant problem for a long time. Kapton polyimide, polyhedral oligomeric silsesquioxane (POSS), silica, and Teflon are the materials extensively used in spacecraft industry, and like many other materials used in spacecraft industry, AO collision degradation is an important issue in their applications on spacecrafts. To investigate the surface chemistry of these materials in exposure to space AO, a computational chemical evaluation of the Kapton polyimide, POSS, amorphous silica, and Teflon was performed in separate simulations under similar conditions. For performing these simulations, the ReaxFF reactive force-field program was used, which provides the computational speed required to perform molecular dynamics (MD) simulations on system sizes sufficiently large to describe the full chemistry of the reactions. Using these simulations, the effects of AO impact on different materials and the role of impact energies, the content of material, and temperature of material on the behavior of the materials are studied. The ReaxFF results indicate that Kapton is less resistant than Teflon toward AO damage. These results are in good agreement with experiment. These simulations indicate that the amorphous silica shows the highest stability among these materials before the start of the highly exothermic silicon oxidation. We have verified that adding silicon to the bulk of the Kapton structure enhances the stability of the Kapton against AO impact. Our canonical MD simulations demonstrate that an increase in the heat transfer in materials during AO impact can provide a considerable decrease in the disintegration of the material. This effect is especially relevant in silica AO collision. Considerable experimental efforts have been undertaken to minimize such AO-based degradations. As our simulations demonstrate, ReaxFF can provide a cost-effective screening tool for future material optimization.
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Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions.
Zhou, H X; Szabo, A
1996-01-01
A general formalism is developed for calculating the time-dependent rate coefficient k(t) of an irreversible diffusion-influenced reaction. This formalism allows one to treat most factors that affect k(t), including rotational Brownian motion and conformational gating of reactant molecules and orientation constraint for product formation. At long times k(t) is shown to have the asymptotic expansion k(infinity)[1 + k(infinity) (pie Dt)-1/2 /4 pie D + ...], where D is the relative translational diffusion constant. An approximate analytical method for calculating k(t) is presented. This is based on the approximation that the probability density of the reactant pair in the reactive region keeps the equilibrium distribution but with a decreasing amplitude. The rate coefficient then is determined by the Green function in the absence of chemical reaction. Within the framework of this approximation, two general relations are obtained. The first relation allows the rate coefficient for an arbitrary amplitude of the reactivity to be found if the rate coefficient for one amplitude of the reactivity is known. The second relation allows the rate coefficient in the presence of conformational gating to be found from that in the absence of conformational gating. The ratio k(t)/k(0) is shown to be the survival probability of the reactant pair at time t starting from an initial distribution that is localized in the reactive region. This relation forms the basis of the calculation of k(t) through Brownian dynamics simulations. Two simulation procedures involving the propagation of nonreactive trajectories initiated only from the reactive region are described and illustrated on a model system. Both analytical and simulation results demonstrate the accuracy of the equilibrium-distribution approximation method. PMID:8913584
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Determination of detonation wave boundary angles via hydrocode simulations using CREST
NASA Astrophysics Data System (ADS)
Whitworth, N. J.; Childs, M.
2017-01-01
A key input parameter to Detonation Shock Dynamics models is the angle that the propagating detonation wave makes with the charge edge. This is commonly referred to as the boundary angle, and is a property of the explosive/confiner material combination. Such angles can be determined: (i) experimentally from measured detonation wave-shapes, (ii) theoretically, or (iii) via hydrocode simulations using a reactive burn model. Of these approaches: (i) is difficult because of resolution, (ii) breaks down for certain configurations, while (iii) requires a well validated model. In this paper, the CREST reactive burn model, which has previously been successful in modelling a wide range of explosive phenomena, is used to simulate recent Detonation Confinement Sandwich Tests conducted at LANL using the insensitive high explosive PBX 9502. Simulated detonation wave-shapes in PBX 9502 for a number of different confiner materials and combinations closely match those recorded from the experiments. Boundary angles were subsequently extracted from the simulated results via a wave-shape analysis toolkit. The results shown demonstrate the usefulness of CREST in determining detonation wave boundary angles for a range of explosive/confiner material combinations.
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A structurally driven analysis of thiol reactivity in mammalian albumins.
Spiga, Ottavia; Summa, Domenico; Cirri, Simone; Bernini, Andrea; Venditti, Vincenzo; De Chiara, Matteo; Priora, Raffaella; Frosali, Simona; Margaritis, Antonios; Di Giuseppe, Danila; Di Simplicio, Paolo; Niccolai, Neri
2011-04-01
Understanding the structural basis of protein redox activity is still an open question. Hence, by using a structural genomics approach, different albumins have been chosen to correlate protein structural features with the corresponding reaction rates of thiol exchange between albumin and disulfide DTNB. Predicted structures of rat, porcine, and bovine albumins have been compared with the experimentally derived human albumin. High structural similarity among these four albumins can be observed, in spite of their markedly different reactivity with DTNB. Sequence alignments offered preliminary hints on the contributions of sequence-specific local environments modulating albumin reactivity. Molecular dynamics simulations performed on experimental and predicted albumin structures reveal that thiolation rates are influenced by hydrogen bonding pattern and stability of the acceptor C34 sulphur atom with donor groups of nearby residues. Atom depth evolution of albumin C34 thiol groups has been monitored during Molecular Dynamic trajectories. The most reactive albumins appeared also the ones presenting the C34 sulphur atom on the protein surface with the highest accessibility. High C34 sulphur atom reactivity in rat and porcine albumins seems to be determined by the presence of additional positively charged amino acid residues favoring both the C34 S⁻ form and the approach of DTNB. Copyright © 2011 Wiley Periodicals, Inc.
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NASA Astrophysics Data System (ADS)
Eckert, Dominik; Kürzinger, Petra; Bauer, Robert; Griebler, Christian; Cirpka, Olaf A.
2015-01-01
Biodegradation in contaminated aquifers has been shown to be most pronounced at the fringe of contaminant plumes, where mixing of contaminated water and ambient groundwater, containing dissolved electron acceptors, stimulates microbial activity. While physical mixing of contaminant and electron acceptor by transverse dispersion has been shown to be the major bottleneck for biodegradation in steady-state plumes, so far little is known on the effect of flow and transport dynamics (caused, e.g., by a seasonally fluctuating groundwater table) on biodegradation in these systems. Towards this end we performed experiments in quasi-two-dimensional flow-through microcosms on aerobic toluene degradation by Pseudomonas putida F1. Plume dynamics were simulated by vertical alteration of the toluene plume position and experimental results were analyzed by reactive-transport modeling. We found that, even after disappearance of the toluene plume for two weeks, the majority of microorganisms stayed attached to the sediment and regained their full biodegradation potential within two days after reappearance of the toluene plume. Our results underline that besides microbial growth, also maintenance and dormancy are important processes that affect biodegradation performance under transient environmental conditions and therefore deserve increased consideration in future reactive-transport modeling.
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Hierarchical Petascale Simulation Framework for Stress Corrosion Cracking
DOE Office of Scientific and Technical Information (OSTI.GOV)
Vashishta, Priya
2014-12-01
Reaction Dynamics in Energetic Materials: Detonation is a prototype of mechanochemistry, in which mechanically and thermally induced chemical reactions far from equilibrium exhibit vastly different behaviors. It is also one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. The CACS group has performed multimillion-atom reactive MD simulations to reveal a novel two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine (RDX) crystal. Rapid production of N2 and H2O within ~10 ps is followed by delayed production of CO molecules within ~ 1 ns. They found that further decomposition towards the final products ismore » inhibited by the formation of large metastable C- and O-rich clusters with fractal geometry. The CACS group has also simulated the oxidation dynamics of close-packed aggregates of aluminum nanoparticles passivated by oxide shells. Their simulation results suggest an unexpectedly active role of the oxide shell as a nanoreactor.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Rahnamoun, A.; Duin, A. C. T. van
We study the dynamics of the collisions between amorphous silica structures and amorphous and crystal ice clusters with impact velocities of 1 km/s, 4 km/s, and 7 km/s using the ReaxFF reactive molecular dynamics simulation method. The initial ice clusters consist of 150 water molecules for the amorphous ice cluster and 128 water molecules for the crystal ice cluster. The ice clusters are collided on the surface of amorphous fully oxidized and suboxide silica. These simulations show that at 1 km/s impact velocities, all the ice clusters accumulate on the surface and at 4 km/s and 7 km/s impact velocities, some of the ice cluster moleculesmore » bounce back from the surface. At 4 km/s and 7 km/s impact velocities, few of the water molecules dissociations are observed. The effect of the second ice cluster impacts on the surfaces which are fully covered with ice, on the mass loss/accumulation is studied. These studies show that at 1 km/s impacts, the entire ice cluster accumulates on the surface at both first and second ice impacts. At higher impact velocities, some ice molecules which after the first ice impacts have been attached to the surface will separate from the surface after the second ice impacts at 7 km/s impact velocity. For the 4 km/s ice cluster impact, ice accumulation is observed for the crystal ice cluster impacts and ice separation is observed for the amorphous ice impacts. Observing the temperatures of the ice clusters during the collisions indicates that the possibility of electron excitement at impact velocities less than 10 km/s is minimal and ReaxFF reactive molecular dynamics simulation can predict the chemistry of these hypervelocity impacts. However, at impact velocities close to 10 km/s the average temperature of the impacting ice clusters increase to about 2000 K, with individual molecules occasionally reaching temperatures of over 8000 K and thus it will be prudent to consider the concept of electron excitation at these higher impact velocities, which goes beyond the current ReaxFF ability.« less
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Shock-induced mechanochemistry in heterogeneous reactive powder mixtures
NASA Astrophysics Data System (ADS)
Gonzales, Manny; Gurumurthy, Ashok; Kennedy, Gregory; Neel, Christopher; Gokhale, Arun; Thadhani, Naresh
The bulk response of compacted powder mixtures subjected to high-strain-rate loading conditions in various configurations is manifested from behavior at the meso-scale. Simulations at the meso-scale can provide an additional confirmation of the possible origins of the observed response. This work investigates the bulk dynamic response of Ti +B +Al reactive powder mixtures under two extreme loading configurations - uniaxial stress and strain loading - leveraging highly-resolved in-situ measurements and meso-scale simulations. Modified rod-on-anvil impact tests on a reactive pellet demonstrate an optimized stoichiometry promoting reaction in Ti +B +Al. Encapsulated powders subjected to shock compression via flyer plate tests provide possible evidence of a shock-induced reaction at high pressures. Meso-scale simulations of the direct experimental configurations employing highly-resolved microstructural features of the Ti +B compacted mixture show complex inhomogeneous deformation responses and reveal the importance of meso-scale features such as particle size and morphology and their effects on the measured response. Funding is generously provided by DTRA through Grant No. HDTRA1-10-1-0038 (Dr. Su Peiris - Program Manager) and by the SMART (AFRL Wright Patterson AFB) and NDSEG fellowships (High Performance Computing and Modernization Office).
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Propagation of gaseous detonation waves in a spatially inhomogeneous reactive medium
NASA Astrophysics Data System (ADS)
Mi, XiaoCheng; Higgins, Andrew J.; Ng, Hoi Dick; Kiyanda, Charles B.; Nikiforakis, Nikolaos
2017-05-01
Detonation propagation in a compressible medium wherein the energy release has been made spatially inhomogeneous is examined via numerical simulation. The inhomogeneity is introduced via step functions in the reaction progress variable, with the local value of energy release correspondingly increased so as to maintain the same average energy density in the medium and thus a constant Chapman-Jouguet (CJ) detonation velocity. A one-step Arrhenius rate governs the rate of energy release in the reactive zones. The resulting dynamics of a detonation propagating in such systems with one-dimensional layers and two-dimensional squares are simulated using a Godunov-type finite-volume scheme. The resulting wave dynamics are analyzed by computing the average wave velocity and one-dimensional averaged wave structure. In the case of sufficiently inhomogeneous media wherein the spacing between reactive zones is greater than the inherent reaction zone length, average wave speeds significantly greater than the corresponding CJ speed of the homogenized medium are obtained. If the shock transit time between reactive zones is less than the reaction time scale, then the classical CJ detonation velocity is recovered. The spatiotemporal averaged structure of the waves in these systems is analyzed via a Favre-averaging technique, with terms associated with the thermal and mechanical fluctuations being explicitly computed. The analysis of the averaged wave structure identifies the super-CJ detonations as weak detonations owing to the existence of mechanical nonequilibrium at the effective sonic point embedded within the wave structure. The correspondence of the super-CJ behavior identified in this study with real detonation phenomena that may be observed in experiments is discussed.
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Computational study of 3-D hot-spot initiation in shocked insensitive high-explosive
NASA Astrophysics Data System (ADS)
Najjar, F. M.; Howard, W. M.; Fried, L. E.; Manaa, M. R.; Nichols, A., III; Levesque, G.
2012-03-01
High-explosive (HE) material consists of large-sized grains with micron-sized embedded impurities and pores. Under various mechanical/thermal insults, these pores collapse generating hightemperature regions leading to ignition. A hydrodynamic study has been performed to investigate the mechanisms of pore collapse and hot spot initiation in TATB crystals, employing a multiphysics code, ALE3D, coupled to the chemistry module, Cheetah. This computational study includes reactive dynamics. Two-dimensional high-resolution large-scale meso-scale simulations have been performed. The parameter space is systematically studied by considering various shock strengths, pore diameters and multiple pore configurations. Preliminary 3-D simulations are undertaken to quantify the 3-D dynamics.
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Marsalek, Ondrej; Markland, Thomas E
2016-02-07
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
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NASA Astrophysics Data System (ADS)
Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi
2017-10-01
Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.
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NASA Astrophysics Data System (ADS)
Jain, S.; Mo, G.; Qiao, L.
2017-02-01
Reactive molecular dynamics simulations were conducted to study the flame speed enhancement phenomenon of a solid mono-propellant, Pentaerythritol Tetranitrate (PETN), when coupled to highly conductive multi-walled carbon nanotubes (MWCNTs). The simulations were based on the first-principles derived reactive force field, ReaxFF, which includes both the physical changes such as thermal transport and the chemical changes such as bond breaking and forming. An annular deposition of a PETN layer around the MWCNTs was considered. The thickness of the PETN layer and the diameter of the MWCNT were varied to understand the effect of the MWCNT loading ratio on the flame propagation. Flame speed enhancements up to 3 times the bulk value were observed. An optimal MWCNT loading ratio was determined. The enhancement was attributed to the layering of the PETN molecules around the MWCNT, which increased the heat transport among the PETN molecules near the MWCNT surface, thus causing the flame to travel faster. Furthermore, a stronger ignition source was required for the MWCNT-PETN complex because of the higher thermal transport among the PETN molecules along the MWCNT, which makes the ignition energy dissipate more quickly. Lastly, the MWCNT remained unburned during the PETN combustion process.
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High-temperature annealing of graphite: A molecular dynamics study
NASA Astrophysics Data System (ADS)
Petersen, Andrew; Gillette, Victor
2018-05-01
A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chao, Y.A.; Chapman, D.M.; Hill, D.J.
2000-12-15
The dynamic rod worth measurement (DRWM) technique is a method of quickly validating the predicted bank worth of control rods and shutdown rods. The DRWM analytic method is based on three-dimensional, space-time kinetic simulations of the rapid rod movements. Its measurement data is processed with an advanced digital reactivity computer. DRWM has been used as the method of bank worth validation at numerous plant startups with excellent results. The process and methodology of DRWM are described, and the measurement results of using DRWM are presented.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Li, L.; Steefel, C.I.; Williams, K.H.
2009-04-20
Injection of organic carbon into the subsurface as an electron donor for bioremediation of redox-sensitive contaminants like uranium often leads to mineral transformation and biomass accumulation, both of which can alter the flow field and potentially bioremediation efficacy. This work combines reactive transport modeling with a column experiment and field measurements to understand the biogeochemical processes and to quantify the biomass and mineral transformation/accumulation during a bioremediation experiment at a uranium contaminated site near Rifle, Colorado. We use the reactive transport model CrunchFlow to explicitly simulate microbial community dynamics of iron and sulfate reducers, and their impacts on reaction rates.more » The column experiment shows clear evidence of mineral precipitation, primarily in the form of calcite and iron monosulfide. At the field scale, reactive transport simulations suggest that the biogeochemical reactions occur mostly close to the injection wells where acetate concentrations are highest, with mineral precipitate and biomass accumulation reaching as high as 1.5% of the pore space. This work shows that reactive transport modeling coupled with field data can be an effective tool for quantitative estimation of mineral transformation and biomass accumulation, thus improving the design of bioremediation strategies.« less
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Li, Li; Steefel, Carl I; Williams, Kenneth H; Wilkins, Michael J; Hubbard, Susan S
2009-07-15
Injection of organic carbon into the subsurface as an electron donor for bioremediation of redox-sensitive contaminants like uranium often leads to mineral transformation and biomass accumulation, both of which can alter the flow field and potentially bioremediation efficacy. This work combines reactive transport modeling with a column experiment and field measurements to understand the biogeochemical processes and to quantify the biomass and mineral transformation/accumulation during a bioremediation experiment at a uranium contaminated site near Rifle, Colorado. We use the reactive transport model CrunchFlow to explicitly simulate microbial community dynamics of iron and sulfate reducers, and their impacts on reaction rates. The column experiment shows clear evidence of mineral precipitation, primarily in the form of calcite and iron monosulfide. At the field scale, reactive transport simulations suggest that the biogeochemical reactions occur mostly close to the injection wells where acetate concentrations are highest, with mineral precipitate and biomass accumulation reaching as high as 1.5% of the pore space. This work shows that reactive transport modeling coupled with field data can bean effective tool for quantitative estimation of mineral transformation and biomass accumulation, thus improving the design of bioremediation strategies.
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Hu, Guodong; Xu, Shicai; Wang, Jihua
2015-12-01
Inhibition of p53-MDM2 interaction by small molecules is considered to be a promising approach to re-activate wild-type p53 for tumor suppression. Several inhibitors of the MDM2-p53 interaction were designed and studied by the experimental methods and the molecular dynamics simulation. However, the unbinding mechanism was still unclear. The steered molecular dynamics simulations combined with Brownian dynamics fluctuation-dissipation theorem were employed to obtain the free-energy landscape of unbinding between MDM2 and their four ligands. It was shown that compounds 4 and 8 dissociate faster than compounds 5 and 7. The absolute binding free energies for these four ligands are in close agreement with experimental results. The open movement of helix II and helix IV in the MDM2 protein-binding pocket upon unbinding is also consistent with experimental MDM2-unbound conformation. We further found that different binding mechanisms among different ligands are associated with H-bond with Lys51 and Glu25. These mechanistic results may be useful for improving ligand design. © 2015 John Wiley & Sons A/S.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.
The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (Cmore » 2H 2) n +, just like ionized acetylene clusters. The fragmentation products result from reactive ion- molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4H 4 + and C 6H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts ( > 2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2H 2) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6H 6 + isomers. Lastly, these results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.« less
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Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; Fang, Yigang; Kostko, Oleg
2017-01-01
The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion–molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C2H2)n+, just like ionized acetylene clusters. The fragmentation products result from reactive ion–molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C4H4+ and C6H6+ structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C2H2)n+ isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C6H6+ isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM. PMID:28484019
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Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P; Fang, Yigang; Kostko, Oleg; Ahmed, Musahid; Head-Gordon, Martin
2017-05-23
The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C 2 H 2 ) n + , just like ionized acetylene clusters. The fragmentation products result from reactive ion-molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4 H 4 + and C 6 H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2 H 2 ) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6 H 6 + isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.
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Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; ...
2017-05-08
The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (Cmore » 2H 2) n +, just like ionized acetylene clusters. The fragmentation products result from reactive ion- molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4H 4 + and C 6H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts ( > 2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2H 2) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6H 6 + isomers. Lastly, these results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.« less
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Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX
NASA Astrophysics Data System (ADS)
Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kiabek
2015-06-01
We consider the ignition of a high-pressure gamma-phase of an explosive crystal of RDX which forms during overdriven shock initiation. Molecular dynamics (MD), with first-principles based or reactive force field based molecular potentials, provides a description of the chemistry as an extremely complex reaction network. The results of the molecular simulation is analyzed by sorting molecular product fragments into high and low molecular groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation, that has a single temperature and stress state for the mixture is used to represent the same RDX material and its chemistry. Each component in the continuum model has a corresponding Gibbs continuum potential, that are in turn inferred from molecular MD informed equation of state libraries such as CHEETAH, or are directly simulated by Monte Carlo MD simulations. Information about transport, kinetic rates and diffusion are derived from the MD simulation and the growth of a reactive hot spot in the RDX is studied with both simulations that mirror the other results to provide an essential, continuum/atomistic link. Supported by N000014-12-1-0555, subaward-36561937 (ONR).
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CCC7-119 Reactive Molecular Dynamics Simulations of Hot Spot Growth in Shocked Energetic Materials
DOE Office of Scientific and Technical Information (OSTI.GOV)
Thompson, Aidan P.
2015-03-01
The purpose of this work is to understand how defects control initiation in energetic materials used in stockpile components; Sequoia gives us the core-count to run very large-scale simulations of up to 10 million atoms and; Using an OpenMP threaded implementation of the ReaxFF package in LAMMPS, we have been able to get good parallel efficiency running on 16k nodes of Sequoia, with 1 hardware thread per core.
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NASA Astrophysics Data System (ADS)
Thompson, Aidan
2013-06-01
Initiation in energetic materials is fundamentally dependent on the interaction between a host of complex chemical and mechanical processes, occurring on scales ranging from intramolecular vibrations through molecular crystal plasticity up to hydrodynamic phenomena at the mesoscale. A variety of methods (e.g. quantum electronic structure methods (QM), non-reactive classical molecular dynamics (MD), mesoscopic continuum mechanics) exist to study processes occurring on each of these scales in isolation, but cannot describe how these processes interact with each other. In contrast, the ReaxFF reactive force field, implemented in the LAMMPS parallel MD code, allows us to routinely perform multimillion-atom reactive MD simulations of shock-induced initiation in a variety of energetic materials. This is done either by explicitly driving a shock-wave through the structure (NEMD) or by imposing thermodynamic constraints on the collective dynamics of the simulation cell e.g. using the Multiscale Shock Technique (MSST). These MD simulations allow us to directly observe how energy is transferred from the shockwave into other processes, including intramolecular vibrational modes, plastic deformation of the crystal, and hydrodynamic jetting at interfaces. These processes in turn cause thermal excitation of chemical bonds leading to initial chemical reactions, and ultimately to exothermic formation of product species. Results will be presented on the application of this approach to several important energetic materials, including pentaerythritol tetranitrate (PETN) and ammonium nitrate/fuel oil (ANFO). In both cases, we validate the ReaxFF parameterizations against QM and experimental data. For PETN, we observe initiation occurring via different chemical pathways, depending on the shock direction. For PETN containing spherical voids, we observe enhanced sensitivity due to jetting, void collapse, and hotspot formation, with sensitivity increasing with void size. For ANFO, we examine the effect of reaction rates on shock direction, fuel oil fraction, and crystal/fuel oil/void microstructural arrangement. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Dept. of Energy's National Nuclear Security Admin. under contract DEAC0494AL85000.
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Molecular Dynamics Simulation of the Titration of Polyoxocations in Aqueous Solution
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rustad, James R.
The aqueous complex ion Al30O8(OH)56(H2O)26 18+(Al30) has a variety of bridging and terminal amphoteric surface functional groups which deprotonate over a pH range of 4–7. Their relative degree of protonation is calculated here from a series of molecular dynamics simulations in what appear to be the first molecular dynamics simulations of an acidometric titration. In these simulations, a model M30O8(OH)56(H2O)26 18+ ion is embedded in aqueous solution and titrated with hydroxide ions in the presence of a charge-compensating background of perchlorate ions. Comparison with titration of a model M13O4(OH)24(H2O)12 7+ reveals that the M30 ion is more acidic than themore » M13 ion due to the presence of acidic nH2O functional groups. The higher acidities of the functional groups on the M30 ion appear to result from enhanced hydration. Metal–oxygen bond lengths are calculated for the ion in solution, an isolated ion in the gas phase, and in its crystalline hydrate sulfate salt. Gas-phase and crystalline bond lengths do not correlate well with those calculated in solution. The acidities do not relate in any simple way to the number of metals coordinating the surface functional group or the M-O bond length. Moreover, the calculated acidity in solution does not correlate with proton affinities calculated for the isolated ion in the absence of solvent. It is concluded that the search for simple indicators of structure–reactivity relationships at the level of individual reactive sites faces major limitations, unless specific information on the hydration states of the functional groups is available.« less
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Molecular Dynamics Modeling of Carbon Nanotube Composite Fracture Using ReaxFF
NASA Technical Reports Server (NTRS)
Jensen, Benjamin D.; Wise, Kristopher E.; Odegard, Gregory M.
2016-01-01
Carbon nanotube (CNT) fiber reinforced composites with specific tensile strengths and moduli approaching those of aerospace grade carbon fiber composites have recently been reported. This achievement was enabled by the emerging availability of high N/tex yarns in kilometer-scale quantities. While the production of this yarn is an impressive advance, its strength is still much lower than that of the individual CNTs comprising the yarn. Closing this gap requires understanding load transfer between CNTs at the nanometer dimensional scale. This work uses reactive molecular dynamics simulations to gain an understanding at the nanometer scale of the key factors that determine CNT nanocomposite mechanical performance, and to place more realistic upper bounds on the target properties. While molecular dynamics simulations using conventional force fields can predict elastic properties, the ReaxFF reactive forcefield can also model fracture behavior because of its ability to accurately describe bond breaking and formation during a simulation. The upper and lower bounds of CNT composite properties are investigated by comparing systems composed of CNTs continuously connected across the periodic boundary with systems composed of finite length CNTs. These lengths, effectively infinite for the continuous tubes and an aspect ratio of 13 for the finite length case, result from practical limitations on the number of atoms that can be included in a simulation. Experimentally measured aspect ratios are typically on the order of 100,000, so the calculated results should represent upper and lower limits on experimental mechanical properties. Finally, the effect of various degrees of covalent crosslinking between the CNTs and amorphous carbon matrix is considered to identify the amount of CNT-matrix covalent bonding that maximizes overall composite properties.
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Molecular dynamics simulations and photoluminescence measurements of annealed ZnO surfaces
NASA Astrophysics Data System (ADS)
Min, Tjun Kit; Yoon, Tiem Leong; Ling, Chuo Ann; Mahmud, Shahrom; Lim, Thong Leng; Saw, Kim Guan
2017-06-01
The effect of thermal annealing on wurtzite ZnO, terminated by two surfaces, (000 1 bar) (which is oxygen-terminated) and (0 0 0 1) (which is Zn-terminated), is investigated via molecular dynamics simulation using reactive force field (ReaxFF). As a result of annealing at a threshold temperature range of 700 K
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Molecular Dynamics Studies of Thermal Induced Chemistry in TATB
NASA Astrophysics Data System (ADS)
Quenneville, Jason; Germann, Timothy
2007-06-01
A reactive force field (ReaxFF^2) is used with molecular dynamics to probe the chemistry induced by intense heating (accelerated `cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 800-atom, simulations, we will show the reaction rate as a function of temperature and density as well as the time evolution of reaction products. A larger simulation (with 14,000 atoms) will illustrate the effect of system size on both carbon clustering and reaction rate. Insight into the mechanisms of product formation will be given, as well as the chemical structure (graphitic or diamond-like) of the carbon clusters obtained. ^2 A. C. T. Van Duin, et al, J. Phys. Chem. A, 1005, 9396 (2001).
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NASA Astrophysics Data System (ADS)
Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng
2015-12-01
To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06016h
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reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.
Müller, Julian; Hartke, Bernd
2016-08-09
Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach.
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Reactivity of Free Malondialdehyde during In Vitro Simulated Gastrointestinal Digestion.
Vandemoortele, Angelique; Babat, Pinar; Yakubu, Mariam; De Meulenaer, Bruno
2017-03-15
An aqueous buffer, a saturated glycerol triheptanoate oil, and a Tween 20 stabilized fully hydrogenated coconut oil-in-water emulsion, all spiked with malondialdehyde, were subjected to in vitro digestion. A dynamic equilibrium between malondialdehyde, its aldol self-condensation products, and its hydrolytic cleavage products was observed. This equilibrium depended upon the kind of sample and the temperature at which these samples were preincubated during 24 h. The presence of oil during gastric digestion protected the aldol self-condensation and cleavage products from conversion to malondialdehyde, which occurred in the aqueous acidic gastric chyme. In parallel, the presence of oil enhanced the reactivity of malondialdehyde throughout the gastrointestinal digestion process. Malondialdehyde recoveries after digestion varied between 42 and 90%, depending upon the model system studied, with the aldol self-condensation as the main reaction pathway. In conclusion, this study revealed that malondialdehyde is a very reactive molecule whose reactivity does not stop at the point of ingestion.
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Reactive collisions for NO(2Π) + N(4S) at temperatures relevant to the hypersonic flight regime.
Denis-Alpizar, Otoniel; Bemish, Raymond J; Meuwly, Markus
2017-01-18
The NO(X 2 Π) + N( 4 S) reaction which occurs entirely in the triplet manifold of N 2 O is investigated using quasiclassical trajectories and quantum simulations. Fully-dimensional potential energy surfaces for the 3 A' and 3 A'' states are computed at the MRCI+Q level of theory and are represented using a reproducing kernel Hilbert space. The N-exchange and N 2 -formation channels are followed by using the multi-state adiabatic reactive molecular dynamics method. Up to 5000 K these reactions occur predominantly on the N 2 O 3 A'' surface. However, for higher temperatures the contributions of the 3 A' and 3 A'' states are comparable and the final state distributions are far from thermal equilibrium. From the trajectory simulations a new set of thermal rate coefficients of up to 20 000 K is determined. Comparison of the quasiclassical trajectory and quantum simulations shows that a classical description is a good approximation as determined from the final state analysis.
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Molecular dynamical simulations of melting Al nanoparticles using a reaxff reactive force field
NASA Astrophysics Data System (ADS)
Liu, Junpeng; Wang, Mengjun; Liu, Pingan
2018-06-01
Molecular dynamics simulations were performed to study thermal properties and melting points of Al nanoparticles by using a reactive force field under canonical (NVT) ensembles. Al nanoparticles (particle size 2–4 nm) were considered in simulations. A combination of structural and thermodynamic parameters such as the Lindemann index, heat capacities, potential energy and radial-distribution functions was employed to decide melting points. We used annealing technique to obtain the initial Al nanoparticle model. Comparison was made between ReaxFF results and other simulation results. We found that ReaxFF force field is reasonable to describe Al cluster melting behavior. The linear relationship between particle size and melting points was found. After validating the ReaxFF force field, more attention was paid on thermal properties of Al nanoparticles with different defect concentrations. 4 nm Al nanoparticles with different defect concentrations (5%–20%) were considered in this paper. Our results revealed that: the melting points are irrelevant with defect concentration at a certain particle size. The extra storage energy of Al nanoparticles is proportional to nanoparticles’ defect concentration, when defect concentration is 5%–15%. While the particle with 20% defect concentration is similar to the cluster with 10% defect concentration. After melting, the extra energy of all nanoparticles decreases sharply, and the extra storage energy is nearly zero at 600 K. The centro-symmetry parameter analysis shows structure evolution of different models during melting processes.
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2016-01-01
An important challenge in the simulation of biomolecular systems is a quantitative description of the protonation and deprotonation process of amino acid residues. Despite the seeming simplicity of adding or removing a positively charged hydrogen nucleus, simulating the actual protonation/deprotonation process is inherently difficult. It requires both the explicit treatment of the excess proton, including its charge defect delocalization and Grotthuss shuttling through inhomogeneous moieties (water and amino residues), and extensive sampling of coupled condensed phase motions. In a recent paper (J. Chem. Theory Comput.2014, 10, 2729−273725061442), a multiscale approach was developed to map high-level quantum mechanics/molecular mechanics (QM/MM) data into a multiscale reactive molecular dynamics (MS-RMD) model in order to describe amino acid deprotonation in bulk water. In this article, we extend the fitting approach (called FitRMD) to create MS-RMD models for ionizable amino acids within proteins. The resulting models are shown to faithfully reproduce the free energy profiles of the reference QM/MM Hamiltonian for PT inside an example protein, the ClC-ec1 H+/Cl– antiporter. Moreover, we show that the resulting MS-RMD models are computationally efficient enough to then characterize more complex 2-dimensional free energy surfaces due to slow degrees of freedom such as water hydration of internal protein cavities that can be inherently coupled to the excess proton charge translocation. The FitRMD method is thus shown to be an effective way to map ab initio level accuracy into a much more computationally efficient reactive MD method in order to explicitly simulate and quantitatively describe amino acid protonation/deprotonation in proteins. PMID:26734942
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Lee, Sangyun; Liang, Ruibin; Voth, Gregory A; Swanson, Jessica M J
2016-02-09
An important challenge in the simulation of biomolecular systems is a quantitative description of the protonation and deprotonation process of amino acid residues. Despite the seeming simplicity of adding or removing a positively charged hydrogen nucleus, simulating the actual protonation/deprotonation process is inherently difficult. It requires both the explicit treatment of the excess proton, including its charge defect delocalization and Grotthuss shuttling through inhomogeneous moieties (water and amino residues), and extensive sampling of coupled condensed phase motions. In a recent paper (J. Chem. Theory Comput. 2014, 10, 2729-2737), a multiscale approach was developed to map high-level quantum mechanics/molecular mechanics (QM/MM) data into a multiscale reactive molecular dynamics (MS-RMD) model in order to describe amino acid deprotonation in bulk water. In this article, we extend the fitting approach (called FitRMD) to create MS-RMD models for ionizable amino acids within proteins. The resulting models are shown to faithfully reproduce the free energy profiles of the reference QM/MM Hamiltonian for PT inside an example protein, the ClC-ec1 H(+)/Cl(-) antiporter. Moreover, we show that the resulting MS-RMD models are computationally efficient enough to then characterize more complex 2-dimensional free energy surfaces due to slow degrees of freedom such as water hydration of internal protein cavities that can be inherently coupled to the excess proton charge translocation. The FitRMD method is thus shown to be an effective way to map ab initio level accuracy into a much more computationally efficient reactive MD method in order to explicitly simulate and quantitatively describe amino acid protonation/deprotonation in proteins.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less
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Nomura, Ken-Ichi; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya; van Duin, Adri C T; Goddard, William A
2007-10-05
Mechanical stimuli in energetic materials initiate chemical reactions at shock fronts prior to detonation. Shock sensitivity measurements provide widely varying results, and quantum-mechanical calculations are unable to handle systems large enough to describe shock structure. Recent developments in reactive force-field molecular dynamics (ReaxFF-MD) combined with advances in parallel computing have paved the way to accurately simulate reaction pathways along with the structure of shock fronts. Our multimillion-atom ReaxFF-MD simulations of l,3,5-trinitro-l,3,5-triazine (RDX) reveal that detonation is preceded by a transition from a diffuse shock front with well-ordered molecular dipoles behind it to a disordered dipole distribution behind a sharp front.
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Yogurtcu, Osman N.; Johnson, Margaret E.
2015-01-01
The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute to dense systems. PMID:26328828
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Rutqvist, Jonny; Cappa, Frederic; Rinaldi, Antonio P.
We summarize recent modeling studies of injection-induced fault reactivation, seismicity, and its potential impact on surface structures and nuisance to the local human population. We used coupled multiphase fluid flow and geomechanical numerical modeling, dynamic wave propagation modeling, seismology theories, and empirical vibration criteria from mining and construction industries. We first simulated injection-induced fault reactivation, including dynamic fault slip, seismic source, wave propagation, and ground vibrations. From co-seismic average shear displacement and rupture area, we determined the moment magnitude to about M w = 3 for an injection-induced fault reactivation at a depth of about 1000 m. We then analyzedmore » the ground vibration results in terms of peak ground acceleration (PGA), peak ground velocity (PGV), and frequency content, with comparison to the U.S. Bureau of Mines’ vibration criteria for cosmetic damage to buildings, as well as human-perception vibration limits. For the considered synthetic M w = 3 event, our analysis showed that the short duration, high frequency ground motion may not cause any significant damage to surface structures, and would not cause, in this particular case, upward CO 2 leakage, but would certainly be felt by the local population.« less
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Emergence of chaos in a spatially confined reactive system
NASA Astrophysics Data System (ADS)
Voorsluijs, Valérie; De Decker, Yannick
2016-11-01
In spatially restricted media, interactions between particles and local fluctuations of density can lead to important deviations of the dynamics from the unconfined, deterministic picture. In this context, we investigated how molecular crowding can affect the emergence of chaos in small reactive systems. We developed to this end an amended version of the Willamowski-Rössler model, where we account for the impenetrability of the reactive species. We analyzed the deterministic kinetics of this model and studied it with spatially-extended stochastic simulations in which the mobility of particles is included explicitly. We show that homogeneous fluctuations can lead to a destruction of chaos through a fluctuation-induced collision between chaotic trajectories and absorbing states. However, an interplay between the size of the system and the mobility of particles can counterbalance this effect so that chaos can indeed be found when particles diffuse slowly. This unexpected effect can be traced back to the emergence of spatial correlations which strongly affect the dynamics. The mobility of particles effectively acts as a new bifurcation parameter, enabling the system to switch from stationary states to absorbing states, oscillations or chaos.
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Eckert, Dominik; Kürzinger, Petra; Bauer, Robert; Griebler, Christian; Cirpka, Olaf A
2015-01-01
Biodegradation in contaminated aquifers has been shown to be most pronounced at the fringe of contaminant plumes, where mixing of contaminated water and ambient groundwater, containing dissolved electron acceptors, stimulates microbial activity. While physical mixing of contaminant and electron acceptor by transverse dispersion has been shown to be the major bottleneck for biodegradation in steady-state plumes, so far little is known on the effect of flow and transport dynamics (caused, e.g., by a seasonally fluctuating groundwater table) on biodegradation in these systems. Towards this end we performed experiments in quasi-two-dimensional flow-through microcosms on aerobic toluene degradation by Pseudomonas putida F1. Plume dynamics were simulated by vertical alteration of the toluene plume position and experimental results were analyzed by reactive-transport modeling. We found that, even after disappearance of the toluene plume for two weeks, the majority of microorganisms stayed attached to the sediment and regained their full biodegradation potential within two days after reappearance of the toluene plume. Our results underline that besides microbial growth, also maintenance and dormancy are important processes that affect biodegradation performance under transient environmental conditions and therefore deserve increased consideration in future reactive-transport modeling. Copyright © 2014 Elsevier B.V. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Holland, Troy; Bhat, Sham; Marcy, Peter
Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive computational fluid dynamics (CFD) simulations are valuable tools in evaluating and deploying oxyfuel and other carbon capture technologies, either as retrofit technologies or for new construction. However, accurate predictive combustor simulations require physically realistic submodels with low computational requirements. A recent sensitivity analysis of a detailed char conversion model (Char Conversion Kinetics (CCK)) found thermal annealing to be an extremely sensitive submodel. In the present work, further analysis of the previous annealing model revealed significant disagreement with numerous datasets from experiments performed after that annealing model was developed. Themore » annealing model was accordingly extended to reflect experimentally observed reactivity loss, because of the thermal annealing of a variety of coals under diverse char preparation conditions. The model extension was informed by a Bayesian calibration analysis. In addition, since oxyfuel conditions include extraordinarily high levels of CO 2, the development of a first-ever CO 2 reactivity loss model due to annealing is presented.« less
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Holland, Troy; Bhat, Sham; Marcy, Peter; ...
2017-08-25
Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive computational fluid dynamics (CFD) simulations are valuable tools in evaluating and deploying oxyfuel and other carbon capture technologies, either as retrofit technologies or for new construction. However, accurate predictive combustor simulations require physically realistic submodels with low computational requirements. A recent sensitivity analysis of a detailed char conversion model (Char Conversion Kinetics (CCK)) found thermal annealing to be an extremely sensitive submodel. In the present work, further analysis of the previous annealing model revealed significant disagreement with numerous datasets from experiments performed after that annealing model was developed. Themore » annealing model was accordingly extended to reflect experimentally observed reactivity loss, because of the thermal annealing of a variety of coals under diverse char preparation conditions. The model extension was informed by a Bayesian calibration analysis. In addition, since oxyfuel conditions include extraordinarily high levels of CO 2, the development of a first-ever CO 2 reactivity loss model due to annealing is presented.« less
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Chowell, Gerardo; Fuentes, R; Olea, A; Aguilera, X; Nesse, H; Hyman, J M
2013-01-01
We use a stochastic simulation model to explore the effect of reactive intervention strategies during the 2002 dengue outbreak in the small population of Easter Island, Chile. We quantified the effect of interventions on the transmission dynamics and epidemic size as a function of the simulated control intensity levels and the timing of initiation of control interventions. Because no dengue outbreaks had been reported prior to 2002 in Easter Island, the 2002 epidemic provided a unique opportunity to estimate the basic reproduction number R0 during the initial epidemic phase, prior to the start of control interventions. We estimated R0 at 27.2 (95%CI: 14.8, 49.3). We found that the final epidemic size is highly sensitive to the timing of start of interventions. However, even when the control interventions start several weeks after the epidemic onset, reactive intervention efforts can have a significant impact on the final epidemic size. Our results indicate that the rapid implementation of control interventions can have a significant effect in reducing the epidemic size of dengue epidemics.
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NASA Astrophysics Data System (ADS)
Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan
2015-11-01
We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).
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A semi-metallic layer in detonating nitromethane
NASA Astrophysics Data System (ADS)
Reed, Evan; Manaa, Riad; Fried, Laurence; Glaesemann, Kurt; Joannopoulos, John
2007-06-01
We present the first ever glimpse behind a detonation front in a chemically reactive quantum molecular dynamics simulation (up to 0.2 ns) of the explosive nitromethane (CH3NO2) represented by the density-functional-based tight-binding method (DFTB). This simulation is enabled by our recently developed multi-scale shock wave molecular dynamics technique (MSST) that opens the door to longer duration simulations by several orders of magnitude. The electronic DOS around the Fermi energy initially increases as metastable material states are produced but then later decreases, perhaps unexpectedly. These changes indicate that the shock front is characterized by an increase in optical thickness followed by a reduction in optical thickness hundreds of picoseconds behind the front, explaining recent experimental observations. We find that a significant population of intermediate metastable molecules are charged and charged species play an important role in the density of states evolution and a possible Mott metal-insulator transition.
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Lee, Mal-Soon; Peter McGrail, B; Rousseau, Roger; Glezakou, Vassiliki-Alexandra
2015-10-12
The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity.
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We performed three column tests to study the behavior of permeable reactive barrier (PRB) materials to remove arsenic under dynamic flow conditions in the absence, as well as in the presence, of added phosphate and silicate. The column consisted of a 10.3-cm depth of 50 : 50 (w :...
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Zhang, Chaoyang; Wen, Yushi; Xue, Xianggui
2014-08-13
Functionalized graphene sheet (FGS) is a promising additive that enhances fuel/propellant combustion, and the determination of its mechanism has attracted much interest. In the present study, a series of molecular dynamic simulations based on a reactive force field (ReaxFF) are performed to explore the catalytic activity (CA) of FGS in the thermal decay of nitromethane (NM, CH3NO2). FGSs and pristine graphene sheets (GSs) are oxidized in hot NM liquid to increase their functionalities and subsequently show self-enhanced CAs during the decay. The CAs result from the interatomic exchanges between the functional groups on the sheets and the NM liquid, i.e., mainly between H and O atoms. CA is dependent on the density of NM, functionalities of sheets, and temperature. The GSs and FGSs that originally exhibit different functionalities tend to possess similar functionalities and consequently similar CAs as temperature increases. Other carbon materials and their oxides can accelerate combustion of other fuels/propellants similar to NM, provided that they can be dispersed and their key reaction steps in combustion are similar to NM.
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NASA Technical Reports Server (NTRS)
Paxson, Daniel E.
2018-01-01
A simplified, two-dimensional, computational fluid dynamic (CFD) simulation, with a reactive Euler solver is used to examine possible causes for the low detonation wave propagation speeds that are consistently observed in air breathing rotating detonation engine (RDE) experiments. Intense, small-scale turbulence is proposed as the primary mechanism. While the solver cannot model this turbulence, it can be used to examine the most likely, and profound effect of turbulence. That is a substantial enlargement of the reaction zone, or equivalently, an effective reduction in the chemical reaction rate. It is demonstrated that in the unique flowfield of the RDE, a reduction in reaction rate leads to a reduction in the detonation speed. A subsequent test of reduced reaction rate in a purely one-dimensional pulsed detonation engine (PDE) flowfield yields no reduction in wave speed. The reasons for this are explained. The impact of reduced wave speed on RDE performance is then examined, and found to be minimal. Two other potential mechanisms are briefly examined. These are heat transfer, and reactive mixture non-uniformity. In the context of the simulation used for this study, both mechanisms are shown to have negligible effect on either wave speed or performance.
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NASA Astrophysics Data System (ADS)
Arshad, Suhana; Raveendran Pillai, Renjith; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Renjith, Rishikesh; Panicker, C. Yohannan; Van Alsenoy, C.
2017-06-01
In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed to fit the title compound into the binding site of MOA-B enzyme.
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NASA Astrophysics Data System (ADS)
Takamatsu, Kuniyoshi; Nakagawa, Shigeaki; Takeda, Tetsuaki
Safety demonstration tests using the High Temperature Engineering Test Reactor (HTTR) are in progress to verify its inherent safety features and improve the safety technology and design methodology for High-temperature Gas-cooled Reactors (HTGRs). The reactivity insertion test is one of the safety demonstration tests for the HTTR. This test simulates the rapid increase in the reactor power by withdrawing the control rod without operating the reactor power control system. In addition, the loss of coolant flow tests has been conducted to simulate the rapid decrease in the reactor power by tripping one, two or all out of three gas circulators. The experimental results have revealed the inherent safety features of HTGRs, such as the negative reactivity feedback effect. The numerical analysis code, which was named-ACCORD-, was developed to analyze the reactor dynamics including the flow behavior in the HTTR core. We have modified this code to use a model with four parallel channels and twenty temperature coefficients. Furthermore, we added another analytical model of the core for calculating the heat conduction between the fuel channels and the core in the case of the loss of coolant flow tests. This paper describes the validation results for the newly developed code using the experimental results. Moreover, the effect of the model is formulated quantitatively with our proposed equation. Finally, the pre-analytical result of the loss of coolant flow test by tripping all gas circulators is also discussed.
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Jain, S; Qiao, L
2018-06-21
This work explored the mechanism of spontaneous combustion of hydrogen-oxygen mixtures inside nanobubbles (which were generated by water electrolysis) using reactive molecular dynamic simulations based on the first-principles derived reactive force field ReaxFF. The effects of surface-assisted dissociation of H 2 and O 2 gases that produced H and O radicals were examined. Additionally, the ignition outcome and species evolution as a function of the initial system pressure (or bubble size) were studied. A significant amount of hydrogen peroxide (H 2 O 2 ), 6-140 times water (H 2 O), was observed in the combustion products. This was attributed to the low-temperature (∼300 K) and high-pressure (2-80 atm) conditions at which the chemical reactions were taking place. In addition, the rate of consumption of H 2 and O 2 molecules was found to increase with an increase in added H and O radical concentrations and initial system pressure. The rate at which heat was being lost from the combustion chamber (nanobubbles) was also compared to the rate at which heat was being released from the chemical reactions. Only a slight rise in the reaction temperature was observed (∼68 K), signifying that, at such small scales, heat losses dominate. The resulting chemistry was quite different from macroscopic combustion, which usually takes place at a much higher temperatures of above 1000 K.
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Dynamic adaptive chemistry with operator splitting schemes for reactive flow simulations
NASA Astrophysics Data System (ADS)
Ren, Zhuyin; Xu, Chao; Lu, Tianfeng; Singer, Michael A.
2014-04-01
A numerical technique that uses dynamic adaptive chemistry (DAC) with operator splitting schemes to solve the equations governing reactive flows is developed and demonstrated. Strang-based splitting schemes are used to separate the governing equations into transport fractional substeps and chemical reaction fractional substeps. The DAC method expedites the numerical integration of reaction fractional substeps by using locally valid skeletal mechanisms that are obtained using the directed relation graph (DRG) reduction method to eliminate unimportant species and reactions from the full mechanism. Second-order temporal accuracy of the Strang-based splitting schemes with DAC is demonstrated on one-dimensional, unsteady, freely-propagating, premixed methane/air laminar flames with detailed chemical kinetics and realistic transport. The use of DAC dramatically reduces the CPU time required to perform the simulation, and there is minimal impact on solution accuracy. It is shown that with DAC the starting species and resulting skeletal mechanisms strongly depend on the local composition in the flames. In addition, the number of retained species may be significant only near the flame front region where chemical reactions are significant. For the one-dimensional methane/air flame considered, speed-up factors of three and five are achieved over the entire simulation for GRI-Mech 3.0 and USC-Mech II, respectively. Greater speed-up factors are expected for larger chemical kinetics mechanisms.
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Reactive molecular simulation on the calcium silicate hydrates/polyethylene glycol composites
NASA Astrophysics Data System (ADS)
Zhou, Yang; Hou, Dongshuai; Jiang, Jinyang; She, Wei; Yu, Jiao
2017-11-01
Calcium silicate hydrates (C-S-H) may potentially exhibit extraordinary performance when modified by polymers, in which way the properties of cement-based materials can be improved from the genetic level. In this molecular dynamics simulation of the interaction between C-S-H and polyethylene glycol, apart from the H bond network connection in the interface, another chemical adsorption was observed. Calcium of C-S-H broke the Csbnd O bond of PEG and formed a new Casbnd C connection, which created a stronger link between the organic and inorganic phases.
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Buckybomb: Reactive Molecular Dynamics Simulation
Chaban, Vitaly V.; Fileti, Eudes Eterno; Prezhdo, Oleg V.
2015-02-24
Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C 60(NO 2) 12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO 2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyballmore » surface. NO oxidizes into NO 2, and C 60 falls apart, liberating CO 2. At the highest temperatures, CO 2 gives rise to diatomic carbon. Lastly, the study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material.« less
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Uribe-Sánchez, Andrés; Savachkin, Alex
2011-01-01
As recently pointed out by the Institute of Medicine, the existing pandemic mitigation models lack the dynamic decision support capability. We develop a large-scale simulation-driven optimization model for generating dynamic predictive distribution of vaccines and antivirals over a network of regional pandemic outbreaks. The model incorporates measures of morbidity, mortality, and social distancing, translated into the cost of lost productivity and medical expenses. The performance of the strategy is compared to that of the reactive myopic policy, using a sample outbreak in Fla, USA, with an affected population of over four millions. The comparison is implemented at different levels of vaccine and antiviral availability and administration capacity. Sensitivity analysis is performed to assess the impact of variability of some critical factors on policy performance. The model is intended to support public health policy making for effective distribution of limited mitigation resources. PMID:23074658
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Scott Stewart, D., E-mail: dss@illinois.edu; Hernández, Alberto; Lee, Kibaek
The estimation of pressure and temperature histories, which are required to understand chemical pathways in condensed phase explosives during detonation, is discussed. We argue that estimates made from continuum models, calibrated by macroscopic experiments, are essential to inform modern, atomistic-based reactive chemistry simulations at detonation pressures and temperatures. We present easy to implement methods for general equation of state and arbitrarily complex chemical reaction schemes that can be used to compute reactive flow histories for the constant volume, the energy process, and the expansion process on the Rayleigh line of a steady Chapman-Jouguet detonation. A brief review of state-of-the-art ofmore » two-component reactive flow models is given that highlights the Ignition and Growth model of Lee and Tarver [Phys. Fluids 23, 2362 (1980)] and the Wide-Ranging Equation of State model of Wescott, Stewart, and Davis [J. Appl. Phys. 98, 053514 (2005)]. We discuss evidence from experiments and reactive molecular dynamic simulations that motivate models that have several components, instead of the two that have traditionally been used to describe the results of macroscopic detonation experiments. We present simplified examples of a formulation for a hypothetical explosive that uses simple (ideal) equation of state forms and detailed comparisons. Then, we estimate pathways computed from two-component models of real explosive materials that have been calibrated with macroscopic experiments.« less
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NASA Astrophysics Data System (ADS)
Ghosh, Shibaji; Chandar, Nellore Bhanu; Jana, Kalyanashis; Ganguly, Bishwajit
2017-08-01
Inhibition of acetylcholinesterase (AChE) with organophosphorus compounds has a detrimental effect on human life. Oxime K203 seems to be one of the promising reactivators for tabun-inhibited AChE than (K027, K127, and K628). These reactivators differ only in the linker units between the two pyridinium rings. The conformational analyses performed with quantum chemical RHF/6-31G* level for K027, K127, K203 and K628 showed that the minimum energy conformers have different orientations of the active and peripheral pyridinium rings for these reactivator molecules. K203 with (-CH2-CH=CH-CH2-) linker unit possesses more open conformation compared to the other reactivators. Such orientation of K203 experiences favorable interaction with the surrounding residues of catalytic anionic site (CAS) and peripheral anionic site (PAS) of tabun-inhibited AChE. From the steered molecular dynamics simulations, it has been observed that the oxygen atom of the oxime group of K203 reactivator approaches nearest to the P-atom of the SUN203 (3.75 Å) at lower time scales (less than 1000 ps) as compared to the other reactivators. K203 experiences less number of hydrophobic interaction with the PAS residues which is suggested to be an important factor for the efficient reactivation process. In addition, K203 crates large number of H-bonding with CAS residues SUN203, Phe295, Tyr337, Phe338 and His447. K203 barely changes its conformation during the SMD simulation process and hence the energy penalty to adopt any other conformation is minimal in this case as compared to the other reactivators. The molecular mechanics and Poisson-Boltzmann surface area binding energies obtained for the interaction of K203 inside the gorge of tabun inhibited AChE is substantially higher (-290.2 kcal/mol) than the corresponding K628 reactivator (-260.4 kcal/mol), which also possess unsaturated aromatic linker unit.
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NASA Astrophysics Data System (ADS)
Saar, Martin O.
2011-11-01
Understanding the fluid dynamics of supercritical carbon dioxide (CO2) in brine- filled porous media is important for predictions of CO2 flow and brine displacement during geologic CO2 sequestration and during geothermal energy capture using sequestered CO2 as the subsurface heat extraction fluid. We investigate multiphase fluid flow in porous media employing particle image velocimetry experiments and lattice-Boltzmann fluid flow simulations at the pore scale. In particular, we are interested in the motion of a drop (representing a CO2 bubble) through an orifice in a plate, representing a simplified porous medium. In addition, we study single-phase/multicomponent reactive transport experimentally by injecting water with dissolved CO2 into rocks/sediments typically considered for CO2 sequestration to investigate how resultant fluid-mineral reactions modify permeability fields. Finally, we investigate numerically subsurface CO2 and heat transport at the geologic formation scale.
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The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.
Yao, Kun; Herr, John E; Toth, David W; Mckintyre, Ryker; Parkhill, John
2018-02-28
Traditional force fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a data-driven approach is naturally inefficient for long-range interatomic forces that have simple physical formulas. In this manuscript we construct a hybrid model chemistry consisting of a nearsighted neural network potential with screened long-range electrostatic and van der Waals physics. This trained potential, simply dubbed "TensorMol-0.1", is offered in an open-source Python package capable of many of the simulation types commonly used to study chemistry: geometry optimizations, harmonic spectra, open or periodic molecular dynamics, Monte Carlo, and nudged elastic band calculations. We describe the robustness and speed of the package, demonstrating its millihartree accuracy and scalability to tens-of-thousands of atoms on ordinary laptops. We demonstrate the performance of the model by reproducing vibrational spectra, and simulating the molecular dynamics of a protein. Our comparisons with electronic structure theory and experimental data demonstrate that neural network molecular dynamics is poised to become an important tool for molecular simulation, lowering the resource barrier to simulating chemistry.
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NASA Astrophysics Data System (ADS)
Sun, Rui; Park, Kyoyeon; de Jong, Wibe A.; Lischka, Hans; Windus, Theresa L.; Hase, William L.
2012-07-01
Electronic structure calculations and direct chemical dynamics simulations are used to study the formation and decomposition of dioxetane on its ground state singlet potential energy surface. The stationary points for 1O2 + C2H4, the singlet .O-O-CH2-CH2. biradical, the transition state (TS) connecting this biradical with dioxetane, and the two transition states and gauche .O-CH2-CH2-O. biradical connecting dioxetane with the formaldehyde product molecules are investigated at different levels of electronic structure theory including UB3LYP, UMP2, MRMP2, and CASSCF and a range of basis sets. The UB3LYP/6-31G* method was found to give representative energies for the reactive system and was used as a model for the simulations. UB3LYP/6-31G* direct dynamics trajectories were initiated at the TS connecting the .O-O-CH2-CH2. biradical and dioxetane by sampling the TS's vibrational energy levels, and rotational and reaction coordinate energies, with Boltzmann distributions at 300, 1000, and 1500 K. This corresponds to the transition state theory model for trajectories that pass the TS. The trajectories were directed randomly towards both the biradical and dioxetane. A small fraction of the trajectories directed towards the biradical recrossed the TS and formed dioxetane. The remainder formed 1O2 + C2H4 and of these ˜ 40% went directly from the TS to 1O2 + C2H4 without getting trapped and forming an intermediate in the .O-O-CH2-CH2. biradical potential energy minimum, a non-statistical result. The dioxetane molecules which are formed dissociate to two formaldehyde molecules with a rate constant two orders of magnitude smaller than that predicted by Rice-Ramsperger-Kassel-Marcus theory. The reaction dynamics from dioxetane to the formaldehyde molecules do not follow the intrinsic reaction coordinate or involve trapping in the gauche .O-CH2-CH2-O. biradical potential energy minimum. Important non-statistical dynamics are exhibited for this reactive system.
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NASA Astrophysics Data System (ADS)
Valentini, Paolo; Schwartzentruber, Thomas E.; Cozmuta, Ioana
2011-12-01
Atomic-level Grand Canonical Monte Carlo (GCMC) simulations equipped with a reactive force field (ReaxFF) are used to study atomic oxygen adsorption on a Pt(111) surface. The off-lattice GCMC calculations presented here rely solely on the interatomic potential and do not necessitate the pre-computation of surface adlayer structures and their interpolation. As such, they provide a predictive description of adsorbate phases. In this study, validation is obtained with experimental evidence (steric heats of adsorption and isotherms) as well as DFT-based state diagrams available in the literature. The ReaxFF computed steric heats of adsorption agree well with experimental data, and this study clearly shows that indirect dissociative adsorption of O2 on Pt(111) is an activated process at non-zero coverages, with an activation energy that monotonically increases with coverage. At a coverage of 0.25 ML, a highly ordered p(2 × 2) adlayer is found, in agreement with several low-energy electron diffraction observations. Isotherms obtained from the GCMC simulations compare qualitatively and quantitatively well with previous DFT-based state diagrams, but are in disagreement with the experimental data sets available. ReaxFF GCMC simulations at very high coverages show that O atoms prefer to bind in fcc hollow sites, at least up to 0.8 ML considered in the present work. At moderate coverages, little to no disorder appears in the Pt lattice. At high coverages, some Pt atoms markedly protrude out of the surface plane. This observation is in qualitative agreement with recent STM images of an oxygen covered Pt surface. The use of the GCMC technique based on a transferable potential is particularly valuable to produce more realistic systems (adsorbent and adsorbate) to be used in subsequent dynamical simulations (Molecular Dynamics) to address recombination reactions (via either Eley-Rideal or Langmuir-Hinshelwood mechanisms) on variously covered surfaces. By using GCMC and Molecular Dynamics simulations, the ReaxFF force field can be a valuable tool for understanding heterogeneous catalysis on a solid surface. Finally, the use of a reactive potential is a necessary requirement to investigate problems where dissociative adsorption occurs, as typical of many important catalytic processes.
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Time-dependent Computational Studies of Premixed Flames in Microgravity
NASA Technical Reports Server (NTRS)
Kailasanath, K.; Patnaik, Gopal; Oran, Elaine S.
1993-01-01
This report describes the research performed at the Center for Reactive Flow and Dynamical Systems in the Laboratory for Computational Physics and Fluid Dynamics, at the Naval Research Laboratory, in support of NASA Microgravity Science and Applications Program. The primary focus of this research is on investigating fundamental questions concerning the propagation and extinction of premixed flames in earth gravity and in microgravity environments. Our approach is to use detailed time-dependent, multispecies, numerical models as tools to simulate flames in different gravity environments. The models include a detailed chemical kinetics mechanism consisting of elementary reactions among the eight reactive species involved in hydrogen combustion, coupled to algorithms for convection, thermal conduction, viscosity, molecular and thermal diffusion, and external forces. The external force, gravity, can be put in any direction relative to flame propagation and can have a range of values. Recently more advanced wall boundary conditions such as isothermal and no-slip have been added to the model. This enables the simulation of flames propagating in more practical systems than before. We have used the numerical simulations to investigate the effects of heat losses and buoyancy forces on the structure and stability of flames, to help resolve fundamental questions on the existence of flammability limits when there are no external losses or buoyancy forces in the system, to understand the interaction between the various processes leading to flame instabilities and extinguishment, and to study the dynamics of cell formation and splitting. Our studies have been able to bring out the differences between upward- and downward-propagating flames and predict the zero-gravity behavior of these flames. The simulations have also highlighted the dominant role of wall heat losses in the case of downward-propagating flames. The simulations have been able to qualitatively predict the formation of multiple cells and the cessation of cell-splitting. Our studies have also shown that some flames in a microgravity environment can be extinguished due to a chemical instability and without any external losses. However, further simulations are needed to more completely understand upward-propagating and zero-gravity flames as well as to understand the potential effect of radiative heat losses.
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An experimental analysis of a doped lithium fluoride direct absorption solar receiver
NASA Technical Reports Server (NTRS)
Kesseli, James; Pollak, Tom; Lacy, Dovie
1988-01-01
An experimental analysis of two key elements of a direct absorption solar receiver for use with Brayton solar dynamic systems was conducted. Experimental data are presented on LiF crystals doped with dysprosium, samarium, and cobalt fluorides. In addition, a simulation of the cavity/window environment was performed and a posttest inspection was conducted to evaluate chemical reactivity, transmissivity, and condensation rate.
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a Transient Semi-Metallic Layer in Detonating Nitromethane
NASA Astrophysics Data System (ADS)
Reed, Evan J.; Manaa, M. Riad; Fried, Laurence E.; Glaesemann, Kurt; Joannopoulos, John D.
2007-12-01
We present the first ever glimpse behind a detonation shock front in a chemically reactive quantum molecular dynamics simulation of the explosive nitromethane (CH3NO2). We discover that the wide-bandgap insulator nitromethane undergoes chemical decomposition and a transformation into a semi-metallic state for a limited distance behind the detonation front. We find this transformation is associated with the production of charged decomposition species.
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NASA Astrophysics Data System (ADS)
Bordwell, Baylee; Brown, Benjamin P.; Oishi, Jeffrey S.
2018-02-01
Disequilibrium chemical processes significantly affect the spectra of substellar objects. To study these effects, dynamical disequilibrium has been parameterized using the quench and eddy diffusion approximations, but little work has been done to explore how these approximations perform under realistic planetary conditions in different dynamical regimes. As a first step toward addressing this problem, we study the localized, small-scale convective dynamics of planetary atmospheres by direct numerical simulation of fully compressible hydrodynamics with reactive tracers using the Dedalus code. Using polytropically stratified, plane-parallel atmospheres in 2D and 3D, we explore the quenching behavior of different abstract chemical species as a function of the dynamical conditions of the atmosphere as parameterized by the Rayleigh number. We find that in both 2D and 3D, chemical species quench deeper than would be predicted based on simple mixing-length arguments. Instead, it is necessary to employ length scales based on the chemical equilibrium profile of the reacting species in order to predict quench points and perform chemical kinetics modeling in 1D. Based on the results of our simulations, we provide a new length scale, derived from the chemical scale height, that can be used to perform these calculations. This length scale is simple to calculate from known chemical data and makes reasonable predictions for our dynamical simulations.
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NASA Astrophysics Data System (ADS)
Galvez, P.; Dalguer, L. A.; Rahnema, K.; Bader, M.
2014-12-01
The 2011 Mw9 Tohoku earthquake has been recorded with a vast GPS and seismic network given unprecedented chance to seismologists to unveil complex rupture processes in a mega-thrust event. In fact more than one thousand near field strong-motion stations across Japan (K-Net and Kik-Net) revealed complex ground motion patterns attributed to the source effects, allowing to capture detailed information of the rupture process. The seismic stations surrounding the Miyagi regions (MYGH013) show two clear distinct waveforms separated by 40 seconds. This observation is consistent with the kinematic source model obtained from the inversion of strong motion data performed by Lee's et al (2011). In this model two rupture fronts separated by 40 seconds emanate close to the hypocenter and propagate towards the trench. This feature is clearly observed by stacking the slip-rate snapshots on fault points aligned in the EW direction passing through the hypocenter (Gabriel et al, 2012), suggesting slip reactivation during the main event. A repeating slip on large earthquakes may occur due to frictional melting and thermal fluid pressurization effects. Kanamori & Heaton (2002) argued that during faulting of large earthquakes the temperature rises high enough creating melting and further reduction of friction coefficient. We created a 3D dynamic rupture model to reproduce this slip reactivation pattern using SPECFEM3D (Galvez et al, 2014) based on a slip-weakening friction with sudden two sequential stress drops . Our model starts like a M7-8 earthquake breaking dimly the trench, then after 40 seconds a second rupture emerges close to the trench producing additional slip capable to fully break the trench and transforming the earthquake into a megathrust event. The resulting sea floor displacements are in agreement with 1Hz GPS displacements (GEONET). The seismograms agree roughly with seismic records along the coast of Japan.The simulated sea floor displacement reaches 8-10 meters of up-lift close to the trench, which may be the cause of such a devastating tsunami followed by the Tohoku earthquake. To investigate the impact of such a huge up-lift, we ran tsunami simulations with the slip reactivation model using sam(oa)2 (O. Meister et al., 2012), a state-of-the-art Finite-Volume framework to simulate the resulting tsunami waves.
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Reactive Molecular Dynamics Investigations of Alkoxysilane Sol-Gel and Surface Coating Processes
NASA Astrophysics Data System (ADS)
Deetz, Joshua David
The ability to generate nanostructured materials with tailored morphology or chemistry is of great technological interest. One proven method of generating metal-oxide materials, and chemically modifying metal-oxide surfaces is through the reactions of molecular building blocks known as alkoxysilanes. Alkoxysilanes are a class of chemicals which contain one or more organic alkoxy groups bonded to silicon atoms. Alkoxysilane (Si-O-R) chemical groups can undergo reactions to form bridges (Si-O-M) with metal oxides. Due to their ability to "attach" to metal-oxides through condensation reactions, alkoxysilanes have a number of interesting applications, such as: the generation of synthetic siloxane materials through the sol-gel process, and the formation of functionalized surface coatings on metal-oxide surfaces. Despite widespread study of sol-gel and surface coatings processes, it is difficult to predict the morphology of the final products due to the large number of process variables involved, such as precursor molecule structure, solvent effects, solution composition, temperature, and pH. To determine the influence of these variables on the products of sol-gel and coatings processes reactive molecular dynamics simulations are used. A reactive force field was used (ReaxFF) to allow the chemical bonds in simulation to dynamically form and break. The force field parameters were optimized using a parallel optimization scheme with a combination of experimental information, and density functional theory calculations. Polycondensation of alkoxysilanes in mixtures of alcohol and water were studied. Steric effects were observed to influence the rates of hydrolysis and condensation in solutions containing different precursor monomers. By restricting the access of nucleophiles to the central silicon atom, the nucleation rate of siloxanes can be controlled. The influence of solution precursor, water, and methanol composition on reaction rates was explored. It was determined that the rate of alkoxysilane hydrolysis is strongly dependent on the concentration of water. The dynamics of siloxane cluster formation are revealed, which provides insight for experimentalists. The silanization of hydroxylated silica surfaces by alkoxysilanes was modeled in pseudo-infinite liquid solution. Butyl-, octyl-, or dodecylsilanes were exposed to hydroxylated silica surfaces in order to observe the influence of silyl headgroup size on the morphology and formation kinetics of silane films on silica substrates. The radius of gyration and order parameter of the hydrocarbon silyl groups were found to increase with grafting density. This was the first simulation study of the dynamic grafting of alkoxysilanes to a substrate.
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Zhou, Tingting; Song, Huajie; Liu, Yi; Huang, Fenglei
2014-07-21
To gain an atomistic-level understanding of the thermal and chemical responses of condensed energetic materials under thermal shock, we developed a thermal shock reactive dynamics (TS-RD) computational protocol using molecular dynamics simulation coupled with ReaxFF force field. β-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) was selected as a a target explosive due to its wide usage in the military and industry. The results show that a thermal shock initiated by a large temperature gradient between the "hot" region and the "cold" region results in thermal expansion of the particles and induces a thermal-mechanical wave propagating back and forth in the system with an averaged velocity of 3.32 km s(-1). Heat propagating along the direction of thermal shock leads to a temperature increment of the system and thus chemical reaction initiation. Applying a continuum reactive heat conduction model combined with the temperature distribution obtained from the RD simulation, a heat conduction coefficient is derived as 0.80 W m(-1) K(-1). The chemical reaction mechanisms during thermal shock were analyzed, showing that the reaction is triggered by N-NO2 bond breaking followed by HONO elimination and ring fission. The propagation rates of the reaction front and reaction center are obtained to be 0.069 and 0.038 km s(-1), based on the time and spatial distribution of NO2. The pressure effect on the thermal shock was also investigated by employing uniaxial compression before the thermal shock. We find that compression significantly accelerates thermal-mechanical wave propagation and heat conduction, resulting in higher temperature and more excited molecules and thus earlier initiation and faster propagation of chemical reactions.
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Raju, Muralikrishna; van Duin, Adri C T; Fichthorn, Kristen A
2014-01-01
Oriented attachment (OA) of nanocrystals is now widely recognized as a key process in the solution-phase growth of hierarchical nanostructures. However, the microscopic origins of OA remain unclear. We perform molecular dynamics simulations using a recently developed ReaxFF reactive force field to study the aggregation of various titanium dioxide (anatase) nanocrystals in vacuum and humid environments. In vacuum, the nanocrystals merge along their direction of approach, resulting in a polycrystalline material. By contrast, in the presence of water vapor the nanocrystals reorient themselves and aggregate via the OA mechanism to form a single or twinned crystal. They accomplish this by creating a dynamic network of hydrogen bonds between surface hydroxyls and surface oxygens of aggregating nanocrystals. We determine that OA is dominant on surfaces that have the greatest propensity to dissociate water. Our results are consistent with experiment, are likely to be general for aqueous oxide systems, and demonstrate the critical role of solvent in nanocrystal aggregation. This work opens up new possibilities for directing nanocrystal growth to fabricate nanomaterials with desired shapes and sizes.
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Thermodynamic interpretation of reactive processes in Ni-Al nanolayers from atomistic simulations
NASA Astrophysics Data System (ADS)
Sandoval, Luis; Campbell, Geoffrey H.; Marian, Jaime
2014-03-01
Metals that can form intermetallic compounds by exothermic reactions constitute a class of reactive materials with multiple applications. Ni-Al laminates of thin alternating layers are being considered as model nanometric metallic multilayers for studying various reaction processes. However, the reaction kinetics at short timescales after mixing are not entirely understood. In this work, we calculate the free energies of Ni-Al alloys as a function of composition and temperature for different solid phases using thermodynamic integration based on state-of-the-art interatomic potentials. We use this information to interpret molecular dynamics (MD) simulations of bilayer systems at 800 K and zero pressure, both in isothermal and isenthalpic conditions. We find that a disordered phase always forms upon mixing as a precursor to a more stable nano crystalline B2 phase. We construe the reactions observed in terms of thermodynamic trajectories governed by the state variables computed. Simulated times of up to 30 ns were achieved, which provides a window to phenomena not previously observed in MD simulations. Our results provide insight into the early experimental reaction timescales and suggest that the path (segregated reactants) → (disordered phase) → (B2 structure) is always realized irrespective of the imposed boundary conditions.
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Yun, Kang-Seop; Pai, Sung Jin; Yeo, Byung Chul; Lee, Kwang-Ryeol; Kim, Sun-Jae; Han, Sang Soo
2017-07-06
We propose the ReaxFF reactive force field as a simulation protocol for predicting the evolution of solid-electrolyte interphase (SEI) components such as gases (C 2 H 4 , CO, CO 2 , CH 4 , and C 2 H 6 ), and inorganic (Li 2 CO 3 , Li 2 O, and LiF) and organic (ROLi and ROCO 2 Li: R = -CH 3 or -C 2 H 5 ) products that are generated by the chemical reactions between the anodes and liquid electrolytes. ReaxFF was developed from ab initio results, and a molecular dynamics simulation with ReaxFF realized the prediction of SEI formation under real experimental conditions and with a reasonable computational cost. We report the effects on SEI formation of different kinds of Si anodes (pristine Si and SiO x ), of the different types and compositions of various carbonate electrolytes, and of the additives. From the results, we expect that ReaxFF will be very useful for the development of novel electrolytes or additives and for further advances in Li-ion battery technology.
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Wen, Yushi; Xue, Xianggui; Long, Xinping; Zhang, Chaoyang
2016-06-09
We carried out reactive molecular dynamics simulations by ReaxFF to study the initial events of an insensitive high explosive 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) against various thermal stimuli including constant-temperature heating, programmed heating, and adiabatic heating to simulate TATB suffering from accidental heating in reality. Cluster evolution at the early stage of the thermal decomposition of condensed TATB was the main focus as cluster formation primarily occurs when TATB is heated. The results show that cluster formation is the balance of the competition of intermolecular collision and molecular decomposition of TATB, that is, an appropriate temperature and certain duration are required for cluster formation and preservation. The temperature in the range of 2000-3000 K was found to be optimum for fast formation and a period of preservation. Besides, the intra- and intermolecular H transfers are always favorable, whereas the C-NO2 partition was favorable at high temperature. The simulation results are helpful to deepen the insight into the thermal properties of condensed TATB.
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NASA Astrophysics Data System (ADS)
Pollet, Rodolphe; Boehme, Christian; Marx, Dominik
2006-08-01
Glycine at the interface of a pyrite surface (001) FeS2, and bulk water at high pressure and temperature conditions relevant to the “iron-sulfur world” scenario of the origin of life is investigated by theoretical means. Car-Parrinello molecular dynamics is used in order to study the desorption process of the zwitterionic form of this amino acid using two different adsorption modes, where either only one or both oxygens of the carboxylate group are anchored to surface iron atoms. It is found that the formation of stabilizing hydrogen bonds plays a key role in the detachment process, leading to longer retention times for the bidentate adsorption mode. In addition, the chemical reactivity of this heterogeneous system is probed by calculating the Fukui functions as site-specific reactivity indices. The most prominent targets for both nucleophilic and electrophilic reactions to occur are surface atoms, whereas the reactivity of glycine is only slightly affected upon anchoring.
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NASA Astrophysics Data System (ADS)
Khosravian, N.; Kamaraj, B.; Neyts, E. C.; Bogaerts, A.
2016-02-01
This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.
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Pore-scale simulation of CO2-water-rock interactions
NASA Astrophysics Data System (ADS)
Deng, H.; Molins, S.; Steefel, C. I.; DePaolo, D. J.
2017-12-01
In Geologic Carbon Storage (GCS) systems, the migration of scCO2 versus CO2-acidifed brine ultimately determines the extent of mineral trapping and caprock integrity, i.e. the long-term storage efficiency and security. While continuum scale multiphase reactive transport models are valuable for large scale investigations, they typically (over-)simplify pore-scale dynamics and cannot capture local heterogeneities that may be important. Therefore, pore-scale models are needed in order to provide mechanistic understanding of how fine scale structural variations and heterogeneous processes influence the transport and geochemistry in the context of multiphase flow, and to inform parameterization of continuum scale modeling. In this study, we investigate the interplay of different processes at pore scale (e.g. diffusion, reactions, and multiphase flow) through the coupling of a well-developed multiphase flow simulator with a sophisticated reactive transport code. The objectives are to understand where brine displaced by scCO2 will reside in a rough pore/fracture, and how the CO2-water-rock interactions may affect the redistribution of different phases. In addition, the coupled code will provide a platform for model testing in pore-scale multiphase reactive transport problems.
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NASA Technical Reports Server (NTRS)
Jaramillo-Botero, A.; Cheng, M-J; Cvicek, V.; Beegle, Luther W.; Hodyss, R.; Goddard, W. A., III
2011-01-01
We report here on the predicted impact of species such as ice-water, CO2, CH4, and NH3, on oxidized titanium, as well as HC species on diamond surfaces. These simulations provide the dynamics of product distributions during and after a hypervelocity impact event, ionization fractions, and dissociation probabilities for the various species of interest as a function of impact velocity (energy). We are using these results to determine the relevance of the fragmentation process to Cassini INMS results, and to quantify its effects on the observed spectra.
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GOBF-ARMA based model predictive control for an ideal reactive distillation column.
Seban, Lalu; Kirubakaran, V; Roy, B K; Radhakrishnan, T K
2015-11-01
This paper discusses the control of an ideal reactive distillation column (RDC) using model predictive control (MPC) based on a combination of deterministic generalized orthonormal basis filter (GOBF) and stochastic autoregressive moving average (ARMA) models. Reactive distillation (RD) integrates reaction and distillation in a single process resulting in process and energy integration promoting green chemistry principles. Improved selectivity of products, increased conversion, better utilization and control of reaction heat, scope for difficult separations and the avoidance of azeotropes are some of the advantages that reactive distillation offers over conventional technique of distillation column after reactor. The introduction of an in situ separation in the reaction zone leads to complex interactions between vapor-liquid equilibrium, mass transfer rates, diffusion and chemical kinetics. RD with its high order and nonlinear dynamics, and multiple steady states is a good candidate for testing and verification of new control schemes. Here a combination of GOBF-ARMA models is used to catch and represent the dynamics of the RDC. This GOBF-ARMA model is then used to design an MPC scheme for the control of product purity of RDC under different operating constraints and conditions. The performance of proposed modeling and control using GOBF-ARMA based MPC is simulated and analyzed. The proposed controller is found to perform satisfactorily for reference tracking and disturbance rejection in RDC. Copyright © 2015 Elsevier Inc. All rights reserved.
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Corley, R A; Minard, K R; Kabilan, S; Einstein, D R; Kuprat, A P; Harkema, J R; Kimbell, J S; Gargas, M L; Kinzell, John H
2009-05-01
The percentages of total airflows over the nasal respiratory and olfactory epithelium of female rabbits were calculated from computational fluid dynamics (CFD) simulations of steady-state inhalation. These airflow calculations, along with nasal airway geometry determinations, are critical parameters for hybrid CFD/physiologically based pharmacokinetic models that describe the nasal dosimetry of water-soluble or reactive gases and vapors in rabbits. CFD simulations were based upon three-dimensional computational meshes derived from magnetic resonance images of three adult female New Zealand White (NZW) rabbits. In the anterior portion of the nose, the maxillary turbinates of rabbits are considerably more complex than comparable regions in rats, mice, monkeys, or humans. This leads to a greater surface area to volume ratio in this region and thus the potential for increased extraction of water soluble or reactive gases and vapors in the anterior portion of the nose compared to many other species. Although there was considerable interanimal variability in the fine structures of the nasal turbinates and airflows in the anterior portions of the nose, there was remarkable consistency between rabbits in the percentage of total inspired airflows that reached the ethmoid turbinate region (approximately 50%) that is presumably lined with olfactory epithelium. These latter results (airflows reaching the ethmoid turbinate region) were higher than previous published estimates for the male F344 rat (19%) and human (7%). These differences in regional airflows can have significant implications in interspecies extrapolations of nasal dosimetry.
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NASA Astrophysics Data System (ADS)
Tian, Zhiwei; Wang, Junye
2018-02-01
Dissolution and precipitation of rock matrix are one of the most important processes of geological CO2 sequestration in reservoirs. They change connections of pore channels and properties of matrix, such as bulk density, microporosity and hydraulic conductivity. This study builds on a recently developed multi-layer model to account for dynamic changes of microporous matrix that can accurately predict variations in hydraulic properties and reaction rates due to dynamic changes in matrix porosity and pore connectivity. We apply the model to simulate the dissolution and precipitation processes of rock matrix in heterogeneous porous media to quantify (1) the effect of the reaction rate on dissolution and matrix porosity, (2) the effect of microporous matrix diffusion on the overall effective diffusion and (3) the effect of heterogeneity on hydraulic conductivity. The results show the CO2 storage influenced by factors including the matrix porosity change, reaction front movement, velocity and initial properties. We also simulated dissolution-induced permeability enhancement as well as effects of initial porosity heterogeneity. The matrix with very low permeability, which can be unresolved on X-ray CT, do contribute to flow patterns and dispersion. The concentration of reactant H+ increases along the main fracture paths where the flow velocity increases. The product Ca++ shows the inversed distribution pattern against the H+ concentration. This demonstrates the capability of this model to investigate the complex CO2 reactive transport in real 3D heterogeneous porous media.
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Reactive Monte Carlo sampling with an ab initio potential
NASA Astrophysics Data System (ADS)
Leiding, Jeff; Coe, Joshua D.
2016-05-01
We present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). We find that there are regions of state space for which RxMC sampling is much more efficient than AIMD due to the "rare-event" character of chemical reactions.
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NASA Astrophysics Data System (ADS)
Wuttke, M. W.; Kessels, W.; Wessling, S.; Han, J.
2007-05-01
Spontaneous combustion is a world wide problem for technical operations in mining, waste disposal and power plant facilities. The principle driving the combustion is every where the same independent of the different reactive materials: Fresh air with the common oxygen content is getting in contact with the reactive material by human operations. The following reaction process produces heat at a usually low but constant rate. The reactive material in operating or abandoned coal mines, heaps of coal, waste or reactive minerals is most times strongly broken or fractured, such that the atmospheric oxygen can deeply penetrate into the porous or fractured media. Because the strongly broken or fractured medium with air filled pores and fractures is often combined with a low thermal conductivity of the bulk material the produced heat accumulates and the temperature increases with time. If the reactivity strongly increases with temperature, the temperature rise accelerates up to the "combustion temperature". Once the temperature is high enough the combustion process is determined by the oxygen transport to the combustion center rather than the chemical reactivity. Spontaneous combustion is thus a self- amplifying process where an initial small variation in the parameters and the starting conditions can create exploding combustion hot spots in an apparently homogenous material. The phenomenon will be discussed by various examples in the context of the German - Sino coal fire project. A temperature monitoring in hot fracture systems documents the strong influence of the weather conditions on the combustion process. Numerical calculations show the sensitivity of the combustion to the model geometries, the boundary conditions and mainly the permeability. The most used fire fighting operations like covering and water injection are discussed. A new method of using saltwater for fire fighting is presented and discussed. References: Kessels, W., Wessling, S., Li, X., and Wuttke, M. W. Numerical element distinction for reactive transport modeling regarding reaction rate. In Proceedings of MODFLOW and MORE 2006: Managing Groundwater Systems, May 21 - 24, 2006, Golden, CO USA (2006). Kessels, W., Wuttke, M. W., Wessling, S., and Li, X. Coal fires between self ignition and fire fighting: Numerical modeling and basic geophysical measurements. In ERSEC Ecological Book Series - 4 on Coal Fire Research (2007). Wessling, S., Litschke, T., Wiegand, J., Schlömer, S., and Kessels, W. Simulating dynamic subsurface coal fires and its applications. In ERSEC Ecological Book Series - 4 on Coal Fire Reserach (2007). Wessling, S., Kessels, W., Schmidt, M., and Krause, U. Investigating dynamic underground coal fires by means of numerical simulation. Geophys. J. Int. (submitted).
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Ahn, Yong Nam; Lee, Sung Hoon; Lee, Goo Soo; Kim, Hyunbin
2017-08-02
Quaternary ammoniums are cations having widespread use in organic electrolytes for high performance electrochemical double layer capacitors (EDLCs) due to their various advantages such as high electrochemical stability and inexpensive production cost. However, the decomposition of quaternary ammoniums via Hofmann elimination hinders their applications for EDLCs operating at elevated temperatures. This study systematically investigates the reactivity of four different quaternary ammoniums (tetraethyl-, triethylmethyl-, diethyldimethyl-, and trimethylethyl-ammonium) in EDLC by utilizing density functional theory calculations and Brownian dynamics simulations complemented with molecular dynamics simulations. It is found that ammonium stability reduces upon increasing the number of ethyl branches that have a stronger positive charge than the methyl groups. However, the contribution of the entropy change to the reaction free energy makes trimethylethylammonium less stable than diethyldimethylammonium at room temperature although the former has less ethyl branches than the latter. Trimethylethylammonium becomes the most stable at a high temperature of 488 K above which the activation free energy becomes effectively negligible and thus the number of reactive sites determines the overall stability. The fundamental understanding of the ammonium decompositions through Hofmann elimination demonstrated in this study is expected to contribute to developing new long-life organic electrolyte systems for high-temperature applications.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lai, Canhai; Xu, Zhijie; Pan, Wenxiao
2016-01-01
To quantify the predictive confidence of a solid sorbent-based carbon capture design, a hierarchical validation methodology—consisting of basic unit problems with increasing physical complexity coupled with filtered model-based geometric upscaling has been developed and implemented. This paper describes the computational fluid dynamics (CFD) multi-phase reactive flow simulations and the associated data flows among different unit problems performed within the said hierarchical validation approach. The bench-top experiments used in this calibration and validation effort were carefully designed to follow the desired simple-to-complex unit problem hierarchy, with corresponding data acquisition to support model parameters calibrations at each unit problem level. A Bayesianmore » calibration procedure is employed and the posterior model parameter distributions obtained at one unit-problem level are used as prior distributions for the same parameters in the next-tier simulations. Overall, the results have demonstrated that the multiphase reactive flow models within MFIX can be used to capture the bed pressure, temperature, CO2 capture capacity, and kinetics with quantitative accuracy. The CFD modeling methodology and associated uncertainty quantification techniques presented herein offer a solid framework for estimating the predictive confidence in the virtual scale up of a larger carbon capture device.« less
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Reactive transport in a partially molten system with binary solid solution
NASA Astrophysics Data System (ADS)
Jordan, J.; Hesse, M. A.
2017-12-01
Melt extraction from the Earth's mantle through high-porosity channels is required to explain the composition of the oceanic crust. Feedbacks from reactive melt transport are thought to localize melt into a network of high-porosity channels. Recent studies invoke lithological heterogeneities in the Earth's mantle to seed the localization of partial melts. Therefore, it is necessary to understand the reaction fronts that form as melt flows across the lithological interface of a heterogeneity and the background mantle. Simplified melting models of such systems aide in the interpretation and formulation of larger scale mantle models. Motivated by the aforementioned facts, we present a chromatographic analysis of reactive melt transport across lithological boundaries, using theory for hyperbolic conservation laws. This is an extension of well-known linear trace element chromatography to the coupling of major elements and energy transport. Our analysis allows the prediction of the feedbacks that arise in reactive melt transport due to melting, freezing, dissolution and precipitation for frontal reactions. This study considers the simplified case of a rigid, partially molten porous medium with binary solid solution. As melt traverses a lithological contact-modeled as a Riemann problem-a rich set of features arise, including a reacted zone between an advancing reaction front and partial chemical preservation of the initial contact. Reactive instabilities observed in this study originate at the lithological interface rather than along a chemical gradient as in most studies of mantle dynamics. We present a regime diagram that predicts where reaction fronts become unstable, thereby allowing melt localization into high-porosity channels through reactive instabilities. After constructing the regime diagram, we test the one-dimensional hyperbolic theory against two-dimensional numerical experiments. The one-dimensional hyperbolic theory is sufficient for predicting the qualitative behavior of reactive melt transport simulations conducted in two-dimensions. The theoretical framework presented can be extended to more complex and realistic phase behavior, and is therefore a useful tool for understanding nonlinear feedbacks in reactive melt transport problems relevant to mantle dynamics.
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Density-dependent liquid nitromethane decomposition: molecular dynamics simulations based on ReaxFF.
Rom, Naomi; Zybin, Sergey V; van Duin, Adri C T; Goddard, William A; Zeiri, Yehuda; Katz, Gil; Kosloff, Ronnie
2011-09-15
The decomposition mechanism of hot liquid nitromethane at various compressions was studied using reactive force field (ReaxFF) molecular dynamics simulations. A competition between two different initial thermal decomposition schemes is observed, depending on compression. At low densities, unimolecular C-N bond cleavage is the dominant route, producing CH(3) and NO(2) fragments. As density and pressure rise approaching the Chapman-Jouget detonation conditions (∼30% compression, >2500 K) the dominant mechanism switches to the formation of the CH(3)NO fragment via H-transfer and/or N-O bond rupture. The change in the decomposition mechanism of hot liquid NM leads to a different kinetic and energetic behavior, as well as products distribution. The calculated density dependence of the enthalpy change correlates with the change in initial decomposition reaction mechanism. It can be used as a convenient and useful global parameter for the detection of reaction dynamics. Atomic averaged local diffusion coefficients are shown to be sensitive to the reactions dynamics, and can be used to distinguish between time periods where chemical reactions occur and diffusion-dominated, nonreactive time periods. © 2011 American Chemical Society
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NASA Astrophysics Data System (ADS)
Ahadi, Zohreh; Shadman Lakmehsari, Muhammad; Kumar Singh, Sandeep; Davoodi, Jamal
2017-12-01
This study is an attempt to perform equilibrium molecular dynamics and non-equilibrium molecular dynamics (NEMD) to evaluate the stability and thermal behavior of molybdenum disulfide nanotubes (MoS2NTs) by reactive empirical bond order potential. The stability of nanotubes, cohesive energy, isobaric heat capacity, and enthalpies of fusion in armchair and zigzag structures with different radii were calculated. The observed results illustrate that SWMoS2NTs, which have larger diameters, are more stable with more negative energy than the smaller ones. Moreover, it was found that the melting point is increased with an increase in the nanotube's radius. During the melting process, the structural transformation of nanotubes was investigated using a mean-square displacement and radial distribution function diagrams. Afterwards, using a NEMD simulation, the thermal conductivity of nanotubes with various diameters was calculated at a constant nanotube length. The obtained results show that the thermal conductivity coefficient increases with increasing nanotube diameters when the nanotube length is constant.
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NASA Astrophysics Data System (ADS)
Yang, Yang; Han, Dandan; Du, Shichao; Wu, Songgu; Gong, Junbo
2018-01-01
Thiamine hydrochloride (THCL) was produced in methanol accompanied with agglomeration in industry, the plate like morphology of THCL in methanol was not deserve to have a good quality. Selecting a suitable solvent should be considered because solvent could be one of the essential factors to impact morphology. Methanol and methanol/ethyl acetate solvent (0.2 vol fraction of methanol) was selected as the solvent system in reactive crystallization of THCL. The experiment results show the THCL crystal morphology in methanol/ethyl acetate solvent system was granular and more regular than that in methanol. In order to explicate the different crystal morphology in different solvents, molecular dynamics (MD) simulation was introduced to simulate crystal morphology in different solvents. The attachment energy (AE) model was employed to investigate the morphology of THCL under vacuum conditions, methanol and methanol/ethyl acetate solvent conditions, respectively. The simulation crystal morphology was in a good agreement with that of experimented. The particle of THCL in methanol/ethyl acetate solvent has less tendency to agglomeration, and then it is favorable to the downstream process, such as filtration, storage and transportation.
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Multiscale modeling of shock wave localization in porous energetic material
NASA Astrophysics Data System (ADS)
Wood, M. A.; Kittell, D. E.; Yarrington, C. D.; Thompson, A. P.
2018-01-01
Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (<6 GPa), atomistic simulations of pore collapse are used to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock waves interacting with pores as a function of this viscoplastic material response. We find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.
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Molecular Modeling of Water Interfaces: From Molecular Spectroscopy to Thermodynamics.
Nagata, Yuki; Ohto, Tatsuhiko; Backus, Ellen H G; Bonn, Mischa
2016-04-28
Understanding aqueous interfaces at the molecular level is not only fundamentally important, but also highly relevant for a variety of disciplines. For instance, electrode-water interfaces are relevant for electrochemistry, as are mineral-water interfaces for geochemistry and air-water interfaces for environmental chemistry; water-lipid interfaces constitute the boundaries of the cell membrane, and are thus relevant for biochemistry. One of the major challenges in these fields is to link macroscopic properties such as interfacial reactivity, solubility, and permeability as well as macroscopic thermodynamic and spectroscopic observables to the structure, structural changes, and dynamics of molecules at these interfaces. Simulations, by themselves, or in conjunction with appropriate experiments, can provide such molecular-level insights into aqueous interfaces. In this contribution, we review the current state-of-the-art of three levels of molecular dynamics (MD) simulation: ab initio, force field, and coarse-grained. We discuss the advantages, the potential, and the limitations of each approach for studying aqueous interfaces, by assessing computations of the sum-frequency generation spectra and surface tension. The comparison of experimental and simulation data provides information on the challenges of future MD simulations, such as improving the force field models and the van der Waals corrections in ab initio MD simulations. Once good agreement between experimental observables and simulation can be established, the simulation can be used to provide insights into the processes at a level of detail that is generally inaccessible to experiments. As an example we discuss the mechanism of the evaporation of water. We finish by presenting an outlook outlining four future challenges for molecular dynamics simulations of aqueous interfacial systems.
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Dynamics of tuberculosis transmission with exogenous reinfections and endogenous reactivation
NASA Astrophysics Data System (ADS)
Khajanchi, Subhas; Das, Dhiraj Kumar; Kar, Tapan Kumar
2018-05-01
We propose and analyze a mathematical model for tuberculosis (TB) transmission to study the role of exogenous reinfection and endogenous reactivation. The model exhibits two equilibria: a disease free and an endemic equilibria. We observe that the TB model exhibits transcritical bifurcation when basic reproduction number R0 = 1. Our results demonstrate that the disease transmission rate β and exogenous reinfection rate α plays an important role to change the qualitative dynamics of TB. The disease transmission rate β give rises to the possibility of backward bifurcation for R0 < 1, and hence the existence of multiple endemic equilibria one of which is stable and another one is unstable. Our analysis suggests that R0 < 1 may not be sufficient to completely eliminate the disease. We also investigate that our TB transmission model undergoes Hopf-bifurcation with respect to the contact rate β and the exogenous reinfection rate α. We conducted some numerical simulations to support our analytical findings.
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Ghosh, Shibaji; Chandar, Nellore Bhanu; Jana, Kalyanashis; Ganguly, Bishwajit
2017-08-01
Inhibition of acetylcholinesterase (AChE) with organophosphorus compounds has a detrimental effect on human life. Oxime K203 seems to be one of the promising reactivators for tabun-inhibited AChE than (K027, K127, and K628). These reactivators differ only in the linker units between the two pyridinium rings. The conformational analyses performed with quantum chemical RHF/6-31G* level for K027, K127, K203 and K628 showed that the minimum energy conformers have different orientations of the active and peripheral pyridinium rings for these reactivator molecules. K203 with (-CH 2 -CH=CH-CH 2 -) linker unit possesses more open conformation compared to the other reactivators. Such orientation of K203 experiences favorable interaction with the surrounding residues of catalytic anionic site (CAS) and peripheral anionic site (PAS) of tabun-inhibited AChE. From the steered molecular dynamics simulations, it has been observed that the oxygen atom of the oxime group of K203 reactivator approaches nearest to the P-atom of the SUN203 (3.75 Å) at lower time scales (less than ~1000 ps) as compared to the other reactivators. K203 experiences less number of hydrophobic interaction with the PAS residues which is suggested to be an important factor for the efficient reactivation process. In addition, K203 crates large number of H-bonding with CAS residues SUN203, Phe295, Tyr337, Phe338 and His447. K203 barely changes its conformation during the SMD simulation process and hence the energy penalty to adopt any other conformation is minimal in this case as compared to the other reactivators. The molecular mechanics and Poisson-Boltzmann surface area binding energies obtained for the interaction of K203 inside the gorge of tabun inhibited AChE is substantially higher (-290.2 kcal/mol) than the corresponding K628 reactivator (-260.4 kcal/mol), which also possess unsaturated aromatic linker unit.
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NASA Astrophysics Data System (ADS)
Jablonski, Piotr; Poe, Gina; Zochowski, Michal
2007-03-01
The hippocampus has the capacity for reactivating recently acquired memories and it is hypothesized that one of the functions of sleep reactivation is the facilitation of consolidation of novel memory traces. The dynamic and network processes underlying such a reactivation remain, however, unknown. We show that such a reactivation characterized by local, self-sustained activity of a network region may be an inherent property of the recurrent excitatory-inhibitory network with a heterogeneous structure. The entry into the reactivation phase is mediated through a physiologically feasible regulation of global excitability and external input sources, while the reactivated component of the network is formed through induced network heterogeneities during learning. We show that structural changes needed for robust reactivation of a given network region are well within known physiological parameters.
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NASA Astrophysics Data System (ADS)
Jablonski, Piotr; Poe, Gina R.; Zochowski, Michal
2007-01-01
The hippocampus has the capacity for reactivating recently acquired memories and it is hypothesized that one of the functions of sleep reactivation is the facilitation of consolidation of novel memory traces. The dynamic and network processes underlying such a reactivation remain, however, unknown. We show that such a reactivation characterized by local, self-sustained activity of a network region may be an inherent property of the recurrent excitatory-inhibitory network with a heterogeneous structure. The entry into the reactivation phase is mediated through a physiologically feasible regulation of global excitability and external input sources, while the reactivated component of the network is formed through induced network heterogeneities during learning. We show that structural changes needed for robust reactivation of a given network region are well within known physiological parameters.
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2011-05-04
pubs.acs.org/JPCB Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics Si-ping Han,†,‡ Adri C. T. van...ABSTRACT: We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH3NO2) using molec- ular dynamics...with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000
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Photodissociation Dynamics of Phenol: Multistate Trajectory Simulations including Tunneling
Xu, Xuefei; Zheng, Jingjing; Yang, Ke R.; ...
2014-10-27
We report multistate trajectory simulations, including coherence, decoherence, and multidimensional tunneling, of phenol photodissociation dynamics. The calculations are based on full-dimensional anchor-points reactive potential surfaces and state couplings fit to electronic structure calculations including dynamical correlation with an augmented correlation-consistent polarized valence double-ζ basis set. The calculations successfully reproduce the experimentally observed bimodal character of the total kinetic energy release spectra and confirm the interpretation of the most recent experiments that the photodissociation process is dominated by tunneling. Analysis of the trajectories uncovers an unexpected dissociation pathway for one quantum excitation of the O–H stretching mode of the S 1more » state, namely, tunneling in a coherent mixture of states starting in a smaller R OH (~0.9–1.0 Å) region than has previously been invoked. The simulations also show that most trajectories do not pass close to the S 1–S 2 conical intersection (they have a minimum gap greater than 0.6 eV), they provide statistics on the out-of-plane angles at the locations of the minimum energy adiabatic gap, and they reveal information about which vibrational modes are most highly activated in the products.« less
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Han, Si-ping; van Duin, Adri C T; Goddard, William A; Strachan, Alejandro
2011-05-26
We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH(3)NO(2)) using molecular dynamics with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000-3000 K) and density 1.97 g/cm(3) for times up to 200 ps. At T = 3000 K the first reaction in the decomposition of nitromethane is an intermolecular proton transfer leading to CH(3)NOOH and CH(2)NO(2). For lower temperatures (T = 2500 and 2000 K) the first reaction during decomposition is often an isomerization reaction involving the scission of the C-N bond the formation of a C-O bond to form methyl nitrate (CH(3)ONO). Also at very early times we observe intramolecular proton transfer events. The main product of these reactions is H(2)O which starts forming following those initiation steps. The appearance of H(2)O marks the beginning of the exothermic chemistry. Recent quantum-mechanics-based molecular dynamics simulations on the chemical reactions and time scales for decomposition of a crystalline sample heated to T = 3000 K for a few picoseconds are in excellent agreement with our results, providing an important, direct validation of ReaxFF.
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NASA Astrophysics Data System (ADS)
Hansen, Scott K.; Pandey, Sachin; Karra, Satish; Vesselinov, Velimir V.
2017-12-01
Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a multi-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, chrotran, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling, and biomass death. Our software implementation handles heterogeneous flow fields, as well as arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hansen, Scott; Pandey, Sachin; Karra, Satish
Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death.more » Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.« less
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Hansen, Scott; Pandey, Sachin; Karra, Satish; ...
2017-04-25
Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death.more » Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.« less
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Zhong, Jian; Cai, Xiao-Ming; Bloss, William James
2015-05-01
This study investigates the dispersion and transport of reactive pollutants in a deep urban street canyon with an aspect ratio of 2 under neutral meteorological conditions using large-eddy simulation. The spatial variation of pollutants is significant due to the existence of two unsteady vortices. The deviation of species abundance from chemical equilibrium for the upper vortex is greater than that for the lower vortex. The interplay of dynamics and chemistry is investigated using two metrics: the photostationary state defect, and the inferred ozone production rate. The latter is found to be negative at all locations within the canyon, pointing to a systematic negative offset to ozone production rates inferred by analogous approaches in environments with incomplete mixing of emissions. This study demonstrates an approach to quantify parameters for a simplified two-box model, which could support traffic management and urban planning strategies and personal exposure assessment. Copyright © 2015 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Jones, T.; Detwiler, R. L.
2017-12-01
Fractures act as dominant pathways for fluid flow in low-permeability rocks. However, in many subsurface environments, fluid rock reactions can lead to mineral precipitation, which alters fracture surface geometry and reduces fracture permeability. In natural fractures, surface mineralogy and roughness are often heterogeneous, leading to variations in both velocity and reactive surface area. The combined effects of surface roughness and mineral heterogeneity can lead to large disparities in local precipitation rates that are difficult to predict due to the strong coupling between dissolved mineral transport and reactions at the fracture surface. Recent experimental observations suggest that mineral precipitation in a heterogeneous fracture may promote preferential flow and focus large dissolved ion concentrations into regions with limited reactive surface area. Here, we build on these observations using reactive transport simulations. Reactive transport is simulated with a quasi-steady-state 2D model that uses a depth-averaged mass-transfer relationship to describe dissolved mineral transport across the fracture aperture and local precipitation reactions. Mineral precipitation-induced changes to fracture surface geometry are accounted for using two different approaches: (1) by only allowing reactive minerals to grow vertically, and (2) by allowing three-dimensional mineral growth at reaction sites. Preliminary results from simulations using (1) suggest that precipitation-induced aperture reduction focuses flow into thin flow paths. This flow focusing causes a reduction in the fracture-scale precipitation rate, and precipitation ceases when the reaction zone extends the entire length of the fracture. This approach reproduces experimental observations at early time reasonably well, but as precipitation proceeds, reaction sites can grow laterally along the fracture surfaces, which is not predicted by (1). To account for three-dimensional mineral growth (2), we have incorporated a level-set-method based approach for tracking the mineral interfaces in three dimensions. This provides a mechanistic approach for simulating the dynamics of the formation, and eventual closing, of preferential flow paths by precipitation-induced aperture alteration, that do not occur using (1).
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2012-02-28
Coupling in Detonation Waves: 1D Dynamics”, Paper 89, 23rd International Colloquium on the Dynamics of Explosions and Reactive ...and temperature, and can be modeled as a constant volume reaction , which is more efficient than a constant pressure reaction . After the detonation ... kinetics , and flow processes using high order numerical methods. A fifth-order WENO (weighted essentially non -oscillatory12,13) scheme was used
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NASA Astrophysics Data System (ADS)
Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.
2010-12-01
Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs to homogeneous and heterogeneous porous media, respectively. In 1D columns, calcium carbonate mineral precipitation was driven by urea hydrolysis catalyzed by urease enzyme, and in 2D flow cells, calcium carbonate mineral forming reactants were injected sequentially, forming migrating reaction fronts that are typically highly nonuniform. The RAT simulation results for the spatial and temporal distributions of precipitates, reaction rates and major species in the system, and also for changes in porosity and permeability, were compared to both laboratory experimental data and computational results obtained using other reactive transport simulators. The comparisons demonstrate the ability of RAT to simulate complex nonlinear systems and the advantages of fully coupled approaches, over de-coupled methods, for accurate simulation of complex, dynamic processes such as engineered mineral precipitation in subsurface environments.
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Multicale modeling of the detonation of aluminized explosives using SPH-MD-QM method
NASA Astrophysics Data System (ADS)
Peng, Qing; Wang, Guangyu; Liu, Gui-Rong; de, Suvranu
Aluminized explosives have been applied in military industry since decades ago. Compared with ideal explosives, aluminized explosives feature both fast detonation and slow metal combustion chemistry, generating a complex multi-phase reactive flow. Here, we introduce a sequential multiscale model of SPH-MD-QM to simulate the detonation behavior of aluminized explosives. At the bottom level, first-principles quantum mechanics (QM) calculations are employed to obtain the training sets for fitting the ReaxFF potentials, which are used in turn in the reactive molecular dynamics (MD) simulations in the middle level to obtain the chemical reaction rates and equations of states. At the up lever, a smooth particle hydrodynamics (SPH) method incorporated ignition and growth model and afterburning model has been used for the simulation of the detonation and combustion of the aluminized explosive. Simulation is compared with experiment and good agreement is observed. The proposed multiscale method of SPH-MD-QM could be used to optimize the performance of aluminized explosives. The authors would like to acknowledge the generous financial support from the Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-13-1-0025 and the Office of Naval Research Grants ONR Award No. N00014-08-1-0462 and No. N00014-12-1-0527.
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Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin
2015-11-12
High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.
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NASA Astrophysics Data System (ADS)
Li, Shaohong L.; Truhlar, Donald G.
2017-02-01
Analytic potential energy surfaces (PESs) and state couplings of the ground and two lowest singlet excited states of thioanisole (C6H5SCH3) are constructed in a diabatic representation based on electronic structure calculations including dynamic correlation. They cover all 42 internal degrees of freedom and a wide range of geometries including the Franck-Condon region and the reaction valley along the breaking S-CH3 bond with the full ranges of the torsion angles. The parameters in the PESs and couplings are fitted to the results of smooth diabatic electronic structure calculations including dynamic electron correlation by the extended multi-configurational quasi-degenerate perturbation theory method for the adiabatic state energies followed by diabatization by the fourfold way. The fit is accomplished by the anchor points reactive potential method with two reactive coordinates and 40 nonreactive degrees of freedom, where the anchor-point force fields are obtained with a locally modified version of the QuickFF package. The PESs and couplings are suitable for study of the topography of the trilayer potential energy landscape and for electronically nonadiabatic molecular dynamics simulations of the photodissociation of the S-CH3 bond.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hansen, Scott K.; Pandey, Sachin; Karra, Satish
2017-04-13
CHROTRAN is a fork of the widely-used PFLOTRAN flow and reactive transport numerical simulation code. It implements custom physics and chemistry appropriate to the design of in-situ reduction of heavy metals such as Cr(VI) in groundwater. CHROTRAN includes full dynamics for five species: the metal to be remediated, an electron donor, biofilm, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, and biofilm inactivation. The software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injectionmore » points, and features full coupling between flow and reactive transport, allowing for assessment of the effect of bio-fouling.« less
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Towards Time Automata and Multi-Agent Systems
NASA Technical Reports Server (NTRS)
Hutzler, G.; Klaudel, H.; Wang, D. Y.
2004-01-01
The design of reactive systems must comply with logical correctness (the system does what it is supposed to do) and timeliness (the system has to satisfy a set of temporal constraints) criteria. In this paper, we propose a global approach for the design of adaptive reactive systems, i.e., systems that dynamically adapt their architecture depending on the context. We use the timed automata formalism for the design of the agents' behavior. This allows evaluating beforehand the properties of the system (regarding logical correctness and timeliness), thanks to model-checking and simulation techniques. This model is enhanced with tools that we developed for the automatic generation of code, allowing to produce very quickly a running multi-agent prototype satisfying the properties of the model.
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NASA Astrophysics Data System (ADS)
Harmon, Michael; Gamba, Irene M.; Ren, Kui
2016-12-01
This work concerns the numerical solution of a coupled system of self-consistent reaction-drift-diffusion-Poisson equations that describes the macroscopic dynamics of charge transport in photoelectrochemical (PEC) solar cells with reactive semiconductor and electrolyte interfaces. We present three numerical algorithms, mainly based on a mixed finite element and a local discontinuous Galerkin method for spatial discretization, with carefully chosen numerical fluxes, and implicit-explicit time stepping techniques, for solving the time-dependent nonlinear systems of partial differential equations. We perform computational simulations under various model parameters to demonstrate the performance of the proposed numerical algorithms as well as the impact of these parameters on the solution to the model.
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Stochastic dynamics for reinfection by transmitted diseases
NASA Astrophysics Data System (ADS)
Barros, Alessandro S.; Pinho, Suani T. R.
2017-06-01
The use of stochastic models to study the dynamics of infectious diseases is an important tool to understand the epidemiological process. For several directly transmitted diseases, reinfection is a relevant process, which can be expressed by endogenous reactivation of the pathogen or by exogenous reinfection due to direct contact with an infected individual (with smaller reinfection rate σ β than infection rate β ). In this paper, we examine the stochastic susceptible, infected, recovered, infected (SIRI) model simulating the endogenous reactivation by a spontaneous reaction, while exogenous reinfection by a catalytic reaction. Analyzing the mean-field approximations of a site and pairs of sites, and Monte Carlo (MC) simulations for the particular case of exogenous reinfection, we obtained continuous phase transitions involving endemic, epidemic, and no transmission phases for the simple approach; the approach of pairs is better to describe the phase transition from endemic phase (susceptible, infected, susceptible (SIS)-like model) to epidemic phase (susceptible, infected, and removed or recovered (SIR)-like model) considering the comparison with MC results; the reinfection increases the peaks of outbreaks until the system reaches endemic phase. For the particular case of endogenous reactivation, the approach of pairs leads to a continuous phase transition from endemic phase (SIS-like model) to no transmission phase. Finally, there is no phase transition when both effects are taken into account. We hope the results of this study can be generalized for the susceptible, exposed, infected, and removed or recovered (SEIRIE) model, for which the state exposed (infected but not infectious), describing more realistically transmitted diseases such as tuberculosis. In future work, we also intend to investigate the effect of network topology on phase transitions when the SIRI model describes both transmitted diseases (σ <1 ) and social contagions (σ >1 ).
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A Uranium Bioremediation Reactive Transport Benchmark
DOE Office of Scientific and Technical Information (OSTI.GOV)
Yabusaki, Steven B.; Sengor, Sevinc; Fang, Yilin
A reactive transport benchmark problem set has been developed based on in situ uranium bio-immobilization experiments that have been performed at a former uranium mill tailings site in Rifle, Colorado, USA. Acetate-amended groundwater stimulates indigenous microorganisms to catalyze the reduction of U(VI) to a sparingly soluble U(IV) mineral. The interplay between the flow, acetate loading periods and rates, microbially-mediated and geochemical reactions leads to dynamic behavior in metal- and sulfate-reducing bacteria, pH, alkalinity, and reactive mineral surfaces. The benchmark is based on an 8.5 m long one-dimensional model domain with constant saturated flow and uniform porosity. The 159-day simulation introducesmore » acetate and bromide through the upgradient boundary in 14-day and 85-day pulses separated by a 10 day interruption. Acetate loading is tripled during the second pulse, which is followed by a 50 day recovery period. Terminal electron accepting processes for goethite, phyllosilicate Fe(III), U(VI), and sulfate are modeled using Monod-type rate laws. Major ion geochemistry modeled includes mineral reactions, as well as aqueous and surface complexation reactions for UO2++, Fe++, and H+. In addition to the dynamics imparted by the transport of the acetate pulses, U(VI) behavior involves the interplay between bioreduction, which is dependent on acetate availability, and speciation-controlled surface complexation, which is dependent on pH, alkalinity and available surface complexation sites. The general difficulty of this benchmark is the large number of reactions (74), multiple rate law formulations, a multisite uranium surface complexation model, and the strong interdependency and sensitivity of the reaction processes. Results are presented for three simulators: HYDROGEOCHEM, PHT3D, and PHREEQC.« less
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Nanocarbon synthesis by high-temperature oxidation of nanoparticles
DOE Office of Scientific and Technical Information (OSTI.GOV)
Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying
High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp 2 carbons with pentagonalmore » and heptagonal defects. Furthermore, this work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.« less
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Molecular dynamics simulations of the surface tension of oxygen-supersaturated water
NASA Astrophysics Data System (ADS)
Jain, S.; Qiao, L.
2017-04-01
In this work, non-reactive molecular dynamic simulations were conducted to determine the surface tension of water as a function of the concentration of the dissolved gaseous molecules (O2), which would in turn help to predict the pressure inside the nanobubbles under supersaturation conditions. Knowing the bubble pressure is a prerequisite for understanding the mechanisms behind the spontaneous combustion of the H2/O2 gases inside the nanobubbles. First, the surface tension of pure water was determined using the planar interface method and the Irving and Kirkwood formula. Next, the surface tension of water containing four different supersaturation concentrations (S) of O2 gas molecules was computed considering the curved interface of a nanobubble. The surface tension of water was found to decrease with an increase in the supersaturation ratio or the concentration of the dissolved O2 gas molecules.
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Seasonality Impact on the Transmission Dynamics of Tuberculosis
2016-01-01
The statistical data of monthly pulmonary tuberculosis (TB) incidence cases from January 2004 to December 2012 show the seasonality fluctuations in Shaanxi of China. A seasonality TB epidemic model with periodic varying contact rate, reactivation rate, and disease-induced death rate is proposed to explore the impact of seasonality on the transmission dynamics of TB. Simulations show that the basic reproduction number of time-averaged autonomous systems may underestimate or overestimate infection risks in some cases, which may be up to the value of period. The basic reproduction number of the seasonality model is appropriately given, which determines the extinction and uniform persistence of TB disease. If it is less than one, then the disease-free equilibrium is globally asymptotically stable; if it is greater than one, the system at least has a positive periodic solution and the disease will persist. Moreover, numerical simulations demonstrate these theorem results. PMID:27042199
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NASA Astrophysics Data System (ADS)
Weingarten, N. Scott; Mattson, William D.; Yau, Anthony D.; Weihs, Timothy P.; Rice, Betsy M.
2010-05-01
To elucidate the mechanisms of energy release in a reacting nickel/aluminum bilayer, we simulate the exothermic alloying reactions using both microcanonical and isoenthalpic-isobaric molecular dynamics simulations and an embedded-atom method type potential. The mechanism of the mixing consists of a sequence of steps in which mixing and reaction first occurs at the interface; the resulting heat generated from the mixing then melts the Al layer; subsequent mixing leads to further heat generation after which the Ni layer melts. The mixing continues until the alloying reactions are completed. The results indicate that pressure has a significant influence on the rates of atomic mixing and alloying reactions. Local pressures and temperatures within the individual layers at the time of melting are calculated, and these results are compared with the pressure-dependent melting curves determined for pure Al and pure Ni using this interaction potential.
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Controlled Detonation Dynamics in Additively Manufactured High Explosives
NASA Astrophysics Data System (ADS)
Schmalzer, Andrew; Tappan, Bryce; Bowden, Patrick; Manner, Virginia; Clements, Brad; Menikoff, Ralph; Ionita, Axinte; Branch, Brittany; Dattelbaum, Dana; Espy, Michelle; Patterson, Brian; Wu, Ruilian; Mueller, Alexander
2017-06-01
The effect of structure in explosives has long been a subject of interest to explosives engineers and scientists. Through structure, detonation dynamics in explosives can be manipulated, introducing a new level of safety and directed performance into these previously difficult to control materials. New advances in additive manufacturing (AM) allow the deliberate introduction of exact internal structures at dimensions approaching the mesoscale of these energetic materials. We show through simulation and experiment that this structure can be used to control detonation behavior by manipulating complex shockwave interactions. We use high-speed video and shorting mag-wires to determine the detonation velocity in AM generated explosive structures, demonstrating, for the first time, a method of controlling the directional propagation of reactive flow through the controlled introduction of structure within a high explosive. With ongoing improvement in the AM methods available coupled with guidance through modeling and simulations, more complex interactions are being explored. LANL LDRD Office.
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Nanocarbon synthesis by high-temperature oxidation of nanoparticles
Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying; ...
2016-04-20
High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp 2 carbons with pentagonalmore » and heptagonal defects. Furthermore, this work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.« less
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Mosey, Nicholas J; Woo, Tom K
2006-09-04
The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.
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Nanocarbon synthesis by high-temperature oxidation of nanoparticles
Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying; Nakano, Aiichiro; Rajak, Pankaj; Sheng, Chunyang; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya
2016-01-01
High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp2 carbons with pentagonal and heptagonal defects. This work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites. PMID:27095061
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NASA Technical Reports Server (NTRS)
Benjamin, Ilan; Pohorille, Andrew
1993-01-01
The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.
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Assessment of CO2 Mineralization and Dynamic Rock Properties at the Kemper Pilot CO2 Injection Site
NASA Astrophysics Data System (ADS)
Qin, F.; Kirkland, B. L.; Beckingham, L. E.
2017-12-01
CO2-brine-mineral reactions following CO2 injection may impact rock properties including porosity, permeability, and pore connectivity. The rate and extent of alteration largely depends on the nature and evolution of reactive mineral interfaces. In this work, the potential for geochemical reactions and the nature of the reactive mineral interface and corresponding hydrologic properties are evaluated for samples from the Lower Tuscaloosa, Washita-Fredericksburg, and Paluxy formations. These formations have been identified as future regionally extensive and attractive CO2 storage reservoirs at the CO2 Storage Complex in Kemper County, Mississippi, USA (Project ECO2S). Samples from these formations were obtained from the Geological Survey of Alabama and evaluated using a suite of complementary analyses. The mineral composition of these samples will be determined using petrography and powder X-ray Diffraction (XRD). Using these compositions, continuum-scale reactive transport simulations will be developed and the potential CO2-brine-mineral interactions will be examined. Simulations will focus on identifying potential reactive minerals as well as the corresponding rate and extent of reactions. The spatial distribution and accessibility of minerals to reactive fluids is critical to understanding mineral reaction rates and corresponding changes in the pore structure, including pore connectivity, porosity and permeability. The nature of the pore-mineral interface, and distribution of reactive minerals, will be determined through imaging analysis. Multiple 2D scanning electron microscopy (SEM) backscattered electron (BSE) images and energy dispersive x-ray spectroscopy (EDS) images will be used to create spatial maps of mineral distributions. These maps will be processed to evaluate the accessibility of reactive minerals and the potential for flow-path modifications following CO2 injection. The "Establishing an Early CO2 Storage Complex in Kemper, MS" project is funded by the U.S. Department of Energy's National Energy Technology Laboratory and cost-sharing partners.
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Azam, Faizul; Alabdullah, Nada Hussin; Ehmedat, Hadeel Mohammed; Abulifa, Abdullah Ramadan; Taban, Ismail; Upadhyayula, Sreedevi
2018-06-01
Aggregation of amyloid beta (Aβ) protein considered as one of contributors in development of Alzheimer's disease (AD). Several investigations have identified the importance of non-steroidal anti-inflammatory drugs (NSAIDs) as Aβ aggregation inhibitors. Here, we have examined the binding interactions of 24 NSAIDs belonging to eight different classes, with Aβ fibrils by exploiting docking and molecular dynamics studies. Minimum energy conformation of the docked NSAIDs were further optimized by density functional theory (DFT) employing Becke's three-parameter hybrid model, Lee-Yang-Parr (B3LYP) correlation functional method. DFT-based global reactivity descriptors, such as electron affinity, hardness, softness, chemical potential, electronegativity, and electrophilicity index were calculated to inspect the expediency of these descriptors for understanding the reactive nature and sites of the molecules. Few selected NSAID-Aβ fibrils complexes were subjected to molecular dynamics simulation to illustrate the stability of these complexes and the most prominent interactions during the simulated trajectory. All of the NSAIDs exhibited potential activity against Aβ fibrils in terms of predicted binding affinity. Sulindac was found to be the most active compound underscoring the contribution of indene methylene substitution, whereas acetaminophen was observed as least active NSAID. General structural requirements for interaction of NSAIDs with Aβ fibril include: aryl/heteroaryl aromatic moiety connected through a linker of 1-2 atoms to a distal aromatic group. Considering these structural requirements and electronic features, new potent agents can be designed and developed as potential Aβ fibril inhibitors for the treatment of AD.
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Dynamic groundwater flows and geochemistry in a sandy nearshore aquifer over a wave event
NASA Astrophysics Data System (ADS)
Malott, Spencer; O'Carroll, Denis M.; Robinson, Clare E.
2016-07-01
Dynamic coastal forcing influences the transport of pollutants in nearshore aquifers and their ultimate flux to coastal waters. In this study, field data are presented that show, for the first time, the influence of a period of intensified wave conditions (wave event) on nearshore groundwater flows and geochemistry in a sandy beach. Field measurements at a freshwater beach allow wave effects to be quantified without other complex forcing that are present along marine shorelines (e.g., tides). Pressure transducer data obtained over an isolated wave event reveal the development of transient groundwater flow recirculations. The groundwater flows were simulated in FEFLOW using a phase-averaged wave setup approach to represent waves acting on the sediment-water interface. Comparison of measured and simulated data indicates that consideration of wave setup alone is able to adequately capture wave-induced perturbations in groundwater flows. While prior studies have shown sharp pH and redox spatial zonations in nearshore aquifers, this study reveals rapid temporal variations in conductivity, pH, and redox (ORP) in shallow sediments (up to 0.5 m depth) in response to varying wave conditions. Comparison of head gradients with calculated conductivity and pH mixing ratios indicates the controlling effect of the wave-induced water exchange and flows in driving the observed geochemical dynamics. While we are not able to conclusively determine the extent to which temporal variations are caused by conservative mixing versus reactive processes, the pH and ORP variations observed will have significant implications for the fate of reactive pollutants discharging through sandy nearshore aquifers.
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Ambrus, Attila; Mizsei, Reka; Adam-Vizi, Vera
2015-07-01
Human dihydrolipoamide dehydrogenase (hLADH) is a flavoenzyme component (E3) of the human alpha-ketoglutarate dehydrogenase complex (α-KGDHc) and few other dehydrogenase complexes. Pathogenic mutations of hLADH cause severe metabolic diseases (atypical forms of E3 deficiency) that often escalate to cardiological or neurological presentations and even premature death; the pathologies are generally accompanied by lactic acidosis. hLADH presents a distinct conformation under acidosis (pH 5.5-6.8) with lower physiological activity and the capacity of generating reactive oxygen species (ROS). It has been shown by our laboratory that selected pathogenic mutations, besides lowering the physiological activity of hLADH, significantly stimulate ROS generation by hLADH, especially at lower pH, which might play a role in the pathogenesis of E3-deficiency in respective cases. Previously, we generated by molecular dynamics (MD) simulation the low-pH hLADH structure and analyzed the structural changes induced in this structure by eight of the pathogenic mutations of hLADH. In the absence of high resolution mutant structures these pieces of information are crucial for the mechanistic investigation of the molecular pathogeneses of the hLADH protein. In the present work we analyzed by molecular dynamics simulation the structural changes induced in the low-pH conformation of hLADH by five pathogenic mutations of hLADH; the structures of these disease-causing mutants of hLADH have never been examined before.
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Shock and Laser Induced Non-Equilibrium Chemistry in Molecular Energetics
NASA Astrophysics Data System (ADS)
Wood, Mitchell; Cherukara, Mathew; Kober, Edward; Strachan, Alejandro
2015-06-01
In this study, we have used large scale reactive molecular dynamics (MD) simulations to study how contrasting initiation mechanisms from either shock or electromagnetic insults compare to traditional thermal initiation. We will show how insults of equal strength but different character can yield vastly different reaction profiles and thus the evolution of hot-spots. For shocked RDX (Up = 2km/s), we find that the collapse of a cylindrical 40 nm diameter pore leads to a significant amount of non-equilibrium reactions followed by the formation of a sustained deflagration wave. In contrast, a hot spot that is seeded into a statically compressed crystal with matching size and temperature will quench over the same timescale, highlighting the importance of insult type. Furthermore, MD simulations of electromagnetic insults coupled to intramolecular vibrations have shown, in some cases, mode specific initial chemistry and altered kinetics of the subsequent decomposition. By leveraging spectroscopic and chemical information gathered in our MD simulations, we have been able to identify and track non-equilibrium vibrational states of these materials and correlate them to these observed changes. Implications of insult dependent reactivity and non-equilibrium chemistry will be discussed.
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Fiebig, Florian; Lansner, Anders
2014-01-01
Declarative long-term memories are not created in an instant. Gradual stabilization and temporally shifting dependence of acquired declarative memories in different brain regions—called systems consolidation—can be tracked in time by lesion experiments. The observation of temporally graded retrograde amnesia (RA) following hippocampal lesions points to a gradual transfer of memory from hippocampus to neocortical long-term memory. Spontaneous reactivations of hippocampal memories, as observed in place cell reactivations during slow-wave-sleep, are supposed to drive neocortical reinstatements and facilitate this process. We propose a functional neural network implementation of these ideas and furthermore suggest an extended three-state framework that includes the prefrontal cortex (PFC). It bridges the temporal chasm between working memory percepts on the scale of seconds and consolidated long-term memory on the scale of weeks or months. We show that our three-stage model can autonomously produce the necessary stochastic reactivation dynamics for successful episodic memory consolidation. The resulting learning system is shown to exhibit classical memory effects seen in experimental studies, such as retrograde and anterograde amnesia (AA) after simulated hippocampal lesioning; furthermore the model reproduces peculiar biological findings on memory modulation, such as retrograde facilitation of memory after suppressed acquisition of new long-term memories—similar to the effects of benzodiazepines on memory. PMID:25071536
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Time-dependent computational studies of flames in microgravity
NASA Technical Reports Server (NTRS)
Oran, Elaine S.; Kailasanath, K.
1989-01-01
The research performed at the Center for Reactive Flow and Dynamical Systems in the Laboratory for Computational Physics and Fluid Dynamics, at the Naval Research Laboratory, in support of the NASA Microgravity Science and Applications Program is described. The primary focus was on investigating fundamental questions concerning the propagation and extinction of premixed flames in Earth gravity and in microgravity environments. The approach was to use detailed time-dependent, multispecies, numerical models as tools to simulate flames in different gravity environments. The models include a detailed chemical kinetics mechanism consisting of elementary reactions among the eight reactive species involved in hydrogen combustion, coupled to algorithms for convection, thermal conduction, viscosity, molecular and thermal diffusion, and external forces. The external force, gravity, can be put in any direction relative to flame propagation and can have a range of values. A combination of one-dimensional and two-dimensional simulations was used to investigate the effects of curvature and dilution on ignition and propagation of flames, to help resolve fundamental questions on the existence of flammability limits when there are no external losses or buoyancy forces in the system, to understand the mechanism leading to cellular instability, and to study the effects of gravity on the transition to cellular structure. A flame in a microgravity environment can be extinguished without external losses, and the mechanism leading to cellular structure is not preferential diffusion but a thermo-diffusive instability. The simulations have also lead to a better understanding of the interactions between buoyancy forces and the processes leading to thermo-diffusive instability.
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NASA Astrophysics Data System (ADS)
Glowacki, David R.; Orr-Ewing, Andrew J.; Harvey, Jeremy N.
2015-07-01
We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ˜23 kcal mol-1 localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of the post-reaction solvation environment results in a red shift. These two competing effects mean that the post-reaction relaxation profile is distinct from what is observed when Franck-Condon vibrational excitation of DF occurs within a microsolvation environment initially at equilibrium. Our conclusions, along with the theoretical and parallel software framework presented in this paper, should be more broadly applicable to a range of complex reactive systems.
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Upscaling heterogeneity in aquifer reactivity via exposure-time concept: forward model.
Seeboonruang, Uma; Ginn, Timothy R
2006-03-20
Reactive properties of aquifer solid phase materials play an important role in solute fate and transport in the natural subsurface on time scales ranging from years in contaminant remediation to millennia in dynamics of aqueous geochemistry. Quantitative tools for dealing with the impact of natural heterogeneity in solid phase reactivity on solute fate and transport are limited. Here we describe the use of a structural variable to keep track of solute flux exposure to reactive surfaces. With this approach, we develop a non-reactive tracer model that is useful for determining the signature of multi-scale reactive solid heterogeneity in terms of solute flux distributions at the field scale, given realizations of three-dimensional reactive site density fields. First, a governing Eulerian equation for the non-reactive tracer model is determined by an upscaling technique in which it is found that the exposure time of solution to reactive surface areas evolves via both a macroscopic velocity and a macroscopic dispersion in the artificial dimension of exposure time. Second, we focus on the Lagrangian approach in the context of a streamtube ensemble and demonstrate the use of the distribution of solute flux over the exposure time dimension in modeling two-dimensional transport of a solute undergoing simplified linear reversible reactions, in hypothetical conditions following prior laboratory experiments. The distribution of solute flux over exposure time in a given case is a signature of the impact of heterogeneous aquifer reactivity coupled with a particular physical heterogeneity, boundary conditions, and hydraulic gradient. Rigorous application of this approach in a simulation sense is limited here to linear kinetically controlled reactions.
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Yang, Zhongyue; Houk, K N
2018-03-15
Jacobus Henricus van 't Hoff was the first Nobel Laureate in Chemistry. He pioneered in the study of chemical dynamics, which referred at that time to chemical kinetics and thermodynamics. The term has evolved in modern times to refer to the exploration of chemical transformations in a time-resolved fashion. Chemical dynamics has been driven by the development of molecular dynamics trajectory simulations, which provide atomic visualization of chemical processes and illuminate how dynamic effects influence chemical reactivity and selectivity. In homage to the legend of van 't Hoff, we review the development of the chemical dynamics of organic reactions, our area of research. We then discuss our trajectory simulations of pericyclic reactions, and our development of dynamic criteria for concerted and stepwise reaction mechanisms. We also describe a method that we call environment-perturbed transition state sampling, which enables trajectory simulations in condensed-media using quantum mechanics and molecular mechanics (QM/MM). We apply the method to reactions in solvent and in enzyme. Jacobus Henricus van 't Hoff (1852, Rotterdam-1911, Berlin) received the Nobel Prize for Chemistry in 1901 "in recognition of the extraordinary services he has rendered by the discovery of the laws of chemical dynamics and osmotic pressure in solutions". van 't Hoff was born the Netherlands, and earned his doctorate in Utrecht in 1874. In 1896 he moved to Berlin, where he was offered a position with more research and less teaching. van 't Hoff is considered one of the founders of physical chemistry. A key step in establishing this new field was the start of Zeitschrift für Physikalische Chemie in 1887. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Multiscale modeling of shock wave localization in porous energetic material
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wood, M. A.; Kittell, D. E.; Yarrington, C. D.
Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (< 6 GPa), atomistic simulations of pore collapse are used here to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock wavesmore » interacting with pores as a function of this viscoplastic material response. Finally, we find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.« less
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Multiscale modeling of shock wave localization in porous energetic material
Wood, M. A.; Kittell, D. E.; Yarrington, C. D.; ...
2018-01-30
Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (< 6 GPa), atomistic simulations of pore collapse are used here to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock wavesmore » interacting with pores as a function of this viscoplastic material response. Finally, we find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.« less
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Role of the Short Distance Order in Glass Reactivity
2018-01-01
In 2005, our group described for the first time the structural characterization at the atomic scale of bioactive glasses and the influence of the glasses’ nanostructure in their reactivity in simulated body fluids. In that study, two bioactive sol-gel glasses with composition 80%SiO2–20%CaO and 80%SiO2–17%CaO–3%P2O5 (in mol-%) were characterized by High-Resolution Transmission Electron Microscopy (HRTEM). Such characterization revealed unknown features of the glasses’ structure at the local scale that allowed the understanding of their different in vitro behaviors as a consequence of the presence or absence of P2O5. Since then, the nanostructure of numerous bioactive glasses, including melt-prepared, sol-gel derived, and mesoporous glasses, was investigated by HRTEM, Nuclear Magnetic Resonance (NMR) spectroscopy, Molecular Dynamics (MD) simulations, and other experimental techniques. These studies have shown that although glasses are amorphous solids, a certain type of short distance order, which greatly influences the in vitro and in vivo reactivity, is always present. This paper reviews the most significant advances in the understanding of bioactive glasses that took place in the last years as a result of the growing knowledge of the glasses’ nanostructure. PMID:29534481
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Zhang, Luzheng; Zybin, Sergey V; van Duin, Adri C T; Dasgupta, Siddharth; Goddard, William A; Kober, Edward M
2009-10-08
We report molecular dynamics (MD) simulations using the first-principles-based ReaxFF reactive force field to study the thermal decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at various densities and temperatures. TATB is known to produce a large amount (15-30%) of high-molecular-weight carbon clusters, whereas detonation of nitramines such as HMX and RDX (1,3,5-trinitroperhydro-1,3,5-triazine) generate predominantly low-molecular-weight products. In agreement with experimental observation, these simulations predict that TATB decomposition quickly (by 30 ps) initiates the formation of large carbonaceous clusters (more than 4000 amu, or approximately 15-30% of the total system mass), and HMX decomposition leads almost exclusively to small-molecule products. We find that HMX decomposes readily on this time scale at lower temperatures, for which the decomposition rate of TATB is about an order of magnitude slower. Analyzing the ReaxFF MD results leads to the detailed atomistic structure of this carbon-rich phase of TATB and allows characterization of the kinetics and chemistry related to this phase and their dependence on system density and temperature. The carbon-rich phase formed from TATB contains mainly polyaromatic rings with large oxygen content, leading to graphitic regions. We use these results to describe the initial reaction steps of thermal decomposition of HMX and TATB in terms of the rates for forming primary and secondary products, allowing comparison to experimentally derived models. These studies show that MD using the ReaxFF reactive force field provides detailed atomistic information that explains such macroscopic observations as the dramatic difference in carbon cluster formation between TATB and HMX. This shows that ReaxFF MD captures the fundamental differences in the mechanisms of such systems and illustrates how the ReaxFF may be applied to model complex chemical phenomena in energetic materials. The studies here illustrate this for modestly sized systems and modest periods; however, ReaxFF calculations of reactive processes have already been reported on systems with approximately 10(6) atoms. Thus, with suitable computational facilities, one can study the atomistic level chemical processes in complex systems under extreme conditions.
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Reactive Oxygen Species (ROS) generation by lunar simulants
NASA Astrophysics Data System (ADS)
Kaur, Jasmeet; Rickman, Douglas; Schoonen, Martin A.
2016-05-01
The current interest in human exploration of the Moon and past experiences of Apollo astronauts has rekindled interest into the possible harmful effects of lunar dust on human health. In comparison to the Apollo-era explorations, human explorers may be weeks on the Moon, which will raise the risk of inhalation exposure. The mineralogical composition of lunar dust is well documented, but its effects on human health are not fully understood. With the aim of understanding the reactivity of dusts that may be encountered on geologically different lunar terrains, we have studied Reactive Oxygen Species (ROS) generation by a suite of lunar simulants of different mineralogical-chemical composition dispersed in water and Simulated Lung Fluid (SLF). To further explore the reactivity of simulants under lunar environmental conditions, we compared the reactivity of simulants both in air and inert atmosphere. As the impact of micrometeorites with consequent shock-induced stresses is a major environmental factor on the Moon, we also studied the effect of mechanical stress on samples. Mechanical stress was induced by hand crushing the samples both in air and inert atmosphere. The reactivity of samples after crushing was analyzed for a period of up to nine days. Hydrogen peroxide (H2O2) in water and SLF was analyzed by an in situ electrochemical probe and hydroxyl radical (•OH) by Electron Spin Resonance (ESR) spectroscopy and Adenine probe. Out of all simulants, CSM-CL-S was found to be the most reactive simulant followed by OB-1 and then JSC-1A simulant. The overall reactivity of samples in the inert atmosphere was higher than in air. Fresh crushed samples showed a higher level of reactivity than uncrushed samples. Simulant samples treated to create agglutination, including the formation of zero-valent iron, showed less reactivity than untreated simulants. ROS generation in SLF is initially slower than in deionized water (DI), but the ROS formation is sustained for as long as 7.5 h. By contrast ROS is formed rapidly within 30 min when simulants are dispersed in DI, but then the concentration either stabilizes or decreases over time. The results indicate that mechanical stress and the absence of molecular oxygen and water, which are important environmental characteristics of the lunar environment, can lead to enhanced production of ROS in general. However, compositional difference among simulants is the most important factor in governing the production of ROS. Simulants with glass content in excess of 40 wt% appear to produce as much as of order of magnitude more ROS than simulants with lower glass content.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Nagaoka, Masataka; Core Research for Evolutional Science and Technology; ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520
A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.
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Mechano-chemical pathways to H2O and CO2 splitting
NASA Astrophysics Data System (ADS)
Vedadi, Mohammad H.; Haas, Stephan
2011-10-01
The shock-induced collapse of CO2-filled nanobubbles is investigated using molecular dynamics simulations based on a reactive force field. The energetic nanojet and high-pressure water hammer shock formed during and after collapse of the nanobubble trigger mechano-chemical H2O-CO2 reactions, some of which lead to splitting of water and formation of O2 molecules. The dominant pathways through which splitting of water molecules occur are identified.
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A NIST Kinetic Data Base for PAH Reaction and Soot Particle Inception During Combusion
2007-12-01
in Computational Fluid Dynamics (CFD) codes hat have lead to the capability of describing complex reactive flow problems and thus simulating... parameters . However in the absence of data estimates must be made. Since the chemistry of combustion is extremely complex and for proper description...118:381-389 9. Babushok, V. and Tsang, W., J. Prop. and Pwr . 20 (2004) 403-414. 10. . Fournet, R., Warth, V., Glaude, P.A., Battin-Leclerc, F
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Mlyniec, A; Ekiert, M; Morawska-Chochol, A; Uhl, T
2016-06-01
In this work, we investigate the influence of the surrounding environment and the initial density on the decomposition kinetics of polylactide (PLA). The decomposition of the amorphous PLA was investigated by means of reactive molecular dynamics simulations. A computational model simulates the decomposition of PLA polymer inside the bulk, due to the assumed lack of removal of reaction products from the polymer matrix. We tracked the temperature dependency of the water and carbon monoxide production to extract the activation energy of thermal decomposition of PLA. We found that an increased density results in decreased activation energy of decomposition by about 50%. Moreover, initiation of decomposition of the amorphous PLA is followed by a rapid decline in activation energy caused by reaction products which accelerates the hydrolysis of esters. The addition of water molecules decreases initial energy of activation as well as accelerates the decomposition process. Additionally, we have investigated the dependency of density on external loading. Comparison of pressures needed to obtain assumed densities shows that this relationship is bilinear and the slope changes around a density equal to 1.3g/cm(3). The conducted analyses provide an insight into the thermal decomposition process of the amorphous phase of PLA, which is particularly susceptible to decomposition in amorphous and semi-crystalline PLA polymers. Copyright © 2016 Elsevier Inc. All rights reserved.
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Wang, Fuping; Chen, Lang; Geng, Deshen; Wu, Junying; Lu, Jianying; Wang, Chen
2018-04-26
Hexanitrohexaazaisowurtzitane (CL-20) has a high detonation velocity and pressure, but its sensitivity is also high, which somewhat limits its applications. Therefore, it is important to understand the mechanism and characteristics of thermal decomposition of CL-20. In this study, a ε-CL-20 supercell was constructed and ReaxFF-lg reactive molecular dynamics simulations were performed to investigate thermal decomposition of ε-CL-20 at various temperatures (2000, 2500, 2750, 3000, 3250, and 3500 K). The mechanism of thermal decomposition of CL-20 was analyzed from the aspects of potential energy evolution, the primary reactions, and the intermediate and final product species. The effect of temperature on thermal decomposition of CL-20 is also discussed. The initial reaction path of thermal decomposition of CL-20 is N-NO 2 cleavage to form NO 2 , followed by C-N cleavage, leading to the destruction of the cage structure. A small number of clusters appear in the early reactions and disappear at the end of the reactions. The initial reaction path of CL-20 decomposition is the same at different temperatures. However, as the temperature increases, the decomposition rate of CL-20 increases and the cage structure is destroyed earlier. The temperature greatly affects the rate constants of H 2 O and N 2 , but it has little effect on the rate constants of CO 2 and H 2 .
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Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials
2007-08-01
code) 2007 Reprint Aug 2006-Aug 2007 Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials W911NF-04-1-0178 sub 2781-USC-DOA...Priya Vashishta 213 821 2663 Reset Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials Priya Vashishta,∗ Rajiv K. Kalia...function of the particle velocity that drives the shock [18]. The MD and experimental data agree very well. Furthermore, the simulation shows a sudden
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Ostadhossein, Alireza; Cubuk, Ekin D.; Tritsaris, Georgios A.; ...
2014-12-18
Silicon (Si) has been recognized as a promising anode material for the next-generation high-capacity lithium (Li)-ion batteries because of its high theoretical energy density. Recent in situ transmission electron microscopy (TEM) revealed that the electrochemical lithiation of crystalline Si nanowires (c-SiNWs) proceeds by the migration of the interface between the lithiated Si (LixSi) shell and the pristine unlithiated core, accompanied by solid-state amorphization. The underlying atomic mechanisms of Li insertion into c-Si remain poorly understood. In this research, we perform molecular dynamics (MD) simulations using the reactive force field (ReaxFF) to characterize the lithiation process of c-SiNWs. Our calculations showmore » that ReaxFF can accurately reproduce the energy barriers of Li migration from DFT calculations in both crystalline (c-Si) and amorphous Si (a-Si). The ReaxFF-based MD simulations reveal that Li insertion into interlayer spacing between two adjacent (111) planes results in the peeling-off of the (111) facets and subsequent amorphization, in agreement with experimental observations. We find that breaking of the Si–Si bonds between (111)-bilayers requires a rather high local Li concentration, which explains the atomically sharp amorphous–crystalline interface (ACI). Our stress analysis shows that lithiation induces compressive stress at the ACI layer, causing retardation or even the stagnation of the reaction front, also in good agreement with TEM observations. Lithiation at high temperatures (e.g. 1200 K) shows that Li insertion into c-SiNW results in an amorphous to crystalline phase transformation at Li : Si composition of ~4.2:1. In conclusion, our modeling results provide a comprehensive picture of the effects of reaction and diffusion-induced stress on the interfacial dynamics and mechanical degradation of SiNW anodes under chemo-mechanical lithiation.« less
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Reactive immunization on complex networks
NASA Astrophysics Data System (ADS)
Alfinito, Eleonora; Beccaria, Matteo; Fachechi, Alberto; Macorini, Guido
2017-01-01
Epidemic spreading on complex networks depends on the topological structure as well as on the dynamical properties of the infection itself. Generally speaking, highly connected individuals play the role of hubs and are crucial to channel information across the network. On the other hand, static topological quantities measuring the connectivity structure are independent of the dynamical mechanisms of the infection. A natural question is therefore how to improve the topological analysis by some kind of dynamical information that may be extracted from the ongoing infection itself. In this spirit, we propose a novel vaccination scheme that exploits information from the details of the infection pattern at the moment when the vaccination strategy is applied. Numerical simulations of the infection process show that the proposed immunization strategy is effective and robust on a wide class of complex networks.
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NASA Astrophysics Data System (ADS)
Grilli, Nicolo; Dandekar, Akshay; Koslowski, Marisol
2017-06-01
The development of high explosive materials requires constitutive models that are able to predict the influence of microstructure and loading conditions on shock sensitivity. In this work a model at the continuum-scale for the polymer-bonded explosive constituted of β-HMX particles embedded in a Sylgard matrix is developed. It includes a Murnaghan equation of state, a crystal plasticity model, based on power-law slip rate and hardening, and a phase field damage model based on crack regularization. The temperature increase due to chemical reactions is introduced by a heat source term, which is validated using results from reactive molecular dynamics simulations. An initial damage field representing pre-existing voids and cracks is used in the simulations to understand the effect of these inhomogeneities on the damage propagation and shock sensitivity. We show the predictions of the crystal plasticity model and the effect of the HMX crystal orientation on the shock initiation and on the dissipated plastic work and damage propagation. The simulation results are validated with ultra-fast dynamic transmission electron microscopy experiments and x-ray experiments carried out at Purdue University. Membership Pending.
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Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations
Pierce, Eric M.; Frugier, Pierre; Criscenti, Louise J.; ...
2014-07-12
Describing the reactions that occur at the glass-water interface and control the development of the altered layer constitutes one of the main scientific challenges impeding existing models from providing accurate radionuclide release estimates. Radionuclide release estimates are a critical component of the safety basis for geologic repositories. The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products) represents a complex region, both physically and chemically, sandwiched between two distinct boundaries pristine glass surface at the inner most interface and aqueous solution at the outer most interface. Computational models, spanning different length and time-scales, are currently being developed tomore » improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include geochemical simulations [i.e., classical reaction path simulations and glass reactivity in allowance for alteration layer (GRAAL) simulations], Monte Carlo simulations, and Molecular Dynamics methods. Finally, in this manuscript, we discuss the advances and limitations of each modeling approach placed in the context of the glass-water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Roy, Santanu; Dang, Liem X.
In this paper, we present the first computer simulation of methanol exchange dynamics between the first and second solvation shells around different cations and anions. After water, methanol is the most frequently used solvent for ions. Methanol has different structural and dynamical properties than water, so its ion solvation process is different. To this end, we performed molecular dynamics simulations using polarizable potential models to describe methanol-methanol and ion-methanol interactions. In particular, we computed methanol exchange rates by employing the transition state theory, the Impey-Madden-McDonald method, the reactive flux approach, and the Grote-Hynes theory. We observed that methanol exchange occursmore » at a nanosecond time scale for Na+ and at a picosecond time scale for other ions. We also observed a trend in which, for like charges, the exchange rate is slower for smaller ions because they are more strongly bound to methanol. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less
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Hot spot initiation and chemical reaction in shocked polymeric bonded explosives
NASA Astrophysics Data System (ADS)
An, Qi; Zybin, Sergey; Jaramillo-Botero, Andres; Goddard, William; Materials; Process Simulation Center, Caltech Team
2011-06-01
A polymer bonded explosive (PBX) model based on PBXN-106 is studied via molecular dynamics (MD) simulations using reactive force field (ReaxFF) under shock loading conditions. Hotspot is observed when shock waves pass through the non-planar interface of explosives and elastomers. Adiabatic shear localization is proposed as the main mechanism of hotspot ignition in PBX for high velocity impact. Our simulation also shows that the coupling of shear localization and chemical reactions at hotspot region play important rules at stress relaxtion for explosives. The phenomenon that shock waves are obsorbed by elastomers is also observed in the MD simulations. This research received supports from ARO (W911NF-05-1-0345; W911NF-08-1-0124), ONR (N00014-05-1-0778), and Los Alamos National Laboratory (LANL).
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NASA Astrophysics Data System (ADS)
Jiang, Shan; Sewell, Thomas D.; Thompson, Donald L.
2015-06-01
We are interested in understanding the fundamental processes that occur during propagation of shock waves across the crystal-melt interface in molecular substances. We have carried out molecular dynamics simulations of shock passage from the nitromethane (100)-oriented crystal into the melt and vice versa using the fully flexible, non-reactive Sorescu, Rice, and Thompson force field. A stable interface was established for a temperature near the melting point by using a combination of isobaric-isothermal (NPT) and isochoric-isothermal (NVT) simulations. The equilibrium bulk and interfacial regions were characterized using spatial-temporal distributions of molecular number density, kinetic and potential energy, and C-N bond orientations. Those same properties were calculated as functions of time during shock propagation. As expected, the local temperatures (intermolecular, intramolecular, and total) and stress states differed significantly between the liquid and crystal regions and depending on the direction of shock propagation. Substantial differences in the spatial distribution of shock-induced defect structures in the crystalline region were observed depending on the direction of shock propagation. Research supported by the U.S. Army Research Office.
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Chen, Gong; Kong, Xian; Lu, Diannan; Wu, Jianzhong; Liu, Zheng
2017-05-10
Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO 2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO 2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO 2 diffusion in hCA-II is a rate-limiting step in the CO 2 diffusion-binding-reaction process. The equilibrium distribution of CO 2 shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO 2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln 136 contributes to the maximal flux. The simulation results offer a new perspective on the CO 2 hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO 2 sequestration and utilization.
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Molecular dynamics study of mechanical properties of carbon nanotube reinforced aluminum composites
NASA Astrophysics Data System (ADS)
Srivastava, Ashish Kumar; Mokhalingam, A.; Singh, Akhileshwar; Kumar, Dinesh
2016-05-01
Atomistic simulations were conducted to estimate the effect of the carbon nanotube (CNT) reinforcement on the mechanical behavior of CNT-reinforced aluminum (Al) nanocomposite. The periodic system of CNT-Al nanocomposite was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The mechanical properties of the nanocomposite were investigated by the application of uniaxial load on one end of the representative volume element (RVE) and fixing the other end. The interactions between the atoms of Al were modeled using embedded atom method (EAM) potentials, whereas Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used for the interactions among carbon atoms and these pair potentials are coupled with the Lennard-Jones (LJ) potential. The results show that the incorporation of CNT into the Al matrix can increase the Young's modulus of the nanocomposite substantially. In the present case, i.e. for approximately 9 with % reinforcement of CNT can increase the axial Young's modulus of the Al matrix up to 77 % as compared to pure Al.
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Multistage reaction pathways in detonating high explosives
NASA Astrophysics Data System (ADS)
Li, Ying; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; CACS Collaboration; ALCF Team
2015-06-01
Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N2 and H2O within 10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct uni-molecular and intermolecular reaction pathways, respectively, for the rapid N2 and H2O productions. This work was supported by the Office of Naval Research Grant No. N000014-12-1-0555 and the Basic Research Program of Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-08-1-0036. All the simulations were performed at USC and Argonne LCF.
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NASA Astrophysics Data System (ADS)
Lindsey, Rebecca; Goldman, Nir; Fried, Laurence
2017-06-01
Atomistic modeling of chemistry at extreme conditions remains a challenge, despite continuing advances in computing resources and simulation tools. While first principles methods provide a powerful predictive tool, the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
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On the gas phase fragmentation of protonated uracil: a statistical perspective.
Rossich Molina, Estefanía; Salpin, Jean-Yves; Spezia, Riccardo; Martínez-Núñez, Emilio
2016-06-01
The potential energy surface of protonated uracil has been explored by an automated transition state search procedure, resulting in the finding of 1398 stationary points and 751 reactive channels, which can be categorized into isomerizations between pairs of isomers, unimolecular fragmentations and bimolecular reactions. The use of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory and Kinetic Monte Carlo (KMC) simulations allowed us to determine the relative abundances of each fragmentation channel as a function of the ion's internal energy. The KMC/RRKM product abundances are compared with novel mass spectrometry (MS) experiments in the collision energy range 1-6 eV. To facilitate the comparison between theory and experiments, further dynamics simulations are carried out to determine the fraction of collision energy converted into the ion's internal energy. The KMC simulations show that the major fragmentation channels are isocyanic acid and ammonia losses, in good agreement with experiments. The third predominant channel is water loss according to both theory and experiments, although the abundance obtained in the KMC simulations is very low, suggesting that non-statistical dynamics might play an important role in this channel. Isocyanic acid (HNCOH(+)) is also an important product in the KMC simulations, although its abundance is only significant at internal energies not accessible in the MS experiments.
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Reactive Monte Carlo sampling with an ab initio potential
Leiding, Jeff; Coe, Joshua D.
2016-05-04
Here, we present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We also discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH 3 to those of ab initio molecular dynamics (AIMD). Furthermore, we find that there are regions of state spacemore » for which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.« less
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Geochemical Reaction Mechanism Discovery from Molecular Simulation
Stack, Andrew G.; Kent, Paul R. C.
2014-11-10
Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less
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Argonne Discovery Yields Self-Healing Diamond-Like Carbon
DOE Office of Scientific and Technical Information (OSTI.GOV)
Cunningham, Greg; Jones, Katie Elyce
We report that large-scale reactive molecular dynamics simulations carried out on the US Department of Energy’s IBM Blue Gene/Q Mira supercomputer at the Argonne Leadership Computing Facility, along with experiments conducted by researchers in Argonne’s Energy Systems Division, enabled the design of a “self-healing” anti-wear coating that drastically reduces friction and related degradation in engines and moving machinery. Now, the computational work advanced for this purpose is being used to identify the friction-fighting potential of other catalysts.
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Argonne Discovery Yields Self-Healing Diamond-Like Carbon
Cunningham, Greg; Jones, Katie Elyce
2016-10-27
We report that large-scale reactive molecular dynamics simulations carried out on the US Department of Energy’s IBM Blue Gene/Q Mira supercomputer at the Argonne Leadership Computing Facility, along with experiments conducted by researchers in Argonne’s Energy Systems Division, enabled the design of a “self-healing” anti-wear coating that drastically reduces friction and related degradation in engines and moving machinery. Now, the computational work advanced for this purpose is being used to identify the friction-fighting potential of other catalysts.
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Effects of Submesoscale Turbulence on Reactive Tracers in the Upper Ocean
NASA Astrophysics Data System (ADS)
Smith, Katherine Margaret
In this dissertation, Large Eddy Simulations (LES) are used to model the coupled turbulence-reactive tracer dynamics within the upper mixed layer of the ocean. Prior work has shown that LES works well over the spatial and time scales relevant to both turbulence and reactive biogeochemistry. Additionally, the code intended for use is able to carry an arbitrary number of tracer equations, allowing for easy expansion of the species reactions. Research in this dissertation includes a study of 15 idealized non-reactive tracers within an evolving large-scale temperature front in order determine and understand the fundamental dynamics underlying turbulence-tracer interaction in the absence of reactions. The focus of this study, in particular, was on understanding the evolution of biogeochemically-relevant, non-reactive tracers in the presence of both large ( 5 km) submesoscale eddies and smallscale ( 100 m) wave-driven Langmuir turbulence. The 15 tracers studied have different initial, boundary, and source conditions and significant differences are seen in their distributions depending on these conditions. Differences are also seen between regions where submesoscale eddies and small-scale Langmuir turbulence are both present, and in regions with only Langmuir turbulence. A second study focuses on the examination of Langmuir turbulence effects on upper ocean carbonate chemistry. Langmuir mixing time scales are similar to those of chemical reactions, resulting in potentially strong tracer-flow coupling effects. The strength of the Langmuir turbulence is varied, from no wave-driven turbulence (i.e., only shear-driven turbulence), to Langmuir turbulence that is much stronger than that found in typical upper ocean conditions. Three different carbonate chemistry models are also used in this study: time-dependent chemistry, equilibrium chemistry, and no-chemistry (i.e., non-reactive tracers). The third and final study described in this dissertation details the development of a reduced-order biogeochemical model with 17 state equations that can accurately reproduce the Bermuda Atlantic Time-series Study (BATS) ecosystem behavior, but that can also be integrated within high-resolution LES.
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Melt focusing and CO2 extraction at mid-ocean ridges: simulations of reactive two-phase flow
NASA Astrophysics Data System (ADS)
Keller, T.; Katz, R. F.; Hirschmann, M. M.
2016-12-01
The deep CO2 cycle is the result of fluxes between near-surface and mantle reservoirs. Outgassing from mid-ocean ridges is one of the primary fluxes of CO2 from the asthenosphere into the ocean-atmosphere reservoir. Focusing of partial melt to the ridge axis crucially controls this flux. However, the role of volatiles, in particular CO2 and H2O, on melt transport processes beneath ridges remains poorly understood. We investigate this transport using numerical simulations of two-phase, multi-component magma/mantle dynamics. The phases are solid mantle and liquid magma; the components are dunite, MORB, hydrated basalt, and carbonated basalt. These effective components capture accepted features of mantle melting with volatiles. The fluid-dynamical model is McKenzie's formulation [1], while melting and reactive transport use the R_DMC method [2,3]. Our results indicate that volatiles cause channelized melt transport, which leads to significant variability in volume and composition of focused melt. The volatile-induced expansion of the melting regime at depth, however, has no influence on melt focusing; distal volatile-rich melts are not focused to the axis. Up to 50% of these melts are instead emplaced along the oceanic LAB. There, crystallization of accumulated melt leads to enrichment of CO2 and H2O in the deep lithosphere, which has implications for LAB rheology and volatile recycling by subduction. Results from a suite of simulations, constrained by catalogued observational data [4,5,6] enable predictions of global MOR CO2 output. By combining observational constraints with self-consistent numerical simulations we obtain a range of CO2 output from the global ridge system of 28-110 Mt CO2/yr, corresponding to mean CO2 contents of 50-200 ppm in the mantle. REFERENCES[1] McKenzie (1984), doi:10.1093/petrology/25.3.713.[2] Rudge, Bercovici & Spiegelman (2011), doi:10.1111/j.1365-246X.2010.04870.x.[3] Keller & Katz (2016), doi:10.1093/petrology/egw030.[4] Dalton, Langmuir & Gale (2014), doi:10.1126/science.1249466.[5] Gale, Langmuir & Dalton (2014), doi:10.1093/petrology/egu017.[6] White et al. (2001), doi:10.1093/petrology/42.6.1171. Fig: Simulation results of MOR magma/mantle dynamics with H2O and CO2, showing Darcy flux magnitude for half-spreading rates of 1 and 5 cm/yr.
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Pai, Sung Jin; Yeo, Byung Chul; Han, Sang Soo
2016-01-21
Liquid CBN (carbon-boron-nitrogen) hydrogen-storage materials such as 3-methyl-1,2-BN-cyclopentane have the advantage of being easily accessible for use in current liquid-fuel infrastructure. To develop practical liquid CBN hydrogen-storage materials, it is of great importance to understand the reaction pathways of hydrogenation/dehydrogenation in the liquid phase, which are difficult to discover by experimental methods. Herein, we developed a reactive force field (ReaxFFCBN) from quantum mechanical (QM) calculations based on density functional theory for the storage of hydrogen in BN-substituted cyclic hydrocarbon materials. The developed ReaxFFCBN provides similar dehydrogenation pathways and energetics to those predicted by QM calculations. Moreover, molecular dynamics (MD) simulations with the developed ReaxFFCBN can predict the stability and dehydrogenation behavior of various liquid CBN hydrogen-storage materials. Our simulations reveal that a unimolecular dehydrogenation mechanism is preferred in liquid CBN hydrogen-storage materials. However, as the temperature in the simulation increases, the contribution of a bimolecular dehydrogenation mechanism also increases. Moreover, our ReaxFF MD simulations show that in terms of thermal stability and dehydrogenation kinetics, liquid CBN materials with a hexagonal structure are more suitable materials than those with a pentagonal structure. We expect that the developed ReaxFFCBN could be a useful protocol in developing novel liquid CBN hydrogen-storage materials.
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Advanced ballistic range technology
NASA Technical Reports Server (NTRS)
Yates, Leslie A.
1993-01-01
Optical images, such as experimental interferograms, schlieren, and shadowgraphs, are routinely used to identify and locate features in experimental flow fields and for validating computational fluid dynamics (CFD) codes. Interferograms can also be used for comparing experimental and computed integrated densities. By constructing these optical images from flow-field simulations, one-to-one comparisons of computation and experiment are possible. During the period from February 1, 1992, to November 30, 1992, work has continued on the development of CISS (Constructed Interferograms, Schlieren, and Shadowgraphs), a code that constructs images from ideal- and real-gas flow-field simulations. In addition, research connected with the automated film-reading system and the proposed reactivation of the radiation facility has continued.
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Design, Control, and Modeling of a New Voltage Source Converter for HVDC System
NASA Astrophysics Data System (ADS)
Mohan, Madhan; Singh, Bhim; Ketan Panigrahi, Bijaya
2013-05-01
Abstract: A New Voltage Source Converter (VSC) based on neutral clamped three-level circuit is proposed for High Voltage DC (HVDC) system. The proposed VSC is designed in a multipulse configuration. The converter is operated by Fundamental Frequency Switching (FFS). A new control method is developed for achieving all the necessary control aspects of HVDC system such as independent real and reactive power control, bidirectional real and reactive power control. The basic of the control method is varying the pulse width and by keeping the dc link voltage constant. The steady state and dynamic performances of HVDC system interconnecting two different frequencies network are demonstrated for active and reactive power control. Total number of transformers used in this system are reduced to half in comparison with the two-level VSCs for both active and reactive power control. The performance of the HVDC system is improved in terms of reduced harmonics level even at fundamental frequency switching. The harmonic performance of the designed converter is also studied for different value of the dead angle (β), and the optimized range of the dead angle is achieved for varying reactive power requirement. Simulation results are presented for the designed three level multipulse voltage source converters with the proposed control algorithm.
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Tailoring non-equilibrium atmospheric pressure plasmas for healthcare technologies
NASA Astrophysics Data System (ADS)
Gans, Timo
2012-10-01
Non-equilibrium plasmas operated at ambient atmospheric pressure are very efficient sources for energy transport through reactive neutral particles (radicals and metastables), charged particles (ions and electrons), UV radiation, and electro-magnetic fields. This includes the unique opportunity to deliver short-lived highly reactive species such as atomic oxygen and atomic nitrogen. Reactive oxygen and nitrogen species can initiate a wide range of reactions in biochemical systems, both therapeutic and toxic. The toxicological implications are not clear, e.g. potential risks through DNA damage. It is anticipated that interactions with biological systems will be governed through synergies between two or more species. Suitable optimized plasma sources are improbable through empirical investigations. Quantifying the power dissipation and energy transport mechanisms through the different interfaces from the plasma regime to ambient air, towards the liquid interface and associated impact on the biological system through a new regime of liquid chemistry initiated by the synergy of delivering multiple energy carrying species, is crucial. The major challenge to overcome the obstacles of quantifying energy transport and controlling power dissipation has been the severe lack of suitable plasma sources and diagnostic techniques. Diagnostics and simulations of this plasma regime are very challenging; the highly pronounced collision dominated plasma dynamics at very small dimensions requires extraordinary high resolution - simultaneously in space (microns) and time (picoseconds). Numerical simulations are equally challenging due to the inherent multi-scale character with very rapid electron collisions on the one extreme and the transport of chemically stable species characterizing completely different domains. This presentation will discuss our recent progress actively combining both advance optical diagnostics and multi-scale computer simulations.
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NASA Astrophysics Data System (ADS)
Sureshkumar, B.; Mary, Y. Sheena; Resmi, K. S.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Narayana, B.; Suma, S.
2018-03-01
Two 8-hydroxyquinoline derivatives, 5,7-dichloro-8-hydroxyquinoline (57DC8HQ) and 5-chloro-7-iodo-8-hydroxy quinoline (5CL7I8HQ) have been investigated in details by means of spectroscopic characterization and computational molecular modelling techniques. FT-IR and FT-Raman experimental spectroscopic approaches have been utilized in order to obtain detailed spectroscopic signatures of title compounds, while DFT calculations have been used in order to visualize and assign vibrations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the title molecules exhibit NLO properties. The evaluated HOMO and LUMO energies demonstrate the chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyperconjugative interactions and charge delocalization. DFT calculations have been also used jointly with MD simulations in order to investigate in details global and local reactivity properties of title compounds. Also, molecular docking has been also used in order to investigate affinity of title compounds against decarboxylase inhibitor and quinoline derivatives can be a lead compounds for developing new antiparkinsonian drug.
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NASA Astrophysics Data System (ADS)
Wang, Mingchao; Yu, Jingui; Lin, Shangchao
Sulfur (S) serves as a promising cathode material in Li-ion batteries owing to its abundance on earth, low cost and high theoretical specific capacity 1670 mAhg-1, which is 3-5 times higher than that of current commercial Li-ion batteries. Nowadays, the most popular strategies of using S cathode are based on producing nanostructured carbon matrices (i.e. hollow carbon nanospheres and nanofibers) to sustain S cathode loading. However, the possible stress evolution and mechanical degradation of the confined S cathode in those carbon matrices have never been explored before. In addition, the associated structural and conductivity changes of the confined S cathode during the lithiation/delithiation process plays a significant role in the battery performance. With the above in mind, here we conduct reactive molecular dynamics simulations to investigate the microstructural and stress evolution of the confined S cathode during lithiation/delithiation process. Simulation results indicate an unusual stress relaxation state in LixS compounds at lower Li concentrations (x >0.7). The strength of corresponding Li-S compounds also increases with respect to the Li concentration.
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NASA Astrophysics Data System (ADS)
Michael, L.; Nikiforakis, N.
2018-02-01
This work is concerned with the effect of cavity collapse in non-ideal explosives as a means of controlling their sensitivity. The main objective is to understand the origin of localised temperature peaks (hot spots) which play a leading order role at the early stages of ignition. To this end, we perform two- and three-dimensional numerical simulations of shock-induced single gas-cavity collapse in liquid nitromethane. Ignition is the result of a complex interplay between fluid dynamics and exothermic chemical reaction. In the first part of this work, we focused on the hydrodynamic effects in the collapse process by switching off the reaction terms in the mathematical formulation. In this part, we reinstate the reactive terms and study the collapse of the cavity in the presence of chemical reactions. By using a multi-phase formulation which overcomes current challenges of cavity collapse modelling in reactive media, we account for the large density difference across the material interface without generating spurious temperature peaks, thus allowing the use of a temperature-based reaction rate law. The mathematical and physical models are validated against experimental and analytic data. In Part I, we demonstrated that, compared to experiments, the generated hot spots have a more complex topological structure and that additional hot spots arise in regions away from the cavity centreline. Here, we extend this by identifying which of the previously determined high-temperature regions in fact lead to ignition and comment on the reactive strength and reaction growth rate in the distinct hot spots. We demonstrate and quantify the sensitisation of nitromethane by the collapse of the isolated cavity by comparing the ignition times of nitromethane due to cavity collapse and the ignition time of the neat material. The ignition in both the centreline hot spots and the hot spots generated by Mach stems occurs in less than half the ignition time of the neat material. We compare two- and three-dimensional simulations to examine the change in topology, temperatures, and reactive strength of the hot spots by the third dimension. It is apparent that belated ignition times can be avoided by the use of three-dimensional simulations. The effect of the chemical reactions on the topology and strength of the hot spots in the timescales considered is also studied, in a comparison between inert and reactive simulations where maximum temperature fields and their growth rates are examined.
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NASA Astrophysics Data System (ADS)
War, Javeed Ahmad; Jalaja, K.; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Srivastava, Santosh Kumar; Van Alsenoy, C.
2017-02-01
IR and Raman spectra of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea (HIPPT) have been recorded in the solid phase and the vibrational wave numbers are calculated theoretically by B3LYP/6-31G(d,p) (6D, 7F) method. All the fundamental vibrational modes have been assigned using potential energy distribution values and the molecular structure was analyzed in terms of parameters like bond length, bond angles and dihedral angles. The ring breathing mode of the phenyl ring is observed at 1016 cm-1 in the IR spectrum, 1014 cm-1 in the Raman spectrum and at 1014 cm-1 theoretically. The values of polarizability and hyperpolarizabilities were calculated and nonlinear optical properties are discussed. The HOMO-LUMO plot reveals the charge transfer possibilities in the molecule. The NBO analysis was computed and possible transitions were correlated with the electronic transitions. In the title compound, the imidazole ring and CH2 groups are tilted from each other and the thiourea group is tilted from the phenyl ring. Using MEP plot the electrophilic and nucleophilic regions are identified. Local reactivity properties were investigated by analysis of ALIE surfaces and Fukui functions. Oxidation and degradation properties were initially assessed by calculation of bond dissociation energies of all single acyclic bonds. Determination of atoms with pronounced interactions with water molecules was performed by calculation of radial distribution functions after molecular dynamics simulations. Chargehopping rates were calculated within Marcus semi-empiric approach, employing both DFT calculations and MD simulations. The molecular docking computational predictions were complemented by the in vitro antibacterial activity evaluation.
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Universal Linear Scaling of Permeability and Time for Heterogeneous Fracture Dissolution
NASA Astrophysics Data System (ADS)
Wang, L.; Cardenas, M. B.
2017-12-01
Fractures are dynamically changing over geological time scale due to mechanical deformation and chemical reactions. However, the latter mechanism remains poorly understood with respect to the expanding fracture, which leads to a positively coupled flow and reactive transport processes, i.e., as a fracture expands, so does its permeability (k) and thus flow and reactive transport processes. To unravel this coupling, we consider a self-enhancing process that leads to fracture expansion caused by acidic fluid, i.e., CO2-saturated brine dissolving calcite fracture. We rigorously derive a theory, for the first time, showing that fracture permeability increases linearly with time [Wang and Cardenas, 2017]. To validate this theory, we resort to the direct simulation that solves the Navier-Stokes and Advection-Diffusion equations with a moving mesh according to the dynamic dissolution process in two-dimensional (2D) fractures. We find that k slowly increases first until the dissolution front breakthrough the outbound when we observe a rapid k increase, i.e., the linear time-dependence of k occurs. The theory agrees well with numerical observations across a broad range of Peclet and Damkohler numbers through homogeneous and heterogeneous 2D fractures. Moreover, the theory of linear scaling relationship between k and time matches well with experimental observations of three-dimensional (3D) fractures' dissolution. To further attest to our theory's universality for 3D heterogeneous fractures across a broad range of roughness and correlation length of aperture field, we develop a depth-averaged model that simulates the process-based reactive transport. The simulation results show that, regardless of a wide variety of dissolution patterns such as the presence of dissolution fingers and preferential dissolution paths, the linear scaling relationship between k and time holds. Our theory sheds light on predicting permeability evolution in many geological settings when the self-enhancing process is relevant. References: Wang, L., and M. B. Cardenas (2017), Linear permeability evolution of expanding conduits due to feedback between flow and fast phase change, Geophys. Res. Lett., 44(9), 4116-4123, doi: 10.1002/2017gl073161.
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Surrogate model approach for improving the performance of reactive transport simulations
NASA Astrophysics Data System (ADS)
Jatnieks, Janis; De Lucia, Marco; Sips, Mike; Dransch, Doris
2016-04-01
Reactive transport models can serve a large number of important geoscientific applications involving underground resources in industry and scientific research. It is common for simulation of reactive transport to consist of at least two coupled simulation models. First is a hydrodynamics simulator that is responsible for simulating the flow of groundwaters and transport of solutes. Hydrodynamics simulators are well established technology and can be very efficient. When hydrodynamics simulations are performed without coupled geochemistry, their spatial geometries can span millions of elements even when running on desktop workstations. Second is a geochemical simulation model that is coupled to the hydrodynamics simulator. Geochemical simulation models are much more computationally costly. This is a problem that makes reactive transport simulations spanning millions of spatial elements very difficult to achieve. To address this problem we propose to replace the coupled geochemical simulation model with a surrogate model. A surrogate is a statistical model created to include only the necessary subset of simulator complexity for a particular scenario. To demonstrate the viability of such an approach we tested it on a popular reactive transport benchmark problem that involves 1D Calcite transport. This is a published benchmark problem (Kolditz, 2012) for simulation models and for this reason we use it to test the surrogate model approach. To do this we tried a number of statistical models available through the caret and DiceEval packages for R, to be used as surrogate models. These were trained on randomly sampled subset of the input-output data from the geochemical simulation model used in the original reactive transport simulation. For validation we use the surrogate model to predict the simulator output using the part of sampled input data that was not used for training the statistical model. For this scenario we find that the multivariate adaptive regression splines (MARS) method provides the best trade-off between speed and accuracy. This proof-of-concept forms an essential step towards building an interactive visual analytics system to enable user-driven systematic creation of geochemical surrogate models. Such a system shall enable reactive transport simulations with unprecedented spatial and temporal detail to become possible. References: Kolditz, O., Görke, U.J., Shao, H. and Wang, W., 2012. Thermo-hydro-mechanical-chemical processes in porous media: benchmarks and examples (Vol. 86). Springer Science & Business Media.
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Dynamic Response of Monolithic and Laminate/Particulate Reactive Mixtures
NASA Astrophysics Data System (ADS)
Wei, Chung-Ting
Two dynamic compression methods were applied to a monolithic metal and reactive mixtures to investigate their responses: (a) Dynamic experiments using a split Hopkinson pressure bar were applied to reactive mixtures densified by explosive consolidation in order to establish their mechanical response and failure mechanisms. (b) Laser compression and release, which can impart high stresses, up to hundreds GPa, in times of nanoseconds and fractions thereof, was applied to establish the spalling strength of vanadium and the reaction threshold for Ni/Al laminates. The spallation and fragmentation exhibited by recovered mono- and poly-crystalline vanadium prove that the laser intensities and crystal structure play important roles in determining spall strength, fragmentation, and microstructural processes. Densified reactive mixtures with different microstructures (Ni, Mo, W, Nb and Ta with Al) were subjected to the quasi-static and dynamic strain rates. Two distinct failure mechanisms, axial splitting and shear failure, were observed in the recovered specimens. Axial splitting occurred when the bonding between the powders was poor; shear failure was primarily associated with extensive deformation of continuous Ta and Nb phases. Finite element simulations provided valuable information in interpreting the experimental results and predicting failure mechanisms akin to those observed. Ni/Al laminates were subjected to laser compression. The strain rates varied from 105 to 108 s-1, and the initial stress varied from 30 to ˜300 GPa. It is found the thickness of the lamellar and the interlaminar bonding strength are the two critical factors in determining mechanical failure. The intermetallic reaction leading to Ni3Al and NiAl were produced by the laser energies and laser pulse durations in direct laser shock experiments. Laser-driven compression was also applied to study the high temperature synthesis in nano-scale Ni/Al laminates with bilayer thickness 54 nm. Intermetallic phases, NiAl and NiAl 3, were found on the plasma stagnated laminates. However, the self-propagating high temperature synthesis (SHS) did not self-sustain in the micro-scale laminate because of the short duration of the pulse.
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Deep analysis of N-cadherin/ADH-1 interaction: a computational survey.
Eslami, Mahboobeh; Nezafat, Navid; Khajeh, Sahar; Mostafavi-Pour, Zohreh; Bagheri Novir, Samaneh; Negahdaripour, Manica; Ghasemi, Younes; Razban, Vahid
2018-01-19
Due to the considerable role of N-cadherin in cancer metastasis, tumor growth, and progression, inhibition of this protein has been highly regarded in recent years. Although ADH-1 has been known as an appropriate inhibitor of N-cadherin in clinical trials, its chemical nature and binding mode with N-cadherin have not been precisely specified yet. Accordingly, in this study, quantum mechanics calculations were used to investigate the chemical nature of ADH-1. These calculations clarify the molecular properties of ADH-1 and determine its reactive sites. Based on the results, the oxygen atoms are suitable for electrophilic reactivity, while the hydrogen atoms that are connected to nitrogen atoms are the favorite sites for nucleophilic reactivity. The higher electronegativity of the oxygen atoms makes them the most reactive portions in this molecule. Molecular docking and molecular dynamics (MD) simulation have also been applied to specify the binding mode of ADH-1 with N-cadherin and determine the important residues of N-cadherin involving in the interaction with ADH-1. Moreover, the verified model by MD simulation has been studied to extract the free energy value and find driving forces. These calculations and molecular electrostatic potential map of ADH-1 indicated that hydrophobic and electrostatic interactions are almost equally involved in the implantation of ADH-1 in the N-cadherin binding site. The presented results not only enable a closer examination of N-cadherin in complex with ADH-1 molecule, but also are very beneficial in designing new inhibitors for N-cadherin and can help to save time and cost in this field.
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NASA Astrophysics Data System (ADS)
Pearl, Thomas; Mantooth, Brent; Varady, Mark; Willis, Matthew
2014-03-01
Chemical warfare agent simulants are often used for environmental testing in place of highly toxic agents. This work sets the foundation for modeling decontamination of absorbing polymeric materials with the focus on determining relationships between agents and simulants. The correlations of agents to simulants must consider the three way interactions in the chemical-material-decontaminant system where transport and reaction occur in polymer materials. To this end, diffusion modeling of the subsurface transport of simulants and live chemical warfare agents was conducted for various polymer systems (e.g., paint coatings) with and without reaction pathways with applied decontamination. The models utilized 1D and 2D finite difference diffusion and reaction models to simulate absorption and reaction in the polymers, and subsequent flux of the chemicals out of the polymers. Experimental data including vapor flux measurements and dynamic contact angle measurements were used to determine model input parameters. Through modeling, an understanding of the relationship of simulant to live chemical warfare agent was established, focusing on vapor emission of agents and simulants from materials.
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Hu, Xiao; Schuster, Jörg; Schulz, Stefan E; Gessner, Thomas
2015-10-28
Atomistic mechanisms for the atomic layer deposition using the Cu(acac)2 (acac = acetylacetonate) precursor are studied using first-principles calculations and reactive molecular dynamics simulations. The results show that Cu(acac)2 chemisorbs on the hollow site of the Cu(110) surface and decomposes easily into a Cu atom and the acac-ligands. A sequential dissociation and reduction of the Cu precursor [Cu(acac)2 → Cu(acac) → Cu] are observed. Further decomposition of the acac-ligand is unfavorable on the Cu surface. Thus additional adsorption of the precursors may be blocked by adsorbed ligands. Molecular hydrogen is found to be nonreactive towards Cu(acac)2 on Cu(110), whereas individual H atoms easily lead to bond breaking in the Cu precursor upon impact, and thus release the surface ligands into the gas-phase. On the other hand, water reacts with Cu(acac)2 on a Cu2O substrate through a ligand-exchange reaction, which produces gaseous H(acac) and surface OH species. Combustion reactions with the main by-products CO2 and H2O are observed during the reaction between Cu(acac)2 and ozone on the CuO surface. The reactivity of different co-reactants toward Cu(acac)2 follows the order H > O3 > H2O.
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Effect of static porosity fluctuations on reactive transport in a porous medium
NASA Astrophysics Data System (ADS)
L'Heureux, Ivan
2018-02-01
Reaction-diffusive transport phenomena in porous media are ubiquitous in engineering applications, biological and geochemical systems. The porosity field is usually random in space, but most models consider the porosity field as a well-defined deterministic function of space and time and ignore the porosity fluctuations. They use a reaction-diffusion equation written in terms of an average porosity and average concentration fields. In this contribution, we treat explicitly the effect of spatial porosity fluctuations on the dynamics of a concentration field for the case of a one-dimensional reaction-transport system with nonlinear kinetics. Three basic assumptions are considered. (i) The porosity fluctuations are assumed to have Gaussian properties and an arbitrary variance; (ii) we assume that the noise correlation length is small compared to the relevant macroscopic length scale; (iii) and we assume that the kinetics of the reactive term in the equations for the fluctuations is a self-consistently determined constant. Elimination of the fluctuating part of the concentration field from the dynamics leads to a renormalized equation involving the average concentration field. It is shown that the noise leads to a renormalized (generally smaller) diffusion coefficient and renormalized kinetics. Within the framework of the approximations used, numerical simulations are in agreement with our theory. We show that the porosity fluctuations may have a significant effect on the transport of a reactive species, even in the case of a homogeneous average porosity.
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Tóth, László; Fekete, Attila; Balogh, Gábor; Bereczky, Zsuzsanna; Komáromi, István
2015-09-01
While antithrombin (AT) has small basal inhibitory activity, it reaches its full inhibitory potential against activated blood coagulation factors, FXa, FIXa, and FIIa (thrombin), via an allosteric and/or template (bridging) mechanism by the action of heparin, heparan sulfate, or heparin-mimetic pentasaccharides (PS). From the numerous X-ray structures available for different conformational states of AT, only indirect and incomplete conclusions can be drawn on the inherently dynamic properties of AT. As a typical example, the basal inhibitory activity of AT cannot be interpreted on the basis of "non-activated" free antithrombin X-ray structures since the Arg393 side chain, playing crucial role in antithrombin-proteinase interaction, is not exposed. In order to reveal the intrinsic dynamic properties and the reason of basal inhibitory activity of antithrombin, 2 μs molecular dynamics simulations were carried out on its native free-forms. It was shown from the simulation trajectories that the reactive center loop which is functioning as "bait" for proteases, even without any biasing potential can populate conformational state in which the Arg393 side chain is solvent exposed. It is revealed from the trajectory analysis that the peptide sequences correspond to the helix D extension, and new helix P formation can be featured with especially large root-mean-square fluctuations. Mutual information analyses of the trajectory showed remarkable (generalized) correlation between those regions of antithrombin which changed their conformations as the consequence of AT-PS complex formation. This suggests that allosteric information propagation pathways are present even in the non-activated native form of AT.
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Influence of the leaving group on the dynamics of a gas-phase SN2 reaction
NASA Astrophysics Data System (ADS)
Stei, Martin; Carrascosa, Eduardo; Kainz, Martin A.; Kelkar, Aditya H.; Meyer, Jennifer; Szabó, István; Czakó, Gábor; Wester, Roland
2016-02-01
In addition to the nucleophile and solvent, the leaving group has a significant influence on SN2 nucleophilic substitution reactions. Its role is frequently discussed with respect to reactivity, but its influence on the reaction dynamics remains unclear. Here, we uncover the influence of the leaving group on the gas-phase dynamics of SN2 reactions in a combined approach of crossed-beam imaging and dynamics simulations. We have studied the reaction F- + CH3Cl and compared it to F- + CH3I. For the two leaving groups, Cl and I, we find very similar structures and energetics, but the dynamics show qualitatively different features. Simple scaling of the leaving group mass does not explain these differences. Instead, the relevant impact parameters for the reaction mechanisms are found to be crucial and the differences are attributed to the relative orientation of the approaching reactants. This effect occurs on short timescales and may also prevail in solution-phase conditions.
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Influence of the leaving group on the dynamics of a gas-phase SN2 reaction.
Stei, Martin; Carrascosa, Eduardo; Kainz, Martin A; Kelkar, Aditya H; Meyer, Jennifer; Szabó, István; Czakó, Gábor; Wester, Roland
2016-02-01
In addition to the nucleophile and solvent, the leaving group has a significant influence on SN2 nucleophilic substitution reactions. Its role is frequently discussed with respect to reactivity, but its influence on the reaction dynamics remains unclear. Here, we uncover the influence of the leaving group on the gas-phase dynamics of SN2 reactions in a combined approach of crossed-beam imaging and dynamics simulations. We have studied the reaction F(-) + CH3Cl and compared it to F(-) + CH3I. For the two leaving groups, Cl and I, we find very similar structures and energetics, but the dynamics show qualitatively different features. Simple scaling of the leaving group mass does not explain these differences. Instead, the relevant impact parameters for the reaction mechanisms are found to be crucial and the differences are attributed to the relative orientation of the approaching reactants. This effect occurs on short timescales and may also prevail in solution-phase conditions.
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Atomistic characterization of the active-site solvation dynamics of a model photocatalyst
van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; ...
2016-11-28
The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir 2(dimen) 4] 2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling themore » solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.« less
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NASA Astrophysics Data System (ADS)
Hantal, György; Picaud, Sylvain; Hoang, Paul N. M.; Voloshin, Vladimir P.; Medvedev, Nikolai N.; Jedlovszky, Pál
2010-10-01
The grand canonical Monte Carlo method is used to simulate the adsorption isotherms of water molecules on different types of model soot particles. These soot models are constructed by first removing atoms from onion-fullerene structures in order to create randomly distributed pores inside the soot, and then performing molecular dynamics simulations, based on the reactive adaptive intermolecular reactive empirical bond order (AIREBO) description of the interaction between carbon atoms, to optimize the resulting structures. The obtained results clearly show that the main driving force of water adsorption on soot is the possibility of the formation of new water-water hydrogen bonds with the already adsorbed water molecules. The shape of the calculated water adsorption isotherms at 298 K strongly depends on the possible confinement of the water molecules in pores of the carbonaceous structure. We found that there are two important factors influencing the adsorption ability of soot. The first of these factors, dominating at low pressures, is the ability of the soot of accommodating the first adsorbed water molecules at strongly hydrophilic sites. The second factor concerns the size and shape of the pores, which should be such that the hydrogen bonding network of the water molecules filling them should be optimal. This second factor determines the adsorption properties at higher pressures.
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Solís-Calero, Christian; Ortega-Castro, Joaquín; Frau, Juan; Muñoz, Francisco
2015-01-01
Phospholipids play multiple and essential roles in cells, as components of biological membranes. Although phospholipid bilayers provide the supporting matrix and surface for many enzymatic reactions, their inherent reactivity and possible catalytic role have not been highlighted. As other biomolecules, phospholipids are frequent targets of nonenzymatic modifications by reactive substances including oxidants and glycating agents which conduct to the formation of advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs). There are some theoretical studies about the mechanisms of reactions related to these processes on phosphatidylethanolamine surfaces, which hypothesize that cell membrane phospholipids surface environment could enhance some reactions through a catalyst effect. On the other hand, the phospholipid bilayers are susceptible to oxidative damage by oxidant agents as reactive oxygen species (ROS). Molecular dynamics simulations performed on phospholipid bilayers models, which include modified phospholipids by these reactions and subsequent reactions that conduct to formation of ALEs and AGEs, have revealed changes in the molecular interactions and biophysical properties of these bilayers as consequence of these reactions. Then, more studies are desirable which could correlate the biophysics of modified phospholipids with metabolism in processes such as aging and diseases such as diabetes, atherosclerosis, and Alzheimer's disease. PMID:25977746
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Chemisorption and Diffusion of H on a Graphene Sheet and Single-Wall Carbon Nanotubes
NASA Technical Reports Server (NTRS)
Srivastava, Deepak; Dzegilenko, Fedor; Menon, Madhu
2000-01-01
Recent experiments on hydrogen storage in single wall nanotubes and nanotube bundles have reported large fractional weight of stored molecular hydrogen which are not in agreement with theoretical estimates based of simulation of hydrogen storage by physisorption mechanisms. Hydrogen storage in catalytically doped nanotube bundles indicate that atomic H might undergo chemisorption changing the basic nature of the storage mechanism under investigation by many groups. Using a generalized tight-binding molecular dynamics (GTBMD) method for reactive C-H dynamics, we investigate chemisorption and diffusion of atomic H on graphene sheet and C nanotubes. Effective potential energy surfaces (EPS) for chemisorption and diffusion are calculated for graphene sheet and nanotubes of different curvatures. Analysis of the activation barriers and quantum rate constants, computed via wave-packet dynamics method, will be discussed in this presentation.
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Insights into the Li Intercalation and SEI Formation on LiSi Nanoclusters
Hankins, Kie; Soto, Fernando A.; Balbuena, Perla B.
2017-01-01
We report a first-principles atomic level assessment of the lithiation and reactivity of pre-lithiated Si clusters. Density functional theory formation energy calculations reveal that the pre-lithiated Li 16Si 16 cluster exposed to two different Li fluxes can store Li between the concentrations of Li 2.5Si and Li 3.5Si. This increase in storage capacity is attributed to the start of an amorphization process in the cluster, and more importantly these results show that the intercalation reaction can be controlled by the flux of the Li-ions. However, in a real battery, the lithiation of the anode occurs simultaneously to the electrode-electrolyte reactions.more » Here we simulate the solid-electrolyte interphase (SEI) formation and simultaneous lithiation of a Li 16Si 16 cluster in contact with two different electrolyte solutions: one with pure ethylene carbonate (EC), and another with a 1 M solution of LiPF 6 in EC. Our ab initio molecular dynamics simulations show that the solvent and salt are decomposed leading to the initial stages of the SEI layer formation and large part of the added Li becomes part of the SEI. Interestingly, the pure EC solution results in lower storage capacity and higher reactivity, whereas the presence of the salt causes the opposite effect: higher lithiation and reduced reactivity.« less
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NASA Astrophysics Data System (ADS)
Voter, Arthur
Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.
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NASA Astrophysics Data System (ADS)
Viegas, Pedro; Damany, Xavier; Iseni, Sylvain; Pouvesle, Jean-Michel; Robert, Eric; Bourdon, Anne
2016-09-01
The use of admixtures (mostly O2 and N2) to a helium buffer has been studied recently to tailor the generation of reactive species in plasma jets for biomedical applications. So far, most experiments have been dedicated to the study of the plasma plume. For endoscopic treatments, it is also important to better understand and optimize the propagation of discharges in long dielectric tubes as catheters. In this work, we present an experimental and numerical study on the dynamics of a μs helium plasma discharge with O2 admixture in a long dielectric tube. In simulations, a 2D fluid model is used. For comparison purposes, the geometries of the set-ups used for simulations and experiments are as close as possible. We compare experiments and simulations for different amounts of O2 admixture added to the buffer gas and present results on the velocity of the discharge front for the various amounts of O2 and different applied voltages. In order to study the influence of different amounts of O2 admixture on the helium discharge dynamics, detailed kinetic schemes have been used. The influence of Penning and charge exchange reactions on the discharge structure and dynamics are studied, as well as the role of negative ions. P.V. is supported by an EDOM fellowship, and X.D. by an INEL/Region Centre-Val de Loire fellowship.
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NASA Astrophysics Data System (ADS)
Sibra, A.; Dupays, J.; Murrone, A.; Laurent, F.; Massot, M.
2017-06-01
In this paper, we tackle the issue of the accurate simulation of evaporating and reactive polydisperse sprays strongly coupled to unsteady gaseous flows. In solid propulsion, aluminum particles are included in the propellant to improve the global performances but the distributed combustion of these droplets in the chamber is suspected to be a driving mechanism of hydrodynamic and acoustic instabilities. The faithful prediction of two-phase interactions is a determining step for future solid rocket motor optimization. When looking at saving computational ressources as required for industrial applications, performing reliable simulations of two-phase flow instabilities appears as a challenge for both modeling and scientific computing. The size polydispersity, which conditions the droplet dynamics, is a key parameter that has to be accounted for. For moderately dense sprays, a kinetic approach based on a statistical point of view is particularly appropriate. The spray is described by a number density function and its evolution follows a Williams-Boltzmann transport equation. To solve it, we use Eulerian Multi-Fluid methods, based on a continuous discretization of the size phase space into sections, which offer an accurate treatment of the polydispersion. The objective of this paper is threefold: first to derive a new Two Size Moment Multi-Fluid model that is able to tackle evaporating polydisperse sprays at low cost while accurately describing the main driving mechanisms, second to develop a dedicated evaporation scheme to treat simultaneously mass, moment and energy exchanges with the gas and between the sections. Finally, to design a time splitting operator strategy respecting both reactive two-phase flow physics and cost/accuracy ratio required for industrial computations. Using a research code, we provide 0D validations of the new scheme before assessing the splitting technique's ability on a reference two-phase flow acoustic case. Implemented in the industrial-oriented CEDRE code, all developments allow to simulate realistic solid rocket motor configurations featuring the first polydisperse reactive computations with a fully Eulerian method.
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Using travel times to simulate multi-dimensional bioreactive transport in time-periodic flows.
Sanz-Prat, Alicia; Lu, Chuanhe; Finkel, Michael; Cirpka, Olaf A
2016-04-01
In travel-time models, the spatially explicit description of reactive transport is replaced by associating reactive-species concentrations with the travel time or groundwater age at all locations. These models have been shown adequate for reactive transport in river-bank filtration under steady-state flow conditions. Dynamic hydrological conditions, however, can lead to fluctuations of infiltration velocities, putting the validity of travel-time models into question. In transient flow, the local travel-time distributions change with time. We show that a modified version of travel-time based reactive transport models is valid if only the magnitude of the velocity fluctuates, whereas its spatial orientation remains constant. We simulate nonlinear, one-dimensional, bioreactive transport involving oxygen, nitrate, dissolved organic carbon, aerobic and denitrifying bacteria, considering periodic fluctuations of velocity. These fluctuations make the bioreactive system pulsate: The aerobic zone decreases at times of low velocity and increases at those of high velocity. For the case of diurnal fluctuations, the biomass concentrations cannot follow the hydrological fluctuations and a transition zone containing both aerobic and obligatory denitrifying bacteria is established, whereas a clear separation of the two types of bacteria prevails in the case of seasonal velocity fluctuations. We map the 1-D results to a heterogeneous, two-dimensional domain by means of the mean groundwater age for steady-state flow in both domains. The mapped results are compared to simulation results of spatially explicit, two-dimensional, advective-dispersive-bioreactive transport subject to the same relative fluctuations of velocity as in the one-dimensional model. The agreement between the mapped 1-D and the explicit 2-D results is excellent. We conclude that travel-time models of nonlinear bioreactive transport are adequate in systems of time-periodic flow if the flow direction does not change. Copyright © 2016 Elsevier B.V. All rights reserved.
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Hernández, Griselda; Anderson, Janet S.; LeMaster, David M.
2012-01-01
The acute sensitivity to conformation exhibited by amide hydrogen exchange reactivity provides a valuable test for the physical accuracy of model ensembles developed to represent the Boltzmann distribution of the protein native state. A number of molecular dynamics studies of ubiquitin have predicted a well-populated transition in the tight turn immediately preceding the primary site of proteasome-directed polyubiquitylation Lys 48. Amide exchange reactivity analysis demonstrates that this transition is 103-fold rarer than these predictions. More strikingly, for the most populated novel conformational basin predicted from a recent 1 ms MD simulation of bovine pancreatic trypsin inhibitor (at 13% of total), experimental hydrogen exchange data indicates a population below 10−6. The most sophisticated efforts to directly incorporate experimental constraints into the derivation of model protein ensembles have been applied to ubiquitin, as illustrated by three recently deposited studies (PDB codes 2NR2, 2K39 and 2KOX). Utilizing the extensive set of experimental NOE constraints, each of these three ensembles yields a modestly more accurate prediction of the exchange rates for the highly exposed amides than does a standard unconstrained molecular simulation. However, for the less frequently exposed amide hydrogens, the 2NR2 ensemble offers no improvement in rate predictions as compared to the unconstrained MD ensemble. The other two NMR-constrained ensembles performed markedly worse, either underestimating (2KOX) or overestimating (2K39) the extent of conformational diversity. PMID:22425325
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NASA Astrophysics Data System (ADS)
Menon, Vidya V.; Foto, Egemen; Mary, Y. Sheena; Karatas, Esin; Panicker, C. Yohannan; Yalcin, Gözde; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Yildiz, Ilkay
2017-02-01
FT-IR and FT-Raman spectra of 5-nitro-2-phenoxymethylbenzimidazole were recorded and analyzed theoretically and experimentally. The splitting of Nsbnd H stretching mode in the IR spectrum with a red shift from the calculated value indicates the weakening of the NH bond. The theoretical calculations give the phenyl ring breathing modes at 999 cm-1 for mono substituted benzene ring and at 1040 cm-1 for tri-substituted benzene ring. The theoretical NMR chemical shifts are in agreement with the experimental chemical shifts. The most reactive sites for electrophilic and nucleophilic attack are predicted from the MEP analysis. HOMO of π nature is delocalized over the entire molecule whereas the LUMO is located over the complete molecule except mono-substituted phenyl ring and oxygen atom. Reactive sites of the title molecule have been located with the help of ALIE surfaces and Fukui functions. In order to determine locations prone to autoxidation and locations interesting for starting of degradation, bond dissociation energies have been calculated for all single acyclic bonds. For the determination of atoms with pronounced interactions with water we have calculated radial distribution functions obtained after molecular dynamics simulations. The calculated first hyperpolarizability of the title compound is 58.03 times that of standard nonlinear optical material urea. The substrate binding site interactions of the title compound with Topo II enzyme is reported by using molecular docking study. Biological activity studies show that the title compound can be leaded for developing new anticancer agents.
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Influence of a Confined Methanol Solvent on the Reactivity of Active Sites in UiO-66.
Caratelli, Chiara; Hajek, Julianna; Rogge, Sven M J; Vandenbrande, Steven; Meijer, Evert Jan; Waroquier, Michel; Van Speybroeck, Veronique
2018-02-19
UiO-66, composed of Zr-oxide bricks and terephthalate linkers, is currently one of the most studied metal-organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this Article, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO-66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen-bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO-66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
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Predicting the crystalline and porous equations of state for secondary explosives
NASA Astrophysics Data System (ADS)
Wixom, Ryan; Damm, David
2013-06-01
Accurate simulations of energetic material response necessitate accurate unreacted equations of state at pressures much higher than even the C-J state. Unfortunately, for reactive materials, experimental data at high pressures may be unattainable, and extrapolation from low-pressure data results in unacceptable uncertainty. In addition to being low-pressure, the available data is typically limited to the porous state. The fully-dense, or crystalline, equation of state is required for building mesoscale simulations of the dynamic response of energetic materials. We have used quantum molecular dynamics to predict the Hugoniots and 300 K isotherms of crystalline PETN, HNS, CL-20 and TATB up to pressures not attainable in experiments. The porous Hugoniots for these materials were then analytically obtained and are validated by comparison with available data. Our calculations for TATB confirm the presence of a kink in the Hugoniot, and the softening of the shock response is explained in terms of a change in molecular conformation and the loss of aromaticity.
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SELF-HEALING NANOMATERIALS: MULTIMILLION-ATOM REACTIVE MOLECULAR DYNAMICS SIMULATIONS
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hakamata, Tomoya; Shimamura, Kohei; Shimojo, Fuyuki
Organometal halide perovskites are attracting great attention as promising material for solar cells because of their high power conversion efficiency. The high performance has been attributed to the existence of free charge carriers and their large diffusion lengths, but the nature of carrier transport at the atomistic level remains elusive. Here, nonadiabatic quantum molecular dynamics simulations elucidate the mechanisms underlying the excellent free-carrier transport in CH 3NH 3PbI 3. Pb and I sublattices act as disjunct pathways for rapid and balanced transport of photoexcited electrons and holes, respectively, while minimizing efficiency-degrading charge recombination. On the other hand, CH 3NH 3more » sublattice quickly screens out electrostatic electron-hole attraction to generate free carriers within 1 ps. Together this nano-architecture lets photoexcited electrons and holes dissociate instantaneously and travel far away to be harvested before dissipated as heat. As a result, this work provides much needed structure-property relationships and time-resolved information that potentially lead to rational design of efficient solar cells.« less
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An automated method to find transition states using chemical dynamics simulations.
Martínez-Núñez, Emilio
2015-02-05
A procedure to automatically find the transition states (TSs) of a molecular system (MS) is proposed. It has two components: high-energy chemical dynamics simulations (CDS), and an algorithm that analyzes the geometries along the trajectories to find reactive pathways. Two levels of electronic structure calculations are involved: a low level (LL) is used to integrate the trajectories and also to optimize the TSs, and a higher level (HL) is used to reoptimize the structures. The method has been tested in three MSs: formaldehyde, formic acid (FA), and vinyl cyanide (VC), using MOPAC2012 and Gaussian09 to run the LL and HL calculations, respectively. Both the efficacy and efficiency of the method are very good, with around 15 TS structures optimized every 10 trajectories, which gives a total of 7, 12, and 83 TSs for formaldehyde, FA, and VC, respectively. The use of CDS makes it a powerful tool to unveil possible nonstatistical behavior of the system under study. © 2014 Wiley Periodicals, Inc.
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Kodavasal, Janardhan; Lavoie, George A.; Assanis, Dennis N.; ...
2015-10-26
Full-cycle computational fluid dynamics simulations with gasoline chemical kinetics were performed to determine the impact of breathing and fuel injection strategies on thermal and compositional stratification, combustion and emissions during homogeneous charge compression ignition combustion. The simulations examined positive valve overlap and negative valve overlap strategies, along with fueling by port fuel injection and direct injection. The resulting charge mass distributions were analyzed prior to ignition using ignition delay as a reactivity metric. The reactivity stratification arising from differences in the distributions of fuel–oxygen equivalence ratio (Φ FO), oxygen molar fraction (χ O2) and temperature (T) was determined for threemore » parametric studies. In the first study, the reactivity stratification and burn duration for positive valve overlap valve events with port fuel injection and early direct injection were nearly identical and were dominated by wall-driven thermal stratification. nitrogen oxide (NO) and carbon monoxide (CO) emissions were negligible for both injection strategies. In the second study, which examined negative valve overlap valve events with direct injection and port fuel injection, reactivity stratification increased for direct injection as the Φ FO and T distributions associated with direct fuel injection into the hot residual gas were positively correlated; however, the latent heat absorbed from the hot residual gas by the evaporating direct injection fuel jet reduced the overall thermal and reactivity stratification. These stratification effects were offsetting, resulting in similar reactivity stratification and burn durations for the two injection strategies. The higher local burned gas temperatures with direct injection resulted in an order of magnitude increase in NO, while incomplete combustion of locally over-lean regions led to a sevenfold increase in CO emissions compared to port fuel injection. The final study evaluated positive valve overlap and negative valve overlap valve events with direct injection. Furthermore, relative to positive valve overlap, the negative valve overlap condition had a wider reactivity stratification, a longer burn duration and higher NO and CO emissions associated with reduced fuel–air mixing.« less
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Gerardin, Jaline; Bever, Caitlin A; Bridenbecker, Daniel; Hamainza, Busiku; Silumbe, Kafula; Miller, John M; Eisele, Thomas P; Eckhoff, Philip A; Wenger, Edward A
2017-06-12
Reactive case detection could be a powerful tool in malaria elimination, as it selectively targets transmission pockets. However, field operations have yet to demonstrate under which conditions, if any, reactive case detection is best poised to push a region to elimination. This study uses mathematical modelling to assess how baseline transmission intensity and local interconnectedness affect the impact of reactive activities in the context of other possible intervention packages. Communities in Southern Province, Zambia, where elimination operations are currently underway, were used as representatives of three archetypes of malaria transmission: low-transmission, high household density; high-transmission, low household density; and high-transmission, high household density. Transmission at the spatially-connected household level was simulated with a dynamical model of malaria transmission, and local variation in vectorial capacity and intervention coverage were parameterized according to data collected from the area. Various potential intervention packages were imposed on each of the archetypical settings and the resulting likelihoods of elimination by the end of 2020 were compared. Simulations predict that success of elimination campaigns in both low- and high-transmission areas is strongly dependent on stemming the flow of imported infections, underscoring the need for regional-scale strategies capable of reducing transmission concurrently across many connected areas. In historically low-transmission areas, treatment of clinical malaria should form the cornerstone of elimination operations, as most malaria infections in these areas are symptomatic and onward transmission would be mitigated through health system strengthening; reactive case detection has minimal impact in these settings. In historically high-transmission areas, vector control and case management are crucial for limiting outbreak size, and the asymptomatic reservoir must be addressed through reactive case detection or mass drug campaigns. Reactive case detection is recommended only for settings where transmission has recently been reduced rather than all low-transmission settings. This is demonstrated in a modelling framework with strong out-of-sample accuracy across a range of transmission settings while including methodologies for understanding the most resource-effective allocations of health workers. This approach generalizes to providing a platform for planning rational scale-up of health systems based on locally-optimized impact according to simplified stratification.
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NASA Astrophysics Data System (ADS)
Taleb, M.; Cherkaoui, M.; Hbib, M.
2018-05-01
Recently, renewable energy sources are impacting seriously power quality of the grids in term of frequency and voltage stability, due to their intermittence and less forecasting accuracy. Among these sources, wind energy conversion systems (WECS) received a great interest and especially the configuration with Doubly Fed Induction Generator. However, WECS strongly nonlinear, are making their control not easy by classical approaches such as a PI. In this paper, we continue deepen study of PI controller used in active and reactive power control of this kind of WECS. Particle Swarm Optimization (PSO) is suggested to improve its dynamic performances and its robustness against parameters variations. This work highlights the performances of PSO optimized PI control against classical PI tuned with poles compensation strategy. Simulations are carried out on MATLAB-SIMULINK software.
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Reactive trajectories of the Ru2+/3+ self-exchange reaction and the connection to Marcus' theory.
Tiwari, Ambuj; Ensing, Bernd
2016-12-22
Outer sphere electron transfer between two ions in aqueous solution is a rare event on the time scale of first principles molecular dynamics simulations. We have used transition path sampling to generate an ensemble of reactive trajectories of the self-exchange reaction between a pair of Ru 2+ and Ru 3+ ions in water. To distinguish between the reactant and product states, we use as an order parameter the position of the maximally localised Wannier center associated with the transferring electron. This allows us to align the trajectories with respect to the moment of barrier crossing and compute statistical averages over the path ensemble. We compare our order parameter with two typical reaction coordinates used in applications of Marcus theory of electron transfer: the vertical gap energy and the solvent electrostatic potential at the ions.
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Sensitivity analysis of reactive ecological dynamics.
Verdy, Ariane; Caswell, Hal
2008-08-01
Ecological systems with asymptotically stable equilibria may exhibit significant transient dynamics following perturbations. In some cases, these transient dynamics include the possibility of excursions away from the equilibrium before the eventual return; systems that exhibit such amplification of perturbations are called reactive. Reactivity is a common property of ecological systems, and the amplification can be large and long-lasting. The transient response of a reactive ecosystem depends on the parameters of the underlying model. To investigate this dependence, we develop sensitivity analyses for indices of transient dynamics (reactivity, the amplification envelope, and the optimal perturbation) in both continuous- and discrete-time models written in matrix form. The sensitivity calculations require expressions, some of them new, for the derivatives of equilibria, eigenvalues, singular values, and singular vectors, obtained using matrix calculus. Sensitivity analysis provides a quantitative framework for investigating the mechanisms leading to transient growth. We apply the methodology to a predator-prey model and a size-structured food web model. The results suggest predator-driven and prey-driven mechanisms for transient amplification resulting from multispecies interactions.
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NASA Astrophysics Data System (ADS)
Godfrey, B.; Majdalani, J.
2014-11-01
This study relies on computational fluid dynamics (CFD) tools to analyse a possible method for creating a stable quadrupole vortex within a simulated, circular-port, cylindrical rocket chamber. A model of the vortex generator is created in a SolidWorks CAD program and then the grid is generated using the Pointwise mesh generation software. The non-reactive flowfield is simulated using an open source computational program, Stanford University Unstructured (SU2). Subsequent analysis and visualization are performed using ParaView. The vortex generation approach that we employ consists of four tangentially injected monopole vortex generators that are arranged symmetrically with respect to the center of the chamber in such a way to produce a quadrupole vortex with a common downwash. The present investigation focuses on characterizing the flow dynamics so that future investigations can be undertaken with increasing levels of complexity. Our CFD simulations help to elucidate the onset of vortex filaments within the monopole tubes, and the evolution of quadrupole vortices downstream of the injection faceplate. Our results indicate that the quadrupole vortices produced using the present injection pattern can become quickly unstable to the extent of dissipating soon after being introduced into simulated rocket chamber. We conclude that a change in the geometrical configuration will be necessary to produce more stable quadrupoles.
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From cellulose to kerogen: molecular simulation of a geological process.
Atmani, Lea; Bichara, Christophe; Pellenq, Roland J-M; Van Damme, Henri; van Duin, Adri C T; Raza, Zamaan; Truflandier, Lionel A; Obliger, Amaël; Kralert, Paul G; Ulm, Franz J; Leyssale, Jean-Marc
2017-12-01
The process by which organic matter decomposes deep underground to form petroleum and its underlying kerogen matrix has so far remained a no man's land to theoreticians, largely because of the geological (Myears) timescale associated with the process. Using reactive molecular dynamics and an accelerated simulation framework, the replica exchange molecular dynamics method, we simulate the full transformation of cellulose into kerogen and its associated fluid phase under prevailing geological conditions. We observe in sequence the fragmentation of the cellulose crystal and production of water, the development of an unsaturated aliphatic macromolecular phase and its aromatization. The composition of the solid residue along the maturation pathway strictly follows what is observed for natural type III kerogen and for artificially matured samples under confined conditions. After expulsion of the fluid phase, the obtained microporous kerogen possesses the structure, texture, density, porosity and stiffness observed for mature type III kerogen and a microporous carbon obtained by saccharose pyrolysis at low temperature. As expected for this variety of precursor, the main resulting hydrocarbon is methane. The present work thus demonstrates that molecular simulations can now be used to assess, almost quantitatively, such complex chemical processes as petrogenesis in fossil reservoirs and, more generally, the possible conversion of any natural product into bio-sourced materials and/or fuel.
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Formation and decay of tetrazane derivatives--a Car-Parrinello molecular dynamics study.
Nonnenberg, Christel; Frank, Irmgard
2008-08-14
The complications during flight 510 of the Ariane Project were ascribed to problems in the upper stage engine that employs the bipropellant monomethylhydrazine (MMH) and nitrogen tetroxide (NTO). This has led to the question what conditions or reactions possibly cause an uncontrolled behaviour in the combustion process of MMH/NTO. We use first-principles molecular dynamics to investigate the reactions of the hypergolic mixture in different chemical situations. It was possible to observe the ultrafast redox reaction between the reactants on the timescale of an unconstrained simulation. We show that electrostatic attraction is crucial for the understanding of this reaction. Besides a cold reaction preceding the ignition, a reaction path leading to the highly reactive compound dimethyltetrazane could be identified.
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Detonation Propagation through Nitromethane Embedded Metal Foam
NASA Astrophysics Data System (ADS)
Lieberthal, Brandon; Maines, Warren R.; Stewart, D. Scott
2015-11-01
There is considerable interest in developing a better understanding of dynamic behaviors of multicomponent systems. We report results of Eulerian hydrodynamic simulations of shock waves propagating through metal foam at approximately 20% relative density and various porosities using a reactive flow model in the ALE3D software package. We investigate the applied pressure and energy of the shock wave and its effects on the fluid and the inert material interface. By varying pore sizes, as well as metal impedance, we predict the overall effects of heterogeneous material systems at the mesoscale. In addition, we observe a radially expanding blast front in these heterogeneous models and apply the theory of Detonation Shock Dynamics to the convergence behavior of the lead shock.
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NASA Astrophysics Data System (ADS)
Rakhimbekova, S.; O'Carroll, D. M.; Robinson, C. E.
2017-12-01
Groundwater-coastal water interactions play an important role in controlling the behavior of inorganic chemicals in nearshore aquifers and the subsequent flux of these chemicals to receiving coastal waters. Previous studies have shown that dynamic groundwater flows and water exchange across the sediment-water interface can set up strong geochemical gradients and an important reaction zone in a nearshore aquifer that affect the fate of reactive chemicals. There is limited understanding of the impact of transient coastal forcing such as wave conditions on groundwater dynamics and geochemistry in a nearshore aquifer. The goal of this study was to assess the impact of intensified wave conditions on the behavior of arsenic in a nearshore aquifer and to determine the hydrological and geochemical factors controlling its fate and ultimate delivery to receiving coastal waters. Field investigations were conducted over the period of intensified wave conditions on a freshwater beach on Lake Erie, Canada. High spatial resolution aqueous and sediment sampling was conducted to characterize the subsurface distribution of inorganic species in the nearshore aquifer. Numerical groundwater flow and transport simulations were conducted to evaluate wave-induced perturbations in the flow dynamics including characterizing changes in the groundwater flow recirculations in the nearshore aquifer. The combination of field data and numerical simulations reveal that varying wave conditions alter groundwater flows and set up geochemical transition zones within the aquifer resulting in the release and sequestration of arsenic. Interactions between oxic surface water, mildly reducing shallow groundwater, and reducing sulfur- and iron-rich deep groundwater promote dynamic iron, sulfur and manganese cycling which control the mobility of arsenic in the aquifer. The findings of this study have potential implications for the fate and transport of other reactive chemicals (e.g. phosphorus, mercury) in nearshore marine and freshwater aquifers exposed to transient coastal forcing. Understanding the fate of chemicals and the dynamics of the reaction zone in nearshore aquifers is critical for evaluating the importance of groundwater as a pathway for delivering pollutants to coastal waters.
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Zhou, Tingting; Lou, Jianfeng; Zhang, Yangeng; Song, Huajie; Huang, Fenglei
2016-07-14
We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives.
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Simulations of photochemical smog formation in complex urban areas
NASA Astrophysics Data System (ADS)
Muilwijk, C.; Schrijvers, P. J. C.; Wuerz, S.; Kenjereš, S.
2016-12-01
In the present study we numerically investigated the dispersion of photochemical reactive pollutants in complex urban areas by applying an integrated Computational Fluid Dynamics (CFD) and Computational Reaction Dynamics (CRD) approach. To model chemical reactions involved in smog generation, the Generic Reaction Set (GRS) approach is used. The GRS model was selected since it does not require detailed modeling of a large set of reactive components. Smog formation is modeled first in the case of an intensive traffic emission, subjected to low to moderate wind conditions in an idealized two-dimensional street canyon with a building aspect ratio (height/width) of one. It is found that Reactive Organic Components (ROC) play an important role in the chemistry of smog formation. In contrast to the NOx/O3 photochemical steady state model that predicts a depletion of the (ground level) ozone, the GRS model predicts generation of ozone. Secondly, the effect of direct sunlight and shadow within the street canyon on the chemical reaction dynamics is investigated for three characteristic solar angles (morning, midday and afternoon). Large differences of up to one order of magnitude are found in the ozone production for different solar angles. As a proof of concept for real urban areas, the integrated CFD/CRD approach is applied for a real scale (1 × 1 km2) complex urban area (a district of the city of Rotterdam, The Netherlands) with high traffic emissions. The predicted pollutant concentration levels give realistic values that correspond to moderate to heavy smog. It is concluded that the integrated CFD/CRD method with the GRS model of chemical reactions is both accurate and numerically robust, and can be used for modeling of smog formation in complex urban areas.
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Convective dynamics and chemical disequilibrium in the atmospheres of substellar objects
NASA Astrophysics Data System (ADS)
Bordwell, Baylee; Brown, Benjamin P.; Oishi, Jeffrey S.
2017-11-01
The thousands of substellar objects now known provide a unique opportunity to test our understanding of atmospheric dynamics across a range of environments. The chemical timescales of certain species transition from being much shorter than the dynamical timescales to being much longer than them at a point in the atmosphere known as the quench point. This transition leads to a state of dynamical disequilibrium, the effects of which can be used to probe the atmospheric dynamics of these objects. Unfortunately, due to computational constraints, models that inform the interpretation of these observations are run at dynamical parameters which are far from realistic values. In this study, we explore the behavior of a disequilibrium chemical process with increasingly realistic planetary conditions, to quantify the effects of the approximations used in current models. We simulate convection in 2-D, plane-parallel, polytropically-stratified atmospheres, into which we add reactive passive tracers that explore disequilibrium behavior. We find that as we increase the Rayleigh number, and thus achieve more realistic planetary conditions, the behavior of these tracers does not conform to the classical predictions of disequilibrium chemistry.
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Assowe, O; Politano, O; Vignal, V; Arnoux, P; Diawara, B; Verners, O; van Duin, A C T
2012-12-06
Corrosion processes occurring in aqueous solutions are critically dependent upon the interaction between the metal electrode and the solvent. In this work, the interaction of a nickel substrate with water molecules has been investigated using reactive force field (ReaxFF) molecular dynamics simulations. This approach was originally developed by van Duin and co-workers to study hydrocarbon chemistry and the catalytic properties of organic compounds. To our knowledge, this method has not previously been used to study the corrosion of nickel. In this work, we studied the interaction of 480 molecules of water (ρ = 0.99 g·cm(-3)) with Ni(111) surfaces at 300 K. The results showed that a water "bilayer" was adsorbed on the nickel surface. In the absence of an applied electric field, no dissociation of water was observed. However, the nickel atoms at the surface were charged positively, whereas the first water layer was charged negatively, indicating the formation of an electric double layer. To study the corrosion of nickel in pure water, we introduced an external electric field between the metal and the solution. The electric field intensity varied between 10 and 20 MeV/cm. The presence of this electric field led to oxidation of the metal surface. The structural and morphological differences associated with the growth of this oxide film in the presence of the electric field were evaluated. The simulated atomic trajectories were used to analyze the atomic displacement during the reactive process. The growth of the oxide scale on the nickel surface was primarily due to the movement of anions toward the interior of the metal substrate and the migration of nickel toward the free surface. We found that increasing the electric field intensity sped up the corrosion of nickel. The results also showed that the oxide film thickness increased linearly with increasing electric field intensity.
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Numerical investigation of coupled density-driven flow and hydrogeochemical processes below playas
NASA Astrophysics Data System (ADS)
Hamann, Enrico; Post, Vincent; Kohfahl, Claus; Prommer, Henning; Simmons, Craig T.
2015-11-01
Numerical modeling approaches with varying complexity were explored to investigate coupled groundwater flow and geochemical processes in saline basins. Long-term model simulations of a playa system gain insights into the complex feedback mechanisms between density-driven flow and the spatiotemporal patterns of precipitating evaporites and evolving brines. Using a reactive multicomponent transport model approach, the simulations reproduced, for the first time in a numerical study, the evaporite precipitation sequences frequently observed in saline basins ("bull's eyes"). Playa-specific flow, evapoconcentration, and chemical divides were found to be the primary controls for the location of evaporites formed, and the resulting brine chemistry. Comparative simulations with the computationally far less demanding surrogate single-species transport models showed that these were still able to replicate the major flow patterns obtained by the more complex reactive transport simulations. However, the simulated degree of salinization was clearly lower than in reactive multicomponent transport simulations. For example, in the late stages of the simulations, when the brine becomes halite-saturated, the nonreactive simulation overestimated the solute mass by almost 20%. The simulations highlight the importance of the consideration of reactive transport processes for understanding and quantifying geochemical patterns, concentrations of individual dissolved solutes, and evaporite evolution.
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NASA Astrophysics Data System (ADS)
Ikuse, Kazumasa; Hamaguchi, Satoshi
2016-09-01
We have used two types of numerical simulations to examine biological effects of reactive oxygen and nitrogen species (RONS) generated in water by an atmospheric-pressure plasma (APP) that irradiates the water surface. One is numerical simulation for the generation and transport of RONS in water based on the reaction-diffusion-advection equations coupled with Poisson equation. The rate constants, mobilities, and diffusion coefficients used in the equations are obtained from the literature. The gaseous species are given as boundary conditions and time evolution of the concentrations of chemical species in pure water is solved numerically as functions of the depth in one dimension. Although it is not clear how living organisms respond to such exogenous RONS, we also use numerical simulation for metabolic reactions of Escherichia coli (E. coli) and examine possible effects of such RONS on an in-silico model organism. The computation model is based on the flux balance analysis (FBA), where the fluxes of the metabolites in a biological system are evaluated in steady state, i.e., under the assumption that the fluxes do not change in time. The fluxes are determined with liner programming to maximize the growth rate of the bacteria under the given conditions. Although FBA cannot be directly applied to dynamical responses of metabolic reactions, the simulation still gives insight into the biological reactions to exogenous chemical species generated by an APP. Partially supported by JSPS Grants-in-Aid for Scientific Research.
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A Generalized Hybrid Multiscale Modeling Approach for Flow and Reactive Transport in Porous Media
NASA Astrophysics Data System (ADS)
Yang, X.; Meng, X.; Tang, Y. H.; Guo, Z.; Karniadakis, G. E.
2017-12-01
Using emerging understanding of biological and environmental processes at fundamental scales to advance predictions of the larger system behavior requires the development of multiscale approaches, and there is strong interest in coupling models at different scales together in a hybrid multiscale simulation framework. A limited number of hybrid multiscale simulation methods have been developed for subsurface applications, mostly using application-specific approaches for model coupling. The proposed generalized hybrid multiscale approach is designed with minimal intrusiveness to the at-scale simulators (pre-selected) and provides a set of lightweight C++ scripts to manage a complex multiscale workflow utilizing a concurrent coupling approach. The workflow includes at-scale simulators (using the lattice-Boltzmann method, LBM, at the pore and Darcy scale, respectively), scripts for boundary treatment (coupling and kriging), and a multiscale universal interface (MUI) for data exchange. The current study aims to apply the generalized hybrid multiscale modeling approach to couple pore- and Darcy-scale models for flow and mixing-controlled reaction with precipitation/dissolution in heterogeneous porous media. The model domain is packed heterogeneously that the mixing front geometry is more complex and not known a priori. To address those challenges, the generalized hybrid multiscale modeling approach is further developed to 1) adaptively define the locations of pore-scale subdomains, 2) provide a suite of physical boundary coupling schemes and 3) consider the dynamic change of the pore structures due to mineral precipitation/dissolution. The results are validated and evaluated by comparing with single-scale simulations in terms of velocities, reactive concentrations and computing cost.
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Superconductivity in human body; myth or necessity.
Alexiou, Athanasios; Rekkas, John
2015-01-01
During the last years there is an increasing trend on the study of mitochondrial populations mainly in neural cells, due to their association with neurological disorders like Alzheimer's disease, Parkinson's disease, Autism, and CMT2A. Several studies concerning modeling of mitochondrial protein pathways, simulation of mitochondrial dynamics, biomarkers associated with Reactive Oxygen Species and many other related topics are already published. In this study we establish the idea of natural superconductivity in mitochondrial level as a necessary theoretical framework for the normal production of ATP and the avoidance of adverse reactions in Central Neural System.
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Application of Improved APO Algorithm in Vulnerability Assessment and Reconstruction of Microgrid
NASA Astrophysics Data System (ADS)
Xie, Jili; Ma, Hailing
2018-01-01
Artificial Physics Optimization (APO) has good global search ability and can avoid the premature convergence phenomenon in PSO algorithm, which has good stability of fast convergence and robustness. On the basis of APO of the vector model, a reactive power optimization algorithm based on improved APO algorithm is proposed for the static structure and dynamic operation characteristics of microgrid. The simulation test is carried out through the IEEE 30-bus system and the result shows that the algorithm has better efficiency and accuracy compared with other optimization algorithms.
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NASA Astrophysics Data System (ADS)
Aswathy, V. V.; Alper-Hayta, Sabiha; Yalcin, Gözde; Mary, Y. Sheena; Panicker, C. Yohannan; Jojo, P. J.; Kaynak-Onurdag, Fatma; Armaković, Stevan; Armaković, Sanja J.; Yildiz, Ilkay; Van Alsenoy, C.
2017-08-01
N-[2-(2-bromophenyl)-1,3-benzoxazol-5-yl]-2-phenylacetamide (NBBPA) was synthesized in this study as an original compound in order to evaluate its antibacterial activity against representative Gram-negative and Gram-positive bacteria, with their drug-resistant clinical isolate. Microbiological results showed that this compound had moderate antibacterial activity. Study also encompassed detailed FT-IR, FT-Raman and NMR experimental and theoretical spectroscopic characterization and assignation of the ring breathing modes of the mono-, ortho- and tri-substituted phenyl rings is in agreement with the literature data. DFT calculations were also used to identify specific reactivity properties of NBBPA molecule based on the molecular orbital, charge distribution and electron density analysis, which indicated the reactive importance of carbonyl and NH2 groups, together with bromine atom. DFT calculations were also used for investigation of sensitivity of the NBBPA molecules towards the autoxidation mechanism, while molecular dynamics (MD) simulations were used to investigate the influence of water. The molecular docking results suggest that the compound might exhibit inhibitory activity against GyrB complex.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lai, Canhai; Xu, Zhijie; Li, Tingwen
In virtual design and scale up of pilot-scale carbon capture systems, the coupled reactive multiphase flow problem must be solved to predict the adsorber’s performance and capture efficiency under various operation conditions. This paper focuses on the detailed computational fluid dynamics (CFD) modeling of a pilot-scale fluidized bed adsorber equipped with vertical cooling tubes. Multiphase Flow with Interphase eXchanges (MFiX), an open-source multiphase flow CFD solver, is used for the simulations with custom code to simulate the chemical reactions and filtered models to capture the effect of the unresolved details in the coarser mesh for simulations with reasonable simulations andmore » manageable computational effort. Previously developed two filtered models for horizontal cylinder drag, heat transfer, and reaction kinetics have been modified to derive the 2D filtered models representing vertical cylinders in the coarse-grid CFD simulations. The effects of the heat exchanger configurations (i.e., horizontal or vertical) on the adsorber’s hydrodynamics and CO2 capture performance are then examined. The simulation result subsequently is compared and contrasted with another predicted by a one-dimensional three-region process model.« less
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Real time implementation and control validation of the wind energy conversion system
NASA Astrophysics Data System (ADS)
Sattar, Adnan
The purpose of the thesis is to analyze dynamic and transient characteristics of wind energy conversion systems including the stability issues in real time environment using the Real Time Digital Simulator (RTDS). There are different power system simulation tools available in the market. Real time digital simulator (RTDS) is one of the powerful tools among those. RTDS simulator has a Graphical User Interface called RSCAD which contains detail component model library for both power system and control relevant analysis. The hardware is based upon the digital signal processors mounted in the racks. RTDS simulator has the advantage of interfacing the real world signals from the external devices, hence used to test the protection and control system equipments. Dynamic and transient characteristics of the fixed and variable speed wind turbine generating systems (WTGSs) are analyzed, in this thesis. Static Synchronous Compensator (STATCOM) as a flexible ac transmission system (FACTS) device is used to enhance the fault ride through (FRT) capability of the fixed speed wind farm. Two level voltage source converter based STATCOM is modeled in both VSC small time-step and VSC large time-step of RTDS. The simulation results of the RTDS model system are compared with the off-line EMTP software i.e. PSCAD/EMTDC. A new operational scheme for a MW class grid-connected variable speed wind turbine driven permanent magnet synchronous generator (VSWT-PMSG) is developed. VSWT-PMSG uses fully controlled frequency converters for the grid interfacing and thus have the ability to control the real and reactive powers simultaneously. Frequency converters are modeled in the VSC small time-step of the RTDS and three phase realistic grid is adopted with RSCAD simulation through the use of optical analogue digital converter (OADC) card of the RTDS. Steady state and LVRT characteristics are carried out to validate the proposed operational scheme. Simulation results show good agreement with real time simulation software and thus can be used to validate the controllers for the real time operation. Integration of the Battery Energy Storage System (BESS) with wind farm can smoothen its intermittent power fluctuations. The work also focuses on the real time implementation of the Sodium Sulfur (NaS) type BESS. BESS is integrated with the STATCOM. The main advantage of this system is that it can also provide the reactive power support to the system along with the real power exchange from BESS unit. BESS integrated with STATCOM is modeled in the VSC small time-step of the RTDS. The cascaded vector control scheme is used for the control of the STATCOM and suitable control is developed to control the charging/discharging of the NaS type BESS. Results are compared with Laboratory standard power system software PSCAD/EMTDC and the advantages of using RTDS in dynamic and transient characteristics analyses of wind farm are also demonstrated clearly.
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Efficient reactive Brownian dynamics
Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho
2018-01-21
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently processmore » reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.« less
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Efficient reactive Brownian dynamics
NASA Astrophysics Data System (ADS)
Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho
2018-01-01
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.
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Efficient reactive Brownian dynamics
DOE Office of Scientific and Technical Information (OSTI.GOV)
Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently processmore » reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.« less
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NASA Astrophysics Data System (ADS)
Bandopadhyay, Aditya; Le Borgne, Tanguy; Méheust, Yves; Dentz, Marco
2017-02-01
Mixing fronts, where fluids of different chemical compositions mix with each other, are known to represent hotspots of chemical reaction in hydrological systems. These fronts are typically subjected to velocity gradients, ranging from the pore scale due to no slip boundary conditions at fluid solid interfaces, to the catchment scale due to permeability variations and complex geometry of the Darcy velocity streamlines. A common trait of these processes is that the mixing interface is strained by shear. Depending on the Péclet number Pe , which represents the ratio of the characteristic diffusion time to the characteristic shear time, and the Damköhler number Da , which represents the ratio of the characteristic diffusion time to the characteristic reaction time, the local reaction rates can be strongly impacted by the dynamics of the mixing interface. So far, this impact has been characterized mostly either in kinetics-limited or in mixing-limited conditions, that is, for either low or high Da. Here the coupling of shear flow and chemical reactivity is investigated for arbitrary Damköhler numbers, for a bimolecular reaction and an initial interface with separated reactants. Approximate analytical expressions for the global production rate and reactive mixing scale are derived based on a reactive lamella approach that allows for a general coupling between stretching enhanced mixing and chemical reactions. While for Pe < Da , reaction kinetics and stretching effects are decoupled, a scenario which we name "weak stretching", for Pe > Da , we uncover a "strong stretching" scenario where new scaling laws emerge from the interplay between reaction kinetics, diffusion, and stretching. The analytical results are validated against numerical simulations. These findings shed light on the effect of flow heterogeneity on the enhancement of chemical reaction and the creation of spatially localized hotspots of reactivity for a broad range of systems ranging from kinetic limited to mixing limited situations.
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Near-Source Shaking and Dynamic Rupture in Plastic Media
NASA Astrophysics Data System (ADS)
Gabriel, A.; Mai, P. M.; Dalguer, L. A.; Ampuero, J. P.
2012-12-01
Recent well recorded earthquakes show a high degree of complexity at the source level that severely affects the resulting ground motion in near and far-field seismic data. In our study, we focus on investigating source-dominated near-field ground motion features from numerical dynamic rupture simulations in an elasto-visco-plastic bulk. Our aim is to contribute to a more direct connection from theoretical and computational results to field and seismological observations. Previous work showed that a diversity of rupture styles emerges from simulations on faults governed by velocity-and-state-dependent friction with rapid velocity-weakening at high slip rate. For instance, growing pulses lead to re-activation of slip due to gradual stress build-up near the hypocenter, as inferred in some source studies of the 2011 Tohoku-Oki earthquake. Moreover, off-fault energy dissipation implied physical limits on extreme ground motion by limiting peak slip rate and rupture velocity. We investigate characteristic features in near-field strong ground motion generated by dynamic in-plane rupture simulations. We present effects of plasticity on source process signatures, off-fault damage patterns and ground shaking. Independent of rupture style, asymmetric damage patterns across the fault are produced that contribute to the total seismic moment, and even dominantly at high angles between the fault and the maximum principal background stress. The off-fault plastic strain fields induced by transitions between rupture styles reveal characteristic signatures of the mechanical source processes during the transition. Comparing different rupture styles in elastic and elasto-visco-plastic media to identify signatures of off-fault plasticity, we find varying degrees of alteration of near-field radiation due to plastic energy dissipation. Subshear pulses suffer more peak particle velocity reduction due to plasticity than cracks. Supershear ruptures are affected even more. The occurrence of multiple rupture fronts affect seismic potency release rate, amplitude spectra, peak particle velocity distributions and near-field seismograms. Our simulations enable us to trace features of source processes in synthetic seismograms, for example exhibiting a re-activation of slip. Such physical models may provide starting points for future investigations of field properties of earthquake source mechanisms and natural fault conditions. In the long-term, our findings may be helpful for seismic hazard analysis and the improvement of seismic source models.
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Curran, Scott J.; Gao, Zhiming; Wagner, Robert M.
2014-12-22
In-cylinder blending of gasoline and diesel to achieve reactivity-controlled compression ignition has been shown to reduce NO X and soot emissions while maintaining or improving brake thermal efficiency as compared with conventional diesel combustion. The reactivity-controlled compression ignition concept has an advantage over many advanced combustion strategies in that the fuel reactivity can be tailored to the engine speed and load, allowing stable low-temperature combustion to be extended over more of the light-duty drive cycle load range. In this paper, a multi-mode reactivity-controlled compression ignition strategy is employed where the engine switches from reactivity-controlled compression ignition to conventional diesel combustionmore » when speed and load demand are outside of the experimentally determined reactivity-controlled compression ignition range. The potential for reactivity-controlled compression ignition to reduce drive cycle fuel economy and emissions is not clearly understood and is explored here by simulating the fuel economy and emissions for a multi-mode reactivity-controlled compression ignition–enabled vehicle operating over a variety of US drive cycles using experimental engine maps for multi-mode reactivity-controlled compression ignition, conventional diesel combustion, and a 2009 port-fuel injected gasoline engine. Drive cycle simulations are completed assuming a conventional mid-size passenger vehicle with an automatic transmission. Multi-mode reactivity-controlled compression ignition fuel economy simulation results are compared with the same vehicle powered by a representative 2009 port-fuel injected gasoline engine over multiple drive cycles. Finally, engine-out drive cycle emissions are compared with conventional diesel combustion, and observations regarding relative gasoline and diesel tank sizes needed for the various drive cycles are also summarized.« less
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Steric Effects of Solvent Molecules on SN2 Substitution Dynamics.
Liu, Xu; Xie, Jing; Zhang, Jiaxu; Yang, Li; Hase, William L
2017-04-20
Influences of solvent molecules on S N 2 reaction dynamics of microsolvated F - (H 2 O) n with CH 3 I, for n = 0-3, are uncovered by direct chemical dynamics simulations. The direct substitution mechanism, which is important without microsolvation, is quenched dramatically upon increasing hydration. The water molecules tend to force reactive encounters to proceed through the prereaction collision complex leading to indirect reaction. In contrast to F - (H 2 O), reaction with higher hydrated ions shows a strong propensity for ion desolvation in the entrance channel, diminishing steric hindrance for nucleophilic attack. Thus, nucleophilic substitution avoids the potential energy barrier with all of the solvent molecules intact and instead occurs through the less solvated barrier, which is energetically unexpected because the former barrier has a lower energy. The work presented here reveals a trade-off between reaction energetics and steric effects, with the latter found to be crucial in understanding how hydration influences microsolvated S N 2 dynamics.
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Computational Design of Graphene Nanoscrolls
NASA Astrophysics Data System (ADS)
Bejagam, Karteek; Singh, Samrendra; Deshmukh, Sanket; Deshmukh Group Team; Samrendra Group Collaboration
Graphene nanoscrolls have obtained a significant interest in recent years due to their potential applications in tribology, nanotechnology, and bioengineering. For example, recently it has been shown that graphene nanoscrolls can be used to experience superlubricity - almost zero friction state. In the present study we employ the metal/non-metal nanoparticles to facilitate the graphene nanoscroll formation. We have conducted reactive molecular dynamics (RMD) simulations of diamond, Nickel, and Gold nanoparticles placed on the 2D graphene sheet. RMD simulations reveal the mechanisms that facilitates or prohibits the graphene nanoscroll formation. Our simulations suggest that the surface chemistry and interactions between nanoparticles and graphene play a crucial in determining the mechanism of scroll formation and the nature of the nanoscroll. We also find that the type of a nanoparticle has strong influence on the elastic and mechanical properties of the nanoscroll. Our study provides a systematic pathway to design graphene nanoscrolls with a wide range of properties.
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NASA Astrophysics Data System (ADS)
WANG, J.; Kim, J.
2014-12-01
In this study, sensitivity of pollutant dispersion on turbulent Schmidt number (Sct) was investigated in a street canyon using a computational fluid dynamics (CFD) model. For this, numerical simulations with systematically varied Sct were performed and the CFD model results were validated against a wind‒tunnel measurement data. The results showed that root mean square error (RMSE) was quite dependent on Sct and dispersion patterns of non‒reactive scalar pollutant with different Sct were quite different among the simulation results. The RMSE was lowest in the case of Sct = 0.35 and the apparent dispersion pattern was most similar to the wind‒tunnel data in the case of Sct = 0.35. Also, numerical simulations using spatially weighted Sct were additionally performed in order for the best reproduction of the wind‒tunnel data. Detailed method and procedure to find the best reproduction will be presented.
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The dynamics of Al/Pt reactive multilayer ignition via pulsed-laser irradiation
DOE Office of Scientific and Technical Information (OSTI.GOV)
Murphy, Ryan D.; Reeves, Robert V.; Yarrington, Cole D.
2015-12-07
Reactive multilayers consisting of alternating layers of Al and Pt were irradiated by single laser pulses ranging from 100 μs to 100 ms in duration, resulting in the initiation of rapid, self-propagating reactions. The threshold intensities for ignition vary with the focused laser beam diameter, bilayer thickness, and pulse length and are affected by solid state reactions and conduction of heat away from the irradiated regions. High-speed photography was used to observe ignition dynamics during irradiation and elucidate the effects of heat transfer into a multilayer foil. For an increasing laser pulse length, the ignition process transitioned from a more uniform tomore » a less uniform temperature profile within the laser-heated zone. A more uniform temperature profile is attributed to rapid heating rates and heat localization for shorter laser pulses, and a less uniform temperature profile is due to slower heating of reactants and conduction during irradiation by longer laser pulses. Finite element simulations of laser heating using measured threshold intensities indicate that micron-scale ignition of Al/Pt occurs at low temperatures, below the melting point of both reactants.« less
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The dynamics of Al/Pt reactive multilayer ignition via pulsed-laser irradiation
Murphy, Ryan D.; Reeves, Robert V.; Yarrington, Cole D.; ...
2015-12-07
Reactive multilayers consisting of alternating layers of Al and Pt were irradiated by single laser pulses ranging from 100 μs to 100 ms in duration, resulting in the initiation of rapid, self-propagating reactions. The threshold intensities for ignition vary with the focused laser beam diameter, bilayer thickness, and pulse length and are affected by solid state reactions and conduction of heat away from the irradiated regions. We used high-speed photography to observe ignition dynamics during irradiation and elucidate the effects of heat transfer into a multilayer foil. For an increasing laser pulse length, the ignition process transitioned from a moremore » uniform to a less uniform temperature profile within the laser-heated zone. A more uniform temperature profile is attributed to rapid heating rates and heat localization for shorter laser pulses, and a less uniform temperature profile is due to slower heating of reactants and conduction during irradiation by longer laser pulses. Lastly, finite element simulations of laser heating using measured threshold intensities indicate that micron-scale ignition of Al/Pt occurs at low temperatures, below the melting point of both reactants.« less
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NASA Astrophysics Data System (ADS)
Spiteri, Claudette; Slomp, Caroline P.; Charette, Matthew A.; Tuncay, Kagan; Meile, Christof
2008-07-01
A two-dimensional (2D) reactive transport model is used to investigate the controls on nutrient ( NO3-, NH4+, PO 4) dynamics in a coastal aquifer. The model couples density-dependent flow to a reaction network which includes oxic degradation of organic matter, denitrification, iron oxide reduction, nitrification, Fe 2+ oxidation and sorption of PO 4 onto iron oxides. Porewater measurements from a well transect at Waquoit Bay, MA, USA indicate the presence of a reducing plume with high Fe 2+, NH4+, DOC (dissolved organic carbon) and PO 4 concentrations overlying a more oxidizing NO3--rich plume. These two plumes travel nearly conservatively until they start to overlap in the intertidal coastal sediments prior to discharge into the bay. In this zone, the aeration of the surface beach sediments drives nitrification and allows the precipitation of iron oxide, which leads to the removal of PO 4 through sorption. Model simulations suggest that removal of NO3- through denitrification is inhibited by the limited overlap between the two freshwater plumes, as well as by the refractory nature of terrestrial DOC. Submarine groundwater discharge is a significant source of NO3- to the bay.
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Study of thermite mixture consolidated by the cold gas dynamic spray process
NASA Astrophysics Data System (ADS)
Bacciochini, A.; Maines, G.; Poupart, C.; Akbarnejad, H.; Radulescu, M.; Jodoin, B.; Zhang, F.; Lee, J. J.
2014-05-01
The present study focused on the cold gas dynamic spray process for manufacturing porosity free, finely structured energetic materials with high reactivity and structural integrity. The experiments have focused the reaction between the aluminium and metal oxide, such as Al-CuO system. The consolidation of the materials used the cold gas dynamic spray technique, where the particles are accelerated to high speeds and consolidated via plastic deformation upon impact. Reactive composites are formed in arbitrary shapes with close to zero porosity and without any reactions during the consolidation phase. Reactivity of mixtures has been investigated through flame propagation analysis on cold sprayed samples and compacted powder mixture. Deflagration tests showed the influence of porosity on the reactivity.
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Molecular simulation studies on chemical reactivity of methylcyclopentadiene.
Wang, Qingsheng; Zhang, Yingchun; Rogers, William J; Mannan, M Sam
2009-06-15
Molecular simulations are important to predict thermodynamic values for reactive chemicals especially when sufficient experimental data are not available. Methylcyclopentadiene (MCP) is an example of a highly reactive and hazardous compound in the chemical process industry. In this work, chemical reactivity of 2-methylcyclopentadiene, including isomerization, dimerization, and oxidation reactions, is investigated in detail by theoretical computational chemistry methods and empirical thermodynamic-energy correlation. On the basis of molecular simulations, an average value of -15.2 kcal/mol for overall heat of dimerization and -45.6 kcal/mol for overall heat of oxidation were obtained in gaseous phase at 298 K and 1 atm. These molecular simulation studies can provide guidance for the design of safer chemical processes, safer handling of MCP, and also provide useful information for an investigation of the T2 Laboratories explosion on December 19, 2007, in Florida.
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Self-assembly of single-wall carbon nanotubes during the cooling process of hot carbon gas.
Wen, Yushi; Zheng, Ke; Long, Xinping; Li, Ming; Xue, Xianggui; Dai, Xiaogan; Deng, Chuan
2018-04-25
In this work, self-assembly mechanism of single-wall carbon nanotube (SWCNT) during the annealing process of hot gaseous carbon is presented using reactive force field (ReaxFF)-based reactive molecular simulations. A series of simulations were performed on the evolution of reactive carbon gas. The simulation results show that the reactive carbon gas can be assembled into regular SWCNT without a catalyst. Five distinct stages of SWCNT self-assembly are proposed. For some initial configurations, the CNT was found to spin at an ultra-high rate after the nucleation. Graphical abstract Self-assembly process of single-wall carbon nanotube from the annealing of hot gaseous carbon.
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Reactive multiphase flow simulation workshop summary
DOE Office of Scientific and Technical Information (OSTI.GOV)
VanderHeyden, W.B.
1995-09-01
A workshop on computer simulation of reactive multiphase flow was held on May 18 and 19, 1995 in the Computational Testbed for Industry at Los Alamos National Laboratory (LANL), Los Alamos, New Mexico. Approximately 35 to 40 people attended the workshop. This included 21 participants from 12 companies representing the petroleum, chemical, environmental and consumer products industries, two representatives from the DOE Office of Industrial Technologies and several from Los Alamos. The dialog at the meeting suggested that reactive multiphase flow simulation represents an excellent candidate for government/industry/academia collaborative research. A white paper on a potential consortium for reactive multiphasemore » flow with input from workshop participants will be issued separately.« less
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HIV dynamics linked to memory CD4+ T cell homeostasis.
Murray, John M; Zaunders, John; Emery, Sean; Cooper, David A; Hey-Nguyen, William J; Koelsch, Kersten K; Kelleher, Anthony D
2017-01-01
The dynamics of latent HIV is linked to infection and clearance of resting memory CD4+ T cells. Infection also resides within activated, non-dividing memory cells and can be impacted by antigen-driven and homeostatic proliferation despite suppressive antiretroviral therapy (ART). We investigated whether plasma viral level (pVL) and HIV DNA dynamics could be explained by HIV's impact on memory CD4+ T cell homeostasis. Median total, 2-LTR and integrated HIV DNA levels per μL of peripheral blood, for 8 primary (PHI) and 8 chronic HIV infected (CHI) individuals enrolled on a raltegravir (RAL) based regimen, exhibited greatest changes over the 1st year of ART. Dynamics slowed over the following 2 years so that total HIV DNA levels were equivalent to reported values for individuals after 10 years of ART. The mathematical model reproduced the multiphasic dynamics of pVL, and levels of total, 2-LTR and integrated HIV DNA in both PHI and CHI over 3 years of ART. Under these simulations, residual viremia originated from reactivated latently infected cells where most of these cells arose from clonal expansion within the resting phenotype. Since virion production from clonally expanded cells will not be affected by antiretroviral drugs, simulations of ART intensification had little impact on pVL. HIV DNA decay over the first year of ART followed the loss of activated memory cells (120 day half-life) while the 5.9 year half-life of total HIV DNA after this point mirrored the slower decay of resting memory cells. Simulations had difficulty reproducing the fast early HIV DNA dynamics, including 2-LTR levels peaking at week 12, and the later slow loss of total and 2-LTR HIV DNA, suggesting some ongoing infection. In summary, our modelling indicates that much of the dynamical behavior of HIV can be explained by its impact on memory CD4+ T cell homeostasis.
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Kondalaji, Samaneh Ghassabi; Khakinejad, Mahdiar; Valentine, Stephen J
2018-06-01
Molecular dynamics (MD) simulations have been utilized to study peptide ion conformer establishment during the electrospray process. An explicit water model is used for nanodroplets containing a model peptide and hydronium ions. Simulations are conducted at 300 K for two different peptide ion charge configurations and for droplets containing varying numbers of hydronium ions. For all conditions, modeling has been performed until production of the gas-phase ions and the resultant conformers have been compared to proposed gas-phase structures. The latter species were obtained from previous studies in which in silico candidate structures were filtered according to ion mobility and hydrogen-deuterium exchange (HDX) reactivity matches. Results from the present study present three key findings namely (1) the evidence from ion production modeling supports previous structure refinement studies based on mobility and HDX reactivity matching, (2) the modeling of the electrospray process is significantly improved by utilizing initial droplets existing below but close to the calculated Rayleigh limit, and (3) peptide ions in the nanodroplets sample significantly different conformers than those in the bulk solution due to altered physicochemical properties of the solvent. Graphical Abstract ᅟ.
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Dynamic autonomous routing technology for IP-based satellite ad hoc networks
NASA Astrophysics Data System (ADS)
Wang, Xiaofei; Deng, Jing; Kostas, Theresa; Rajappan, Gowri
2014-06-01
IP-based routing for military LEO/MEO satellite ad hoc networks is very challenging due to network and traffic heterogeneity, network topology and traffic dynamics. In this paper, we describe a traffic priority-aware routing scheme for such networks, namely Dynamic Autonomous Routing Technology (DART) for satellite ad hoc networks. DART has a cross-layer design, and conducts routing and resource reservation concurrently for optimal performance in the fluid but predictable satellite ad hoc networks. DART ensures end-to-end data delivery with QoS assurances by only choosing routing paths that have sufficient resources, supporting different packet priority levels. In order to do so, DART incorporates several resource management and innovative routing mechanisms, which dynamically adapt to best fit the prevailing conditions. In particular, DART integrates a resource reservation mechanism to reserve network bandwidth resources; a proactive routing mechanism to set up non-overlapping spanning trees to segregate high priority traffic flows from lower priority flows so that the high priority flows do not face contention from low priority flows; a reactive routing mechanism to arbitrate resources between various traffic priorities when needed; a predictive routing mechanism to set up routes for scheduled missions and for anticipated topology changes for QoS assurance. We present simulation results showing the performance of DART. We have conducted these simulations using the Iridium constellation and trajectories as well as realistic military communications scenarios. The simulation results demonstrate DART's ability to discriminate between high-priority and low-priority traffic flows and ensure disparate QoS requirements of these traffic flows.
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SAFSIM theory manual: A computer program for the engineering simulation of flow systems
NASA Astrophysics Data System (ADS)
Dobranich, Dean
1993-12-01
SAFSIM (System Analysis Flow SIMulator) is a FORTRAN computer program for simulating the integrated performance of complex flow systems. SAFSIM provides sufficient versatility to allow the engineering simulation of almost any system, from a backyard sprinkler system to a clustered nuclear reactor propulsion system. In addition to versatility, speed and robustness are primary SAFSIM development goals. SAFSIM contains three basic physics modules: (1) a fluid mechanics module with flow network capability; (2) a structure heat transfer module with multiple convection and radiation exchange surface capability; and (3) a point reactor dynamics module with reactivity feedback and decay heat capability. Any or all of the physics modules can be implemented, as the problem dictates. SAFSIM can be used for compressible and incompressible, single-phase, multicomponent flow systems. Both the fluid mechanics and structure heat transfer modules employ a one-dimensional finite element modeling approach. This document contains a description of the theory incorporated in SAFSIM, including the governing equations, the numerical methods, and the overall system solution strategies.
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NASA Astrophysics Data System (ADS)
Biswas, Sohag; Dasgupta, Teesta; Mallik, Bhabani S.
2016-09-01
We present the reactivity of an organic intermediate by studying the proton transfer process from water to ketyl radical anion using gas phase electronic structure calculations and the metadynamics method based first principles molecular dynamics (FPMD) simulations. Our results indicate that during the micro solvation of anion by water molecules systematically, the presence of minimum three water molecules in the gas phase cluster is sufficient to observe the proton transfer event. The analysis of trajectories obtained from initial FPMD simulation of an aqueous solution of the anion does not show any evident of complete transfer of the proton from water. The cooperativity of water molecules and the relatively weak anion-water interaction in liquid state prohibit the full release of the proton. Using biasing potential through first principles metadynamics simulations, we report the observation of proton transfer reaction from water to ketyl radical anion with a barrier height of 16.0 kJ/mol.
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NASA Astrophysics Data System (ADS)
Guo, Lei; Safi, Zaki S.; Kaya, Savas; Shi, Wei; Tüzün, Burak; Altunay, Nail; Kaya, Cemal
2018-05-01
It is known that iron is one of the most widely used metals in industrial production. In this work, the inhibition performances of three thiophene derivatives on the corrosion of iron were investigated in the light of several theoretical approaches. In the section including DFT calculations, several global reactivity descriptors such as EHOMO, ELUMO, ionization energy (I), electron affinity (A), HOMO-LUMO energy gap (ΔE), chemical hardness (η), softness (σ), as well as local reactivity descriptors like Fukui indices, local softness, and local electrophilicity were considered and discussed. The adsorption behaviors of considered thiophene derivatives on Fe(110) surface were investigated using molecular dynamics simulation approach. To determine the most active corrosion inhibitor among studied thiophene derivatives, we used the principle component analysis (PCA) and agglomerative hierarchical cluster analysis (AHCA). Accordingly, all data obtained using various theoretical calculation techniques are consistent with experiments.
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All-atom calculation of protein free-energy profiles
NASA Astrophysics Data System (ADS)
Orioli, S.; Ianeselli, A.; Spagnolli, G.; Faccioli, P.
2017-10-01
The Bias Functional (BF) approach is a variational method which enables one to efficiently generate ensembles of reactive trajectories for complex biomolecular transitions, using ordinary computer clusters. For example, this scheme was applied to simulate in atomistic detail the folding of proteins consisting of several hundreds of amino acids and with experimental folding time of several minutes. A drawback of the BF approach is that it produces trajectories which do not satisfy microscopic reversibility. Consequently, this method cannot be used to directly compute equilibrium observables, such as free energy landscapes or equilibrium constants. In this work, we develop a statistical analysis which permits us to compute the potential of mean-force (PMF) along an arbitrary collective coordinate, by exploiting the information contained in the reactive trajectories calculated with the BF approach. We assess the accuracy and computational efficiency of this scheme by comparing its results with the PMF obtained for a small protein by means of plain molecular dynamics.
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Electrolyte Structure near Electrode Interfaces in Lithium-Ion Batteries
NASA Astrophysics Data System (ADS)
Lordi, Vincenzo; Ong, Mitchell; Verners, Osvalds; van Duin, Adri; Draeger, Erik; Pask, John
2014-03-01
The performance of lithium-ion secondary batteries (LIBs) is strongly tied to electrochemistry and ionic transport near the electrode-electrolyte interface. Changes in ion solvation near the interface affect ion conductivity and also are associated with the formation and evolution of solid-electrolyte interphase (SEI) layers, which impede transport but also passivate the interface. Thus, understanding these effects is critical to optimizing battery performance. Here we present molecular dynamics (MD) simulations of typical organic liquid LIB electrolytes in contact with graphite electrodes to understand differences in molecular structure and solvation near the interface compared to the bulk electrolyte. Results for different graphite terminations are presented. We compare the results of density-functional based MD to the empirical reactive forcefield ReaxFF and the non-reactive, non-polarizable COMPASS forcefield. Notable differences in the predictive power of each of these techniques are discussed. Prepared by LLNL under Contract DE-AC52-07NA27344.
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Tabelin, Carlito Baltazar; Sasaki, Ryosuke; Igarashi, Toshifumi; Park, Ilhwan; Tamoto, Shuichi; Arima, Takahiko; Ito, Mayumi; Hiroyoshi, Naoki
2017-12-01
Predicting the fates of arsenic (As) and selenium (Se) in natural geologic media like rocks and soils necessitates the understanding of how their various oxyanionic species behave and migrate under dynamic conditions. In this study, geochemical factors and processes crucial in the leaching and transport of arsenite (As III ), arsenate (As V ), selenite (Se IV ) and selenate (Se VI ) in tunnel-excavated rocks of marine origin were investigated using microscopic/extraction techniques, column experiments, dissolution-precipitation kinetics and one-dimensional reactive transport modeling. The results showed that evaporite salts were important because aside from containing As and Se, they played crucial roles in the evolution of pH and concentrations of coexisting ions, both of which had strong effects on adsorption-desorption reactions of As and Se species with iron oxyhydroxide minerals/phases. The observed leaching trends of As V , As III , Se IV and Se VI were satisfactorily simulated by one-dimensional reactive transport models, which predict that preferential adsorptions of As V and Se IV were magnified by geochemical changes in the columns due to water flow. Moreover, our results showed that migrations of As III , Se IV and Se VI could be predicted adequately by 1D solute transport with simple activity-K' d approach, but surface complexation was more reliable to simulate adsorption-desorption behavior of As V . Copyright © 2017 Elsevier Ltd. All rights reserved.
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A Film Depositional Model of Permeability for Mineral Reactions in Unsaturated Media.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Freedman, Vicky L.; Saripalli, Prasad; Bacon, Diana H.
2004-11-15
A new modeling approach based on the biofilm models of Taylor et al. (1990, Water Resources Research, 26, 2153-2159) has been developed for modeling changes in porosity and permeability in saturated porous media and implemented in an inorganic reactive transport code. Application of the film depositional models to mineral precipitation and dissolution reactions requires that calculations of mineral films be dynamically changing as a function of time dependent reaction processes. Since calculations of film thicknesses do not consider mineral density, results show that the film porosity model does not adequately describe volumetric changes in the porous medium. These effects canmore » be included in permeability calculations by coupling the film permeability models (Mualem and Childs and Collis-George) to a volumetric model that incorporates both mineral density and reactive surface area. Model simulations demonstrate that an important difference between the biofilm and mineral film models is in the translation of changes in mineral radii to changes in pore space. Including the effect of tortuosity on pore radii changes improves the performance of the Mualem permeability model for both precipitation and dissolution. Results from simulation of simultaneous dissolution and secondary mineral precipitation provides reasonable estimates of porosity and permeability. Moreover, a comparison of experimental and simulated data show that the model yields qualitatively reasonable results for permeability changes due to solid-aqueous phase reactions.« less
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NASA Astrophysics Data System (ADS)
Maes, Julien; Geiger, Sebastian
2018-01-01
Laboratory experiments have shown that oil production from sandstone and carbonate reservoirs by waterflooding could be significantly increased by manipulating the composition of the injected water (e.g. by lowering the ionic strength). Recent studies suggest that a change of wettability induced by a change in surface charge is likely to be one of the driving mechanism of the so-called low-salinity effect. In this case, the potential increase of oil recovery during waterflooding at low ionic strength would be strongly impacted by the inter-relations between flow, transport and chemical reaction at the pore-scale. Hence, a new numerical model that includes two-phase flow, solute reactive transport and wettability alteration is implemented based on the Direct Numerical Simulation of the Navier-Stokes equations and surface complexation modelling. Our model is first used to match experimental results of oil droplet detachment from clay patches. We then study the effect of wettability change on the pore-scale displacement for simple 2D calcite micro-models and evaluate the impact of several parameters such as water composition and injected velocity. Finally, we repeat the simulation experiments on a larger and more complex pore geometry representing a carbonate rock. Our simulations highlight two different effects of low-salinity on oil production from carbonate rocks: a smaller number of oil clusters left in the pores after invasion, and a greater number of pores invaded.
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Multiphase Reactive Transport and Platelet Ice Accretion in the Sea Ice of McMurdo Sound, Antarctica
NASA Astrophysics Data System (ADS)
Buffo, J. J.; Schmidt, B. E.; Huber, C.
2018-01-01
Sea ice seasonally to interannually forms a thermal, chemical, and physical boundary between the atmosphere and hydrosphere over tens of millions of square kilometers of ocean. Its presence affects both local and global climate and ocean dynamics, ice shelf processes, and biological communities. Accurate incorporation of sea ice growth and decay, and its associated thermal and physiochemical processes, is underrepresented in large-scale models due to the complex physics that dictate oceanic ice formation and evolution. Two phenomena complicate sea ice simulation, particularly in the Antarctic: the multiphase physics of reactive transport brought about by the inhomogeneous solidification of seawater, and the buoyancy driven accretion of platelet ice formed by supercooled ice shelf water onto the basal surface of the overlying ice. Here a one-dimensional finite difference model capable of simulating both processes is developed and tested against ice core data. Temperature, salinity, liquid fraction, fluid velocity, total salt content, and ice structure are computed during model runs. The model results agree well with empirical observations and simulations highlight the effect platelet ice accretion has on overall ice thickness and characteristics. Results from sensitivity studies emphasize the need to further constrain sea ice microstructure and the associated physics, particularly permeability-porosity relationships, if a complete model of sea ice evolution is to be obtained. Additionally, implications for terrestrial ice shelves and icy moons in the solar system are discussed.
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Impact Ignition and Combustion Behavior of Amorphous Metal-Based Reactive Composites
NASA Astrophysics Data System (ADS)
Mason, Benjamin; Groven, Lori; Son, Steven
2013-06-01
Recently published molecular dynamic simulations have shown that metal-based reactive powder composites consisting of at least one amorphous component could lead to improved reaction performance due to amorphous materials having a zero heat of fusion, in addition to having high energy densities and potential uses such as structural energetic materials and enhanced blast materials. In order to investigate the feasibility of these systems, thermochemical equilibrium calculations were performed on various amorphous metal/metalloid based reactive systems with an emphasis on commercially available or easily manufactured amorphous metals, such as Zr and Ti based amorphous alloys in combination with carbon, boron, and aluminum. Based on the calculations and material availability material combinations were chosen. Initial materials were either mixed via a Resodyn mixer or mechanically activated using high energy ball milling where the microstructure of the milled material was characterized using x-ray diffraction, optical microscopy and scanning electron microscopy. The mechanical impact response and combustion behavior of select reactive systems was characterized using the Asay shear impact experiment where impact ignition thresholds, ignition delays, combustion velocities, and temperatures were quantified, and reported. Funding from the Defense Threat Reduction Agency (DTRA), Grant Number HDTRA1-10-1-0119. Counter-WMD basic research program, Dr. Suhithi M. Peiris, program director is gratefully acknowledged.
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Simulations of reactive transport and precipitation with smoothed particle hydrodynamics
NASA Astrophysics Data System (ADS)
Tartakovsky, Alexandre M.; Meakin, Paul; Scheibe, Timothy D.; Eichler West, Rogene M.
2007-03-01
A numerical model based on smoothed particle hydrodynamics (SPH) was developed for reactive transport and mineral precipitation in fractured and porous materials. Because of its Lagrangian particle nature, SPH has several advantages for modeling Navier-Stokes flow and reactive transport including: (1) in a Lagrangian framework there is no non-linear term in the momentum conservation equation, so that accurate solutions can be obtained for momentum dominated flows and; (2) complicated physical and chemical processes such as surface growth due to precipitation/dissolution and chemical reactions are easy to implement. In addition, SPH simulations explicitly conserve mass and linear momentum. The SPH solution of the diffusion equation with fixed and moving reactive solid-fluid boundaries was compared with analytical solutions, Lattice Boltzmann [Q. Kang, D. Zhang, P. Lichtner, I. Tsimpanogiannis, Lattice Boltzmann model for crystal growth from supersaturated solution, Geophysical Research Letters, 31 (2004) L21604] simulations and diffusion limited aggregation (DLA) [P. Meakin, Fractals, scaling and far from equilibrium. Cambridge University Press, Cambridge, UK, 1998] model simulations. To illustrate the capabilities of the model, coupled three-dimensional flow, reactive transport and precipitation in a fracture aperture with a complex geometry were simulated.
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Taking the plunge: chemical reaction dynamics in liquids.
Orr-Ewing, Andrew J
2017-12-11
The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.
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Quadrature Moments Method for the Simulation of Turbulent Reactive Flows
NASA Technical Reports Server (NTRS)
Raman, Venkatramanan; Pitsch, Heinz; Fox, Rodney O.
2003-01-01
A sub-filter model for reactive flows, namely the DQMOM model, was formulated for Large Eddy Simulation (LES) using the filtered mass density function. Transport equations required to determine the location and size of the delta-peaks were then formulated for a 2-peak decomposition of the FDF. The DQMOM scheme was implemented in an existing structured-grid LES solver. Simulations of scalar shear layer using an experimental configuration showed that the first and second moments of both reactive and inert scalars are in good agreement with a conventional Lagrangian scheme that evolves the same FDF. Comparisons with LES simulations performed using laminar chemistry assumption for the reactive scalar show that the new method provides vast improvements at minimal computational cost. Currently, the DQMOM model is being implemented for use with the progress variable/mixture fraction model of Pierce. Comparisons with experimental results and LES simulations using a single-environment for the progress-variable are planned. Future studies will aim at understanding the effect of increase in environments on predictions.
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Dutta, Saheb; Kundu, Soumya; Saha, Amrita; Nandi, Nilashis
2018-03-01
Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri ( mk SerRS) and histidyl tRNA synthetases from Thermus thermophilus ( tt HisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain. Catalytic residues of the loops form a network of interaction with the substrates to form a reactive state. The loops undergo transitions between closed state and open state and the relaxation of the constituent residues occurs in femtosecond to nanosecond time scale. Order parameters are higher for constituent catalytic residues which form a specific network of interaction with the substrates to form a reactive state compared to the Gly residues within the loop. The development of interaction is supported from mutation studies where the catalytic domain with mutated loop exhibits unfavorable binding energy with the substrates. During the open-close motion of the loops, the catalytic residues make relaxation by ultrafast librational motion as well as fast diffusive motion and subsequently relax rather slowly via slower diffusive motion. The Gly residues act as a hinge to facilitate the loop closing and opening by their faster relaxation behavior. The role of bound water is analyzed by comparing implicit solvent-based and explicit solvent-based simulations. Loops fail to form catalytically competent geometry in absence of water. The present result, for the first time reveals the nature of the active site loop dynamics in aaRS and their influence on catalysis.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Yang, Liang; Wang, C. Z.; Lin, Shiwei
Understanding of metal oxidation is very critical to corrosion control, catalysis synthesis, and advanced materials engineering. Metal oxidation is a very complex phenomenon, with many different processes which are coupled and involved from the onset of reaction. In this work, the initial stage of oxidation on titanium surface was investigated in atomic scale by molecular dynamics (MD) simulations using a reactive force field (ReaxFF). We show that oxygen transport is the dominant process during the initial oxidation. Our simulation also demonstrate that a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Titaniummore » (0001) surface and further prevented oxidation in the deeper layers. As a result, the mechanism of initial oxidation observed in this work can be also applicable to other self-limiting oxidation.« less
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Vöhringer-Martinez, E; Link, O; Lugovoy, E; Siefermann, K R; Wiederschein, F; Grubmüller, H; Abel, B
2014-09-28
Supercritical water and methanol have recently drawn much attention in the field of green chemistry. It is crucial to an understanding of supercritical solvents to know their dynamics and to what extent hydrogen (H) bonds persist in these fluids. Here, we show that with femtosecond infrared (IR) laser pulses water and methanol can be heated to temperatures near and above their critical temperature Tc and their molecular dynamics can be studied via ultrafast photoelectron spectroscopy at liquid jet interfaces with high harmonics radiation. As opposed to previous studies, the main focus here is the comparison between the hydrogen bonded systems of methanol and water and their interpretation by theory. Superheated water initially forms a dense hot phase with spectral features resembling those of monomers in gas phase water. On longer timescales, this phase was found to build hot aggregates, whose size increases as a function of time. In contrast, methanol heated to temperatures near Tc initially forms a broad distribution of aggregate sizes and some gas. These experimental features are also found and analyzed in extended molecular dynamics simulations. Additionally, the simulations enabled us to relate the origin of the different behavior of these two hydrogen-bonded liquids to the nature of the intermolecular potentials. The combined experimental and theoretical approach delivers new insights into both superheated phases and may contribute to understand their different chemical reactivities.
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Melt focusing and geochemical evolution at mid-ocean ridges: simulations of reactive two-phase flow
NASA Astrophysics Data System (ADS)
Keller, T.; Katz, R. F.; Hirschmann, M. M.
2017-12-01
The geochemical character of MORB and related off-axis volcanic products reflects the signature of chemical reservoirs in the mantle, the processes of melt transport from source to surface, or both. Focusing of partial melt to the ridge axis controls the proportion of deep, volatile- and incompatible-rich melts that contribute to MORB formation. However, the effect of volatiles, including CO2 and H2O, on melt segregation and focusing remains poorly understood. We investigate this transport using 2-D numerical simulations of reactive two-phase flow. The phases are solid mantle and liquid magma. Major elements and volatiles are represented by a system with 4 or 6 pseudo-components. This captures accepted features of mantle melting with volatiles. The fluid-dynamical model is McKenzie's formulation [1], while melting and reactive transport use the R_DMC method [2,3]. Trace element transport is computed for 5 idealized elements between highly incompatible and compatible behavior. Our results indicate that volatiles cause channelized melt transport, which leads to fluctuations in volume and composition of melt focused to the axis. The volatile-induced expansion of the melting regime at depth, however, has no influence on melt focusing. Up to 50% of deep, volatile-rich melts are not focused to the axis, but are emplaced along the oceanic LAB. There, crystallization of accumulated melt leads to enrichment of volatiles and incompatibles in the deep lithosphere. This has implications for volatile recycling by subduction, seismic properties of the oceanic LAB, and potential sources for seamount volcanism. Results from a suite of simulations, constrained by catalogued observational data [4,5,6], enable prediction of global MORB and volatile output and systematic variations of major, volatile and trace element concentrations as a function of mantle conditions and dynamic properties. REFERENCES[1] McKenzie (1984), doi:10.1093/petrology/25.3.713.[2] Rudge, Bercovici & Spiegelman (2011), doi:10.1111/j.1365-246X.2010.04870.x.[3] Keller & Katz (2016), doi:10.1093/petrology/egw030.[4] Dalton, Langmuir & Gale (2014), doi:10.1126/science.1249466.[5] Gale, Langmuir & Dalton (2014), doi:10.1093/petrology/egu017.[6] White et al. (2001), doi:10.1093/petrology/42.6.1171.
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Proceedings of "Optical Probes of Dynamics in Complex Environments"
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sension, R; Tokmakoff, A
2008-04-01
This document contains the proceedings from the symposium on Optical Probes of Dynamics in Complex Environments, which organized as part of the 235th National Meeting of the American Chemical Society in New Orleans, LA from April 6 to 10, 2008. The study of molecular dynamics in chemical reaction and biological processes using time ÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂresolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE Office of Science because of their role in the development of alternative energy sources, themore » understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time resolved spectroscopy is central to all of DOEs grand challenges for fundamental energy science. This symposium brought together leaders in the field of ultrafast spectroscopy, including experimentalists, theoretical chemists, and simulators, to discuss the most recent scientific and technological advances. DOE support for this conference was used to help young US and international scientists travel to the meeting. The latest technology in ultrafast infrared, optical, and xray spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.« less
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Simulations relevant to the beam instability in the foreshock
NASA Technical Reports Server (NTRS)
Cairns, I. H.; Nishikawa, K.-I.
1989-01-01
The results presently obtained from two-dimensional simulations of the reactive instability for Maxwellian beams and cutoff distributions are noted to be consistent with recent suggestions that electrons backstreaming into earth's foreshock have steep-sided cutoff distributions, which are initially unstable to the reactive instability, and that the back-reaction to the wave growth causes the instability to pass into its kinetic phase. It is demonstrated that the reactive instability is a bunching instability, and that the reactive instability saturates and passes over into the kinetic phase by particle trapping.
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Dynamics of basaltic glass dissolution - Capturing microscopic effects in continuum scale models
NASA Astrophysics Data System (ADS)
Aradóttir, E. S. P.; Sigfússon, B.; Sonnenthal, E. L.; Björnsson, G.; Jónsson, H.
2013-11-01
The method of 'multiple interacting continua' (MINC) was applied to include microscopic rate-limiting processes in continuum scale reactive transport models of basaltic glass dissolution. The MINC method involves dividing the system up to ambient fluid and grains, using a specific surface area to describe the interface between the two. The various grains and regions within grains can then be described by dividing them into continua separated by dividing surfaces. Millions of grains can thus be considered within the method without the need to explicity discretizing them. Four continua were used for describing a dissolving basaltic glass grain; the first one describes the ambient fluid around the grain, while the second, third and fourth continuum refer to a diffusive leached layer, the dissolving part of the grain and the inert part of the grain, respectively. The model was validated using the TOUGHREACT simulator and data from column flow through experiments of basaltic glass dissolution at low, neutral and high pH values. Successful reactive transport simulations of the experiments and overall adequate agreement between measured and simulated values provides validation that the MINC approach can be applied for incorporating microscopic effects in continuum scale basaltic glass dissolution models. Equivalent models can be used when simulating dissolution and alteration of other minerals. The study provides an example of how numerical modeling and experimental work can be combined to enhance understanding of mechanisms associated with basaltic glass dissolution. Column outlet concentrations indicated basaltic glass to dissolve stoichiometrically at pH 3. Predictive simulations with the developed MINC model indicated significant precipitation of secondary minerals within the column at neutral and high pH, explaining observed non-stoichiometric outlet concentrations at these pH levels. Clay, zeolite and hydroxide precipitation was predicted to be most abundant within the column.
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Length and temperature dependence of the mechanical properties of finite-size carbyne
NASA Astrophysics Data System (ADS)
Yang, Xueming; Huang, Yanhui; Cao, Bingyang; To, Albert C.
2017-09-01
Carbyne is an ideal one-dimensional conductor and the thinnest interconnection in an ultimate nano-device and it requires an understanding of the mechanical properties that affect device performance and reliability. Here, we report the mechanical properties of finite-size carbyne, obtained by a molecular dynamics simulation study based on the adaptive intermolecular reactive empirical bond order potential. To avoid confusion in assigning the effective cross-sectional area of carbyne, the value of the effective cross-sectional area of carbyne (4.148 Å2) was deduced via experiment and adopted in our study. Ends-constraints effects on the ultimate stress (maximum force) of the carbyne chains are investigated, revealing that the molecular dynamics simulation results agree very well with the experimental results. The ultimate strength, Young's Modulus and maximum strain of carbyne are rather sensitive to the temperature and all decrease with the temperature. Opposite tendencies of the length dependence of the overall ultimate strength and maximum strain of carbyne at room temperature and very low temperature have been found, and analyses show that this originates in the ends effect of carbyne.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Dang, Liem X.; Vo, Quynh N.; Nilsson, Mikael
We report one of the first simulations using a classical rate theory approach to predict the mechanism of the exchange process between water and aqueous uranyl ions. Using our water and ion-water polarizable force fields and molecular dynamics techniques, we computed the potentials of mean force for the uranyl ion-water pair as the function of pressures at ambient temperature. Subsequently, these simulated potentials of mean force were used to calculate rate constants using the transition rate theory; the time dependent transmission coefficients were also examined using the reactive flux method and Grote-Hynes treatments of the dynamic response of the solvent.more » The computed activation volumes using transition rate theory and the corrected rate constants are positive, thus the mechanism of this particular water-exchange is a dissociative process. We discuss our rate theory results and compare them with previously studies in which non-polarizable force fields were used. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less
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Multiscale Investigations of the Early Stage Oxidation on Cu Surfaces
NASA Astrophysics Data System (ADS)
Zhu, Qing; Xiao, Penghao; Lian, Xin; Yang, Shen-Che; Henkelman, Grame; Saidi, Wissam; Yang, Judith; University of Pittsburgh Team; University of Texas at Austin Team
Previous in situ TEM experiments have shown that the oxidation of the three low index Cu surfaces (100), (110) and (111) exhibit different oxide nucleation rates, and the resulting oxides have 3-dimensional (3D) island shapes or 2D rafts under different conditions. In order to better understand these results, we have investigated the early stages of Cu oxidation using a multiscale computational approach that employs density functional theory (DFT), reactive force field (ReaxFF), and kinetic Mote Carlo (KMC). With DFT calculation, we have compared O2 dissociation barriers on Cu (100), (110) and (111) surfaces at high oxygen coverage to evaluate the kinetic barrier of sublayer oxidization. We found that O2 dissociation barriers on Cu(111) surface are all lower than those on (110) and (100) surfaces. This trend agrees with experimental observations that (111) surface is easier to oxidize. These DFT calculated energy barriers are then incorporated into KMC simulations. The large scale ReaxFF molecular dynamics and KMC simulations detail the oxidation dynamics of the different Cu surfaces, and show the formation of various oxide morphologies that are consistent with experimental observations.
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NASA Astrophysics Data System (ADS)
Lindsey, Rebecca; Goldman, Nir; Fried, Laurence
Understanding chemistry at extreme conditions is crucial in fields including geochemistry, astrobiology, and alternative energy. First principles methods can provide valuable microscopic insights into such systems while circumventing the risks of physical experiments, however the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
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Collision-induced evaporation of water clusters and contribution of momentum transfer
NASA Astrophysics Data System (ADS)
Calvo, Florent; Berthias, Francis; Feketeová, Linda; Abdoul-Carime, Hassan; Farizon, Bernadette; Farizon, Michel
2017-05-01
The evaporation of water molecules from high-velocity argon atoms impinging on protonated water clusters has been computationally investigated using molecular dynamics simulations with the reactive OSS2 potential to model water clusters and the ZBL pair potential to represent their interaction with the projectile. Swarms of trajectories and an event-by-event analysis reveal the conditions under which a specific number of molecular evaporation events is found one nanosecond after impact, thereby excluding direct knockout events from the analysis. These simulations provide velocity distributions that exhibit two main features, with a major statistical component arising from a global redistribution of the collision energy into intermolecular degrees of freedom, and another minor but non-ergodic feature at high velocities. The latter feature is produced by direct impacts on the peripheral water molecules and reflects a more complete momentum transfer. These two components are consistent with recent experimental measurements and confirm that electronic processes are not explicitly needed to explain the observed non-ergodic behavior. Contribution to the Topical Issue "Dynamics of Systems at the Nanoscale", edited by Andrey Solov'yov and Andrei Korol.
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Breen, Kristin J; DeBlase, Andrew F; Guasco, Timothy L; Voora, Vamsee K; Jordan, Kenneth D; Nagata, Takashi; Johnson, Mark A
2012-01-26
The transition states of a chemical reaction in solution are generally accessed through exchange of thermal energy between the solvent and the reactants. As such, an ensemble of reacting systems approaches the transition state configuration of reactant and surrounding solvent in an incoherent manner that does not lend itself to direct experimental observation. Here we describe how gas-phase cluster chemistry can provide a detailed picture of the microscopic mechanics at play when a network of six water molecules mediates the trapping of a highly reactive "hydrated electron" onto a neutral CO(2) molecule to form a radical anion. The exothermic reaction is triggered from a metastable intermediate by selective excitation of either the reactant CO(2) or the water network, which is evidenced by the evaporative decomposition of the product cluster. Ab initio molecular dynamics simulations of energized CO(2)·(H(2)O)(6)(-) clusters are used to elucidate the nature of the network deformations that mediate intracluster electron capture, thus revealing the detailed solvent fluctuations implicit in the Marcus theory for electron-transfer kinetics in solution.
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Limones-Herrero, Daniel; Pérez-Ruiz, Raúl; Lence, Emilio; González-Bello, Concepción; Miranda, Miguel A; Jiménez, M Consuelo
2017-04-01
A multidisciplinary strategy to obtain structural information on the intraprotein region is described here. As probe ligands, ( S )- and ( R )- CPFMe (the methyl esters of the chiral drug carprofen) have been selected, while bovine α 1 -acid glycoprotein (BAAG) has been chosen as a biological host. The procedure involves the separate irradiation of the BAAG/( S )- CPFMe and BAAG/( R )- CPFMe complexes, coupled with fluorescence spectroscopy, laser flash photolysis, proteomic analysis, docking and molecular dynamics simulations. Thus, irradiation of the BAAG/ CPFMe complexes at λ = 320 nm was followed by fluorescence spectroscopy. The intensity of the emission band obtained after irradiation indicated photodehalogenation, whereas its structureless shape suggested covalent binding of the resulting radical CBZMe˙ to the biopolymer. After gel filtration chromatography, the spectra still displayed emission, in agreement with covalent attachment of CBZMe˙ to BAAG. Stereodifferentiation was observed in this process. After trypsin digestion and ESI-MS/MS, the incorporation of CBZMe was detected at Phe68. Docking and molecular dynamics simulation studies, which were carried out using a homology model of BAAG, reveal that the closer proximity of the aromatic moiety of the ( S )-enantiomer to the phenyl group of Phe68 would be responsible for the experimentally observed, more effective chemical modification of the protein. The proposed tridimensional structure of BAAG covalently modified by the two enantiomers is also provided. In principle, this approach can be extended to a variety of protein/ligand complexes.
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Shi, Zhenzhen; Chapes, Stephen K; Ben-Arieh, David; Wu, Chih-Hang
2016-01-01
We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as "sepsis". Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-α ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies.
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Chapes, Stephen K.; Ben-Arieh, David; Wu, Chih-Hang
2016-01-01
We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as “sepsis”. Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-α ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies. PMID:27556404
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Zhong, Jian; Cai, Xiao-Ming; Bloss, William James
2017-05-01
A large eddy simulation (LES) model coupled with O 3 -NO x -VOC chemistry is implemented to simulate the coupled effects of emissions, mixing and chemical pre-processing within an idealised deep (aspect ratio = 2) urban street canyon under a weak wind condition. Reactive pollutants exhibit significant spatial variations in the presence of two vertically aligned unsteady vortices formed in the canyon. Comparison of the LES results from two chemical schemes (simple NO x -O 3 chemistry and a more comprehensive Reduced Chemical Scheme (RCS) chemical mechanism) shows that the concentrations of NO 2 and O x inside the street canyon are enhanced by approximately 30-40% via OH/HO 2 chemistry. NO, NO x , O 3 , OH and HO 2 are chemically consumed, while NO 2 and O x (total oxidant) are chemically produced within the canyon environment. Within-canyon pre-processing increases oxidant fluxes from the canyon to the overlying boundary layer, and this effect is greater for deeper street canyons (as found in many traditional European urban centres) than shallower (lower aspect ratio) streets. There is clear evidence of distinct behaviours for emitted chemical species and entrained chemical species, and positive (or negative) values of intensities of segregations are found between pairs of species with similar (or opposite) behaviour. The simplified two-box model underestimated NO and O 3 levels, but overestimated NO 2 levels for both the lower and upper canyon compared with the more realistic LES-chemistry model. This suggests that the segregation effect due to incomplete mixing reduces the chemical conversion rate of NO to NO 2 . This study reveals the impacts of nonlinear O 3 -NO x -VOC photochemical processes in the incomplete mixing environment and provides a better understanding of the pre-processing of emissions within canyons, prior to their release to the urban boundary layer, through the coupling of street canyon dynamics and chemistry. Copyright © 2017 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
De Lucia, Marco; Kempka, Thomas; Kühn, Michael
2014-05-01
Fully-coupled reactive transport simulations involving multiphase hydrodynamics and chemical reactions in heterogeneous settings are extremely challenging from a computational point of view. This often leads to oversimplification of the investigated system: coarse spatial discretization, to keep the number of elements in the order of few thousands; simplified chemistry, disregarding many potentially important reactions. A novel approach for coupling non-reactive hydrodynamic simulations with the outcome of single batch geochemical simulations was therefore introduced to assess the potential long-term mineral trapping at the Ketzin pilot site for underground CO2 storage in Germany [1],[2]. The advantage of the coupling is the ability to use multi-million grid non-reactive hydrodynamics simulations on one side and few batch 0D geochemical simulations on the other, so that the complexity of both systems does not need to be reduced. This contribution shows the approach which was taken to validate this simplified coupling scheme. The procedure involved batch simulations of the reference geochemical model, then performing both non-reactive and fully coupled 1D and 3D reactive transport simulations and finally applying the simplified coupling scheme based on the non-reactive and geochemical batch model. The TOUGHREACT/ECO2N [3] simulator was adopted for the validation. The degree of refinement of the spatial grid and the complexity and velocity of the mineral reactions, along with a cut-off value for the minimum concentration of dissolved CO2 allowed to originate precipitates in the simplified approach were found out to be the governing parameters for the convergence of the two schemes. Systematic discrepancies between the approaches are not reducible, simply because there is no feedback between chemistry and hydrodynamics, and can reach 20 % - 30 % in unfavourable cases. However, even such discrepancy is completely acceptable, in our opinion, given the amount of uncertainty underlying the geochemical models. References [1] Klein, E., De Lucia, M., Kempka, T. Kühn, M. 2013. Evaluation of longterm mineral trapping at the Ketzin pilot site for CO2 storage: an integrative approach using geochemical modelling and reservoir simulation. International Journal of Greenhouse Gas Control 19: 720-730, doi:10.1016/j.ijggc.2013.05.014 [2] Kempka, T., Klein, E., De Lucia, M., Tillner, E. Kühn, M. 2013. Assessment of Long-term CO2 Trapping Mechanisms at the Ketzin Pilot Site (Germany) by Coupled Numerical Modelling. Energy Procedia 37: 5419-5426, doi:10.1016/j.egypro.2013.06.460 [3] Xu, T., Spycher, N., Sonnenthal, E., Zhang, G., Zheng, L., Pruess, K. 2010. TOUGHREACT Version 2.0: A simulator for subsurface reactive transport under non-isothermal multiphase flow conditions, Computers & Geosciences 37(6), doi:10.1016/j.cageo.2010.10.007
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Study on improved Ip-iq APF control algorithm and its application in micro grid
NASA Astrophysics Data System (ADS)
Xie, Xifeng; Shi, Hua; Deng, Haiyingv
2018-01-01
In order to enhance the tracking velocity and accuracy of harmonic detection by ip-iq algorithm, a novel ip-iq control algorithm based on the Instantaneous reactive power theory is presented, the improved algorithm adds the lead correction link to adjust the zero point of the detection system, the Fuzzy Self-Tuning Adaptive PI control is introduced to dynamically adjust the DC-link Voltage, which meets the requirement of the harmonic compensation of the micro grid. Simulation and experimental results verify the proposed method is feasible and effective in micro grid.
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A semi-empirical approach for the chemoviscosity modeling of reactive resin system
NASA Technical Reports Server (NTRS)
Hou, T. H.; Bai, J. M.
1988-01-01
A new analytical model for simulating chemoviscosity of a thermosetting resin is presented. The model is developed on the basis of the Williams-Landel-Ferry (WLF, 1955) polymer rheology theory for the thermoplastic materials, which was modified to account for the factor of reaction time by introducing a relationship between the glass transition temperature and the degree of cure of the resin system. Theoretical predictions of the chemoviscosity profiles under dynamic curing conditions are shown to compare favorably with the experimental data obtained on the Hercules 3501-6 resin system cured under seven isothermal conditions.
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NASA Astrophysics Data System (ADS)
Xiao, Qiran; Chen, Yanping; Bereau, Tristan; Shi, Yunfeng
2016-08-01
The paradox of biomimetic research is to perform bio-functionality, usually associated with sophisticated structures optimized by nature, with minimal structural complexity for the ease of fabrication. Here we show that a three-particle trimer can exhibit kinesin-like autonomous walk on a track via reactive molecular dynamics simulations. The autonomous motion is due to imbalanced transitions resulting from exothermic catalytic reactions, and the spatial asymmetry from the track. This molecular design can be realized by reproducing the particle-particle interactions in functionalized nano- or colloidal particles. Our results open up the possibility of fabricating bio-mimetic nano-systems in a minimalist approach.
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Kumar, Ashish; Kaur, Harmeet; Jain, Abha; Nair, Deepak T; Salunke, Dinakar M
2018-01-12
Sequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure. At an optimal temperature, MP-4 achieves maximal binding while above and below the optimum temperature, its functional activity is hampered due to unfavourable flexibility and relative rigidity, respectively. The low activity at normal temperature is due to the widening of the conformational spectrum of the Reactive Site Loop (RSL) that reduces the probability of formation of stabilizing contacts with trypsin. The unique sequence of the RSL enhances flexibility at ambient temperature and thus reduces its ability to inhibit trypsin. This study shows that temperature influences the function of a protein through modulation in the structure of functional domain of the protein. Modulation of function through appearance of new sequences that are more sensitive to temperature may be a general strategy for evolution of new proteins.
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Dynamic Stabilization of Metal Oxide–Water Interfaces
DOE Office of Scientific and Technical Information (OSTI.GOV)
McBriarty, Martin E.; von Rudorff, Guido Falk; Stubbs, Joanne E.
2017-02-08
The interaction of water with metal oxide surfaces plays a crucial role in the catalytic and geochemical behavior of metal oxides. In a vast majority of studies, the interfacial structure is assumed to arise from a relatively static lowest energy configuration of atoms, even at room temperature. Using hematite (α-Fe2O3) as a model oxide, we show through a direct comparison of in situ synchrotron X-ray scattering with density functional theory-based molecular dynamics simulations that the structure of the (1102) termination is dynamically stabilized by picosecond water exchange. Simulations show frequent exchanges between terminal aquo groups and adsorbed water in locationsmore » and with partial residence times consistent with experimentally determined atomic sites and fractional occupancies. Frequent water exchange occurs even for an ultrathin adsorbed water film persisting on the surface under a dry atmosphere. The resulting time-averaged interfacial structure consists of a ridged lateral arrangement of adsorbed water molecules hydrogen bonded to terminal aquo groups. Surface pKa prediction based on bond valence analysis suggests that water exchange will influence the proton-transfer reactions underlying the acid/base reactivity at the interface. Our findings provide important new insights for understanding complex interfacial chemical processes at metal oxide–water interfaces.« less
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Dynamics and kinetics of reversible homo-molecular dimerization of polycyclic aromatic hydrocarbons
NASA Astrophysics Data System (ADS)
Mao, Qian; Ren, Yihua; Luo, K. H.; van Duin, Adri C. T.
2017-12-01
Physical dimerization of polycyclic aromatic hydrocarbons (PAHs) has been investigated via molecular dynamics (MD) simulation with the ReaxFF reactive force field that is developed to bridge the gap between the quantum mechanism and classical MD. Dynamics and kinetics of homo-molecular PAH collision under different temperatures, impact parameters, and orientations are studied at an atomic level, which is of great value to understand and model the PAH dimerization. In the collision process, the enhancement factors of homo-molecular dimerizations are quantified and found to be larger at lower temperatures or with smaller PAH instead of size independent. Within the capture radius, the lifetime of the formed PAH dimer decreases as the impact parameter increases. Temperature and PAH characteristic dependent forward and reverse rate constants of homo-molecular PAH dimerization are derived from MD simulations, on the basis of which a reversible model is developed. This model can predict the tendency of PAH dimerization as validated by pyrene dimerization experiments [H. Sabbah et al., J. Phys. Chem. Lett. 1(19), 2962 (2010)]. Results from this study indicate that the physical dimerization cannot be an important source under the typical flame temperatures and PAH concentrations, which implies a more significant role played by the chemical route.
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Zeng, Fanlin; Peng, Chao; Liu, Yizhi; Qu, Jianmin
2015-07-30
Poly(vinylidene fluoride) (PVDF) is a kind of important piezoelectric polymer used in spacecraft industry. But the atomic oxygen (AO) is the most abundant element in the low Earth orbit (LEO) environment. AO collision degradation is an important issue in the application of PVDF on spacecrafts. To investigate the erosion behaviors of PVDF during AO impacts and how to improve the stability of PVDF against AO impacts, the temperature evolution, mass loss, and erosion yields of neat PVDF, neat polyhedral oligomeric silsesquioxanes compound (3,3,3-trifluoropropyl)8Si8O12 (FP-POSS) and the PVDF/FP-POSS composite under AO impacts, as well as some key disintegrated structures and separated chemical compositions, were researched using the molecular dynamics (MD) simulations and the reactive ReaxFF force field. The simulation erosion yield result of PVDF is very close to the experiment results, which shows our simulations are reliable. The results of the temperature evolution, mass loss, and erosion yield of three materials show that the antierosion performance of PVDF is not outstanding. However, incorporating FP-POSS into PVDF matrix enhances the stability of PVDF against AO impact greatly and reduces the temperature rise, mass loss, and the erosion yield of PVDF rapidly. A detailed analysis on the flight chemical compositions and key snapshots of the structures reveals that the erosion process on PVDF and PVDF/FP-POSS is continuous and should be derived from the same PVDF matrix in two materials. In contrast, the erosion process on FP-POSS is stepped. The erosion will not take place until the number of AO reaches a specific value. There is a barrier for the erosion of high-energy AO because of the stable cagelike Si-O frame in FP-POSS molecules. This should be chiefly responsible for the high stability of FP-POSS and the reinforcement mechanism of FP-POSS on PVDF against AO impacts. This work is helpful for people to understand the erosion details of PVDF and POSS and provides valuable information to design effective protective structure for PVDF against AO impacts in LEO environment.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Fröhlich, Markus G., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu; Sewell, Thomas D., E-mail: SewellT@missouri.edu; Thompson, Donald L., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu
2014-01-14
The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup −1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structuralmore » properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.« less
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NASA Astrophysics Data System (ADS)
Toyota, K.; McConnell, J. C.; Lupu, A.; Neary, L.; McLinden, C. A.; Richter, A.; Kwok, R.; Semeniuk, K.; Kaminski, J. W.; Gong, S.-L.; Jarosz, J.; Chipperfield, M. P.; Sioris, C. E.
2011-04-01
Episodes of high bromine levels and surface ozone depletion in the springtime Arctic are simulated by an online air-quality model, GEM-AQ, with gas-phase and heterogeneous reactions of inorganic bromine species and a simple scheme of air-snowpack chemical interactions implemented for this study. Snowpack on sea ice is assumed to be the only source of bromine to the atmosphere and to be capable of converting relatively stable bromine species to photolabile Br2 via air-snowpack interactions. A set of sensitivity model runs are performed for April 2001 at a horizontal resolution of approximately 100 km×100 km in the Arctic, to provide insights into the effects of temperature and the age (first-year, FY, versus multi-year, MY) of sea ice on the release of reactive bromine to the atmosphere. The model simulations capture much of the temporal variations in surface ozone mixing ratios as observed at stations in the high Arctic and the synoptic-scale evolution of areas with enhanced BrO column amount ("BrO clouds") as estimated from satellite observations. The simulated "BrO clouds" are in modestly better agreement with the satellite measurements when the FY sea ice is assumed to be more efficient at releasing reactive bromine to the atmosphere than on the MY sea ice. Surface ozone data from coastal stations used in this study are not sufficient to evaluate unambiguously the difference between the FY sea ice and the MY sea ice as a source of bromine. The results strongly suggest that reactive bromine is released ubiquitously from the snow on the sea ice during the Arctic spring while the timing and location of the bromine release are largely controlled by meteorological factors. It appears that a rapid advection and an enhanced turbulent diffusion associated with strong boundary-layer winds drive transport and dispersion of ozone to the near-surface air over the sea ice, increasing the oxidation rate of bromide (Br-) in the surface snow. Also, if indeed the surface snowpack does supply most of the reactive bromine in the Arctic boundary layer, it appears to be capable of releasing reactive bromine at temperatures as high as -10 °C, particularly on the sea ice in the central and eastern Arctic Ocean. Dynamically-induced BrO column variability in the lowermost stratosphere appears to interfere with the use of satellite BrO column measurements for interpreting BrO variability in the lower troposphere but probably not to the extent of totally obscuring "BrO clouds" that originate from the surface snow/ice source of bromine in the high Arctic. A budget analysis of the simulated air-surface exchange of bromine compounds suggests that a "bromine explosion" occurs in the interstitial air of the snowpack and/or is accelerated by heterogeneous reactions on the surface of wind-blown snow in ambient air, both of which are not represented explicitly in our simple model but could have been approximated by a parameter adjustment for the yield of Br2 from the trigger.
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Collinear Collision Chemistry: 1. A Simple Model for Inelastic and Reactive Collision Dynamics
ERIC Educational Resources Information Center
Mahan, Bruce H.
1974-01-01
Discusses a model for the collinear collision of an atom with a diatomic molecule on a simple potential surface. Indicates that the model can provide a framework for thinking about molecular collisions and reveal many factors which affect the dynamics of reactive and inelastic collisions. (CC)
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Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.
Yang, Qian; Sing-Long, Carlos A; Reed, Evan J
2017-08-01
We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.
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Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics
Sing-Long, Carlos A.
2017-01-01
We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates. PMID:28989618
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Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics
Yang, Qian; Sing-Long, Carlos A.; Reed, Evan J.
2017-06-19
Here, we propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. Conversely, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our methodmore » on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. Furthermore, we describe a framework in this work that paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.« less
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Simulation and Theory of Ions at Atmospherically Relevant Aqueous Liquid-Air Interfaces
DOE Office of Scientific and Technical Information (OSTI.GOV)
Tobias, Douglas J.; Stern, Abraham C.; Baer, Marcel D.
2013-04-01
Chemistry occurring at or near the surfaces of aqueous droplets and thin films in the atmosphere influences air quality and climate. Molecular dynamics simulations are becoming increasingly useful for gaining atomic-scale insight into the structure and reactivity of aqueous interfaces in the atmosphere. Here we review simulation studies of atmospherically relevant aqueous liquid-air interfaces, with an emphasis on ions that play important roles in the chemistry of atmospheric aerosols. In addition to surveying results from simulation studies, we discuss challenges to the refinement and experimental validation of the methodology for simulating ion adsorption to the air-water interface, and recent advancesmore » in elucidating the driving forces for adsorption. We also review the recent development of a dielectric continuum theory that is capable of reproducing simulation and experimental data on ion behavior at aqueous interfaces. MDB and CJM acknowledge support from the US Department of Energy's Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is supported by the Linus Pauling Distinguished Postdoctoral Fellowship Program at PNNL.« less
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suk O, Jin; Jeen, Sung-Wook; Gillham, Robert W; Gui, Lai
2009-01-26
Column experiments and numerical simulation were conducted to test the hypothesis that iron material having a high corrosion rate is not beneficial for the long-term performance of iron permeable reactive barriers (PRBs) because of faster passivation of iron and greater porosity loss close to the influent face of the PRBs. Four iron materials (Connelly, Gotthart-Maier, Peerless, and ISPAT) were used for the column experiments, and the changes in reactivity toward cis-dichloroethene (cis-DCE) degradation in the presence of dissolved CaCO3 were evaluated. The experimental results showed that the difference in distribution of the accumulated precipitates, resulting from differences in iron corrosion rate, caused a difference in the migration rate of the cis-DCE profiles and a significant difference in the pattern of passivation, indicating a faster passivation in the region close to the influent end for the material having a higher corrosion rate. For the numerical simulation, the accumulation of secondary minerals and reactivity loss of iron were coupled using an empirically-derived relationship that was incorporated into a multi-component reactive transport model. The simulation results provided a reasonable representation of the evolution of iron reactivity toward cis-DCE treatment and the changes in geochemical conditions for each material, consistent with the observed data. The simulations for long-term performance were also conducted to further test the hypothesis and predict the differences in performance over a period of 40 years under typical groundwater conditions. The predictions showed that the cases of higher iron corrosion rates had earlier cis-DCE breakthrough and more reduction in porosity starting from near the influent face, due to more accumulation of carbonate minerals in that region. Therefore, both the experimental and simulation results appear to support the hypothesis and suggest that reactivity changes of iron materials resulting from evolution of geochemical conditions should be considered in the design of iron PRBs.
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Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P; Daggett, Valerie; Adkins, Joshua N
2014-06-01
Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS(3) ) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine-lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS(3), a distance constraint of 26-30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods. © 2014 The Protein Society.
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Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P; Daggett, Valerie; Adkins, Joshua N
2014-01-01
Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS3) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS3, a distance constraint of 26–30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods. PMID:24639379
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Kinetics of SiHCl3 chemical vapor deposition and fluid dynamic simulations.
Cavallotti, Carlo; Masi, Maurizio
2011-09-01
Though most of the current silicon photovoltaic technology relies on trichlorosilane (SiHCl3) as a precursor gas to deposit Si, only a few studies have been devoted to the investigation of its gas phase and surface kinetics. In the present work we propose a new kinetic mechanism apt to describe the gas phase and surface chemistry active during the deposition of Si from SiHCl3. Kinetic constants of key reactions were either taken from the literature or determined through ab initio calculations. The capability of the mechanism to reproduce experimental data was tested through the implementation of the kinetic scheme in a fluid dynamic model and in the simulation of both deposition and etching of Si in horizontal reactors. The results of the simulations show that the reactivity of HCl is of key importance in order to control the Si deposition rate. When HCl reaches a critical concentration in the gas phase it starts etching the Si surface, so that the net deposition rate is the net sum of the adsorption rate of the gas phase precursors and the etching rate due to HCl. In these conditions the possibility to further deposit Si is directly related to the rate of consumption of HCl through its reaction with SiHCl3 to give SiCl4. The proposed reaction mechanism was implemented in a 3D fluid dynamic model of a simple Siemens reactor. The simulation results indicate that the proposed interpretation of the growth process applies also to this class of reactors, which operate in what can be defined as a mixed kinetic-transport controlled regime.
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Yao, Jianzhuang; Chu, Yuzhuo; An, Ran; Guo, Hong
2012-02-27
The results of hybrid quantum mechanical/molecular mechanical (QM/MM) free energy (potential of mean force) simulations for methyl-transfer processes in SET7/9 and its Y245A mutant are compared to address the question concerning the change of the product specificity as well as catalytic efficiency due to the mutation. One of the key questions is whether or not the free energy profiles of methyl transfers may be used to predict the change of the product specificity as a result of the mutations for the residues that are not located at the Tyr/Phe switch position. The simulations show that while the wild-type SET7/9 is a monomethylase, the Y245→A mutation increases the ability of the enzyme to add more methyl groups on the target lysine (i.e., acting as a trimethylase). However, the first methyl-transfer process seems to become less efficient in the mutant compared to that in wild-type. All these results are consistent with experimental observations concerning the effects of the mutation on the product specificity and catalytic efficiency. Thus, the previous suggestion that the energetics of the methyl-transfer reactions may determine the product specificity, at least in some cases, is confirmed by the present work. Moreover, the dynamic information of the reactant complexes obtained from the QM/MM molecular dynamics simulations shows that the ability of the reactant complexes to form the reactive transition-state-like configurations may be used as an important indicator for the prediction of the product specificity of PKMTs, consistent with previous computational studies.
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Reactive Burn Model Calibration for PETN Using Ultra-High-Speed Phase Contrast Imaging
NASA Astrophysics Data System (ADS)
Johnson, Carl; Ramos, Kyle; Bolme, Cindy; Sanchez, Nathaniel; Barber, John; Montgomery, David
2017-06-01
A 1D reactive burn model (RBM) calibration for a plastic bonded high explosive (HE) requires run-to-detonation data. In PETN (pentaerythritol tetranitrate, 1.65 g/cc) the shock to detonation transition (SDT) is on the order of a few millimeters. This rapid SDT imposes experimental length scales that preclude application of traditional calibration methods such as embedded electromagnetic gauge methods (EEGM) which are very effective when used to study 10 - 20 mm thick HE specimens. In recent work at Argonne National Laboratory's Advanced Photon Source we have obtained run-to-detonation data in PETN using ultra-high-speed dynamic phase contrast imaging (PCI). A reactive burn model calibration valid for 1D shock waves is obtained using density profiles spanning the transition to detonation as opposed to particle velocity profiles from EEGM. Particle swarm optimization (PSO) methods were used to operate the LANL hydrocode FLAG iteratively to refine SURF RBM parameters until a suitable parameter set attained. These methods will be presented along with model validation simulations. The novel method described is generally applicable to `sensitive' energetic materials particularly those with areal densities amenable to radiography.
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Quantitative 3D evolution of colloidal nanoparticle oxidation in solution
Sun, Yugang; Zuo, Xiaobing; Sankaranarayanan, Subramanian K. R. S.; ...
2017-04-21
Real-time tracking three-dimensional (3D) evolution of colloidal nanoparticles in solution is essential for understanding complex mechanisms involved in nanoparticle growth and transformation. We simultaneously use time-resolved small-angle and wide-angle x-ray scattering to monitor oxidation of highly uniform colloidal iron nanoparticles, enabling the reconstruction of intermediate 3D morphologies of the nanoparticles with a spatial resolution of ~5 Å. The in-situ probing combined with large-scale reactive molecular dynamics simulations reveals the transformational details from the solid metal nanoparticles to hollow metal oxide nanoshells via nanoscale Kirkendall process, for example, coalescence of voids upon their growth, reversing of mass diffusion direction depending onmore » crystallinity, and so forth. In conclusion, our results highlight the complex interplay between defect chemistry and defect dynamics in determining nanoparticle transformation and formation.« less
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The Evolution of Latent Genes in Subdivided Populations
Moody, M. E.; Basten, C. J.
1990-01-01
We define latent genes as phenotypically silent DNA sequences which may be reactivated by various genetic mechanisms. Of interest is how they and their functional counterparts can be maintained at high frequency in the face of mutation and selection pressure. We propose a two-deme, three-allele model incorporating viability selection, mutation and migration in haploid populations. It is shown that polymorphism for the three alleles can be easily maintained for a wide range of biologically meaningful parameter values. Computer simulations were employed to gain qualitative insight into the global dynamics of the system. It was found that the dynamics of the latent allele is closely correlated with that of the functional allele. In addition, bias in the migration rates can strengthen or weaken selective conditions for preservation of the functional and latent alleles. PMID:2307354
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Quantitative 3D evolution of colloidal nanoparticle oxidation in solution
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sun, Yugang; Zuo, Xiaobing; Sankaranarayanan, Subramanian K. R. S.
Real-time tracking three-dimensional (3D) evolution of colloidal nanoparticles in solution is essential for understanding complex mechanisms involved in nanoparticle growth and transformation. We simultaneously use time-resolved small-angle and wide-angle x-ray scattering to monitor oxidation of highly uniform colloidal iron nanoparticles, enabling the reconstruction of intermediate 3D morphologies of the nanoparticles with a spatial resolution of ~5 Å. The in-situ probing combined with large-scale reactive molecular dynamics simulations reveals the transformational details from the solid metal nanoparticles to hollow metal oxide nanoshells via nanoscale Kirkendall process, for example, coalescence of voids upon their growth, reversing of mass diffusion direction depending onmore » crystallinity, and so forth. In conclusion, our results highlight the complex interplay between defect chemistry and defect dynamics in determining nanoparticle transformation and formation.« less
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NASA Astrophysics Data System (ADS)
Koizumi, Kenichi; Boero, Mauro; Shigeta, Yasuteru; Oshiyama, Atsushi; Dept. of Applied Physics Team; Institute of Physics and Chemistry of Strasbourg (IPCMS) Collaboration; Department Of Materials Engineering Science Collaboration
2013-03-01
Oxygen plasma etching is a crucial step in the fabrication of electronic circuits and has recently received a renovated interest in view of the realization of carbon-based nanodevices. In an attempt at unraveling the atomic-scale details and to provide guidelines for the control of the etching processes mechanisms, we inspected the possible reaction pathways via reactive first principles simulations. These processes involve breaking and formation of several chemical bonds and are characterized by different free-energy barriers. Free-energy sampling techniques (metadynamics and blue moon), used to enhance the standard Car-Parrinello molecular dynamics, provide us a detailed microscopic picture of the etching of graphene surfaces and a comprehensive scenario of the activation barriers involved in the various steps. MEXT, Japan - contract N. 22104005
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NASA Astrophysics Data System (ADS)
Murthy, P. Krishna; Krishnaswamy, G.; Armaković, Stevan; Armaković, Sanja J.; Suchetan, P. A.; Desai, Nivedita R.; Suneetha, V.; SreenivasaRao, R.; Bhargavi, G.; Aruna Kumar, D. B.
2018-06-01
The title compound 2-(6-hydroxy-1-benzofuran-3-yl) acetic acid (abbreviated as HBFAA) has been synthetized and characterized by FT-IR, FT-Raman and NMR spectroscopic techniques. Solid state crystal structure of HBFAA has been determined by single crystal X-ray diffraction technique. The crystal structure features O-H⋯O and C-H⋯O intermolecular interactions resulting in a two dimensional supramolecular architecture. The presence of various intermolecular interactions is well supported by the Hirshfeld surface analysis. The molecular properties of HBFAA were performed by Density functional theory (DFT) using B3LYP/6-311G++(d,p) method at ground state in gas phase, compile these results with experimental values and shows mutual agreement. The vibrational spectral analysis were carried out using FT-IR and FT-Raman spectroscopic techniques and assignment of each vibrational wavenumber made on the basis of potential energy distribution (PED). And also frontier orbital analysis (FMOs), global reactivity descriptors, non-linear optical properties (NLO) and natural bond orbital analysis (NBO) of HBFAA were computed with same method. Efforts were made in order to understand global and local reactivity properties of title compound by calculations of MEP, ALIE, BDE and Fukui function surfaces in gas phase, together with thermodynamic properties. Molecular dynamics simulation and radial distribution functions were also used in order to understand the influence of water to the stability of title compound. Charge transfer between molecules of HBFAA has been investigated thanks to the combination of MD simulations and DFT calculations.
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Dynamic power flow controllers
Divan, Deepakraj M.; Prasai, Anish
2017-03-07
Dynamic power flow controllers are provided. A dynamic power flow controller may comprise a transformer and a power converter. The power converter is subject to low voltage stresses and not floated at line voltage. In addition, the power converter is rated at a fraction of the total power controlled. A dynamic power flow controller controls both the real and the reactive power flow between two AC sources having the same frequency. A dynamic power flow controller inserts a voltage with controllable magnitude and phase between two AC sources; thereby effecting control of active and reactive power flows between two AC sources.
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Monopoly models with time-varying demand function
NASA Astrophysics Data System (ADS)
Cavalli, Fausto; Naimzada, Ahmad
2018-05-01
We study a family of monopoly models for markets characterized by time-varying demand functions, in which a boundedly rational agent chooses output levels on the basis of a gradient adjustment mechanism. After presenting the model for a generic framework, we analytically study the case of cyclically alternating demand functions. We show that both the perturbation size and the agent's reactivity to profitability variation signals can have counterintuitive roles on the resulting period-2 cycles and on their stability. In particular, increasing the perturbation size can have both a destabilizing and a stabilizing effect on the resulting dynamics. Moreover, in contrast with the case of time-constant demand functions, the agent's reactivity is not just destabilizing, but can improve stability, too. This means that a less cautious behavior can provide better performance, both with respect to stability and to achieved profits. We show that, even if the decision mechanism is very simple and is not able to always provide the optimal production decisions, achieved profits are very close to those optimal. Finally, we show that in agreement with the existing empirical literature, the price series obtained simulating the proposed model exhibit a significant deviation from normality and large volatility, in particular when underlying deterministic dynamics become unstable and complex.
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A quantum dynamics study of the benzopyran ring opening guided by laser pulses
NASA Astrophysics Data System (ADS)
Saab, Mohamad; Doriol, Loïc Joubert; Lasorne, Benjamin; Guérin, Stéphane; Gatti, Fabien
2014-10-01
The ring-opening photoisomerization of benzopyran, which occurs via a photochemical route involving a conical intersection, has been studied with quantum dynamics calculations using the multi-configuration time-dependent Hartree method (MCTDH). We introduce a mechanistic strategy to control the conversion of benzopyran to merocyanine with laser pulses. We use a six-dimensional model developed in a previous work for the potential energy surfaces (PES) based on an extension of the vibronic-coupling Hamiltonian model (diabatization method by ansatz), which depends on the most active degrees of freedom. The main objective of these quantum dynamics simulations is to provide a set of strategies that could help experimentalists to control the photoreactivity vs. photostability ratio (selectivity). In this work we present: (i) a pump-dump technique used to control the photostability, (ii) a two-step strategy to enhance the reactivity of the system: first, a pure vibrational excitation in the electronic ground state that prepares the system and, second, an ultraviolet excitation that brings the system to the first adiabatic electronic state; (iii) finally the effect of a non-resonant pulse (Stark effect) on the dynamics.
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NASA Astrophysics Data System (ADS)
Meile, C. D.; Dwyer, I.; Zhu, Q.; Polerecky, L.; Volkenborn, N.
2017-12-01
Mineralization of organic matter in marine sediments leads to the depletion of oxygen, while activities of infauna introduce oxygenated seawater to the subsurface. In permeable sediments solutes can be transported from animals and their burrows into the surrounding sediment through advection over several centimeters. The intermittency of pumping leads to a spatially heterogeneous distribution of oxidants, with the temporal dynamics depending on sediment reactivity and activity patterns of the macrofauna. Here, we present results from a series of experiments in which these dynamics are studied at high spatial and temporal resolution using planar optodes. From O2, pH and pCO2 optode data, we quantify rates of O2 consumption and dissolved inorganic carbon production, as well alkalinity dynamics, with millimeter-scale resolution. Simulating intermittent irrigation by imposed pumping patterns in thin aquaria, we derive porewater flow patterns, which together with the production and consumption rates cause the chemical distributions and the establishment of reaction fronts. Our analysis thus establishes a quantitative connection between the locally dynamic redox conditions relevant for biogeochemical transformations and macroscopic observations commonly made with sediment cores.
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NASA Astrophysics Data System (ADS)
Hossain, Mossaraf; Thomas, Renjith; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Vijayakumar, G.; Van Alsenoy, C.
2018-04-01
Two newly synthetized imidazole derivatives (1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (MPDIA) and 1-(4-bromophenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (BPDIA)) have been prepared by solvent-free synthesis pathway and their specific spectroscopic and reactive properties have been discussed based on combined experimental and computational approaches. Aside of synthesis, experimental part of this work included measurements of IR, FT-Raman and NMR spectra. All of the aforementioned spectra were also obtained computationally, within the framework of density functional theory (DFT) approach. Additionally, DFT calculations have been used in order to investigate local reactivity properties based on molecular orbital theory, molecular electrostatic potential (MEP), average local ionization energy (ALIE), Fukui functions and bond dissociation energy (BDE). Molecular dynamics (MD) simulations have been used in order to obtain radial distribution functions (RDF), which were used for identification of the atoms with pronounced interactions with water molecules. MEP showed negative regions are mainly localized over N28, O29, O35 atoms, it is represent with red colour in rainbow color scheme for MPDIA and BPDIA (which are most reactive sites for electrophilic attack). The first order hyperpolarizabilities of MPDIA and BPDIA are 20.15 and 6.10 times that of the standard NLO material urea. Potential interaction with antihypertensive protein hydrolase.
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Parker, Daniel M; Landier, Jordi; von Seidlein, Lorenz; Dondorp, Arjen; White, Lisa; Hanboonkunupakarn, Borimas; Maude, Richard J; Nosten, François H
2016-11-25
Reactive case detection is an approach that has been proposed as a tool for malaria elimination in low-transmission settings. It is an intuitively justified approach based on the concept of space-time clustering of malaria cases. When an index malaria clinical case is detected, it triggers reactive screening and treatment in the index house and neighbouring houses. However, the efficacy of this approach at varying screening radii and malaria prevalence remains ill defined. Data were obtained from a detailed demographic and geographic surveillance study in four villages on the Myanmar-Thailand border. Clinical cases were recorded at village malaria clinics and were linked back to patients' residencies. These data were used to simulate the efficacy of reactive case detection for clinical cases using rapid diagnostic tests (RDT). Simulations took clinical cases in a given month and tabulated the number of cases that would have been detected in the following month at varying screening radii around the index houses. Simulations were run independently for both falciparum and vivax malaria. Each simulation of a reactive case detection effort was run in comparison with a strategy using random selection of houses for screening. In approximately half of the screenings for falciparum and 10% for vivax it would have been impossible to detect any malaria cases regardless of the screening strategy because the screening would have occurred during times when there were no cases. When geographically linked cases were present in the simulation, reactive case detection would have only been successful at detecting most malaria cases using larger screening radii (150-m radius and above). At this screening radius and above, reactive case detection does not perform better than random screening of an equal number of houses in the village. Screening within very small radii detects only a very small proportion of cases, but despite this low performance is better than random screening with the same sample size. The results of these simulations indicate that reactive case detection for clinical cases using RDTs has limited ability in halting transmission in regions of low and unstable transmission. This is linked to high spatial heterogeneity of cases, acquisition of malaria infections outside the village, as well missing asymptomatic infections. When cases are few and sporadic, reactive case detection would result in major time and budgetary losses.
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McKnight, Diane M.; Bencala, K.E.
1989-01-01
A pH perturbation experiment was conducted in an acidic, metal-enriched, mountain stream to identify relative rates of chemical and hydrologic processes as they influence iron transport. During the experiment the pH was lowered from 4.2 to 3.2 for three hours by injection of sulfuric acid. Amorphous iron oxides are abundant on the streambed, and dissolution and photoreduction reactions resulted in a rapid increase in the dissolved iron concentration. The increase occurred simultaneously with the decrease in pH. Ferrous iron was the major aqueous iron species. The changes in the iron concentration during the experiment indicate that variation exists in the solubility properties of the hydrous iron oxides on the streambed with dissolution of at least two compartments of hydrous iron oxides contributing to the iron pulse. Spatial variations of the hydrologic properties along the stream were quantified by simulating the transport of a coinjected tracer, lithium. A simulation of iron transport, as a conservative solute, indicated that hydrologie transport had a significant role in determining downstream changes in the iron pulse. The rapidity of the changes in iron concentration indicates that a model based on dynamic equilibrium may be adequate for simulating iron transport in acid streams. A major challenge for predictive solute transport models of geochemical processes may be due to substantial spatial and seasonal variations in chemical properties of the reactive hydrous oxides in such streams, and in the physical and hydrologic properties of the stream. ?? 1989.
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Dynamic Monte Carlo description of thermal desorption processes
NASA Astrophysics Data System (ADS)
Weinketz, Sieghard
1994-07-01
The applicability of the dynamic Monte Carlo method of Fichthorn and Weinberg, in which the time evolution of a system is described in terms of the absolute number of different microscopic possible events and their associated transition rates, is discussed for the case of thermal desorption simulations. It is shown that the definition of the time increment at each successful event leads naturally to the macroscopic differential equation of desorption, in the case of simple first- and second-order processes in which the only possible events are desorption and diffusion. This equivalence is numerically demonstrated for a second-order case. In the sequence, the equivalence of this method with the Monte Carlo method of Sales and Zgrablich for more complex desorption processes, allowing for lateral interactions between adsorbates, is shown, even though the dynamic Monte Carlo method does not bear their limitation of a rapid surface diffusion condition, thus being able to describe a more complex ``kinetics'' of surface reactive processes, and therefore be applied to a wider class of phenomena, such as surface catalysis.
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NASA Astrophysics Data System (ADS)
Rodriguez Lucatero, C.; Schaum, A.; Alarcon Ramos, L.; Bernal-Jaquez, R.
2014-07-01
In this study, the dynamics of decisions in complex networks subject to external fields are studied within a Markov process framework using nonlinear dynamical systems theory. A mathematical discrete-time model is derived using a set of basic assumptions regarding the convincement mechanisms associated with two competing opinions. The model is analyzed with respect to the multiplicity of critical points and the stability of extinction states. Sufficient conditions for extinction are derived in terms of the convincement probabilities and the maximum eigenvalues of the associated connectivity matrices. The influences of exogenous (e.g., mass media-based) effects on decision behavior are analyzed qualitatively. The current analysis predicts: (i) the presence of fixed-point multiplicity (with a maximum number of four different fixed points), multi-stability, and sensitivity with respect to the process parameters; and (ii) the bounded but significant impact of exogenous perturbations on the decision behavior. These predictions were verified using a set of numerical simulations based on a scale-free network topology.
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Ballistic Fracturing of Carbon Nanotubes.
Ozden, Sehmus; Machado, Leonardo D; Tiwary, ChandraSekhar; Autreto, Pedro A S; Vajtai, Robert; Barrera, Enrique V; Galvao, Douglas S; Ajayan, Pulickel M
2016-09-21
Advanced materials with multifunctional capabilities and high resistance to hypervelocity impact are of great interest to the designers of aerospace structures. Carbon nanotubes (CNTs) with their lightweight and high strength properties are alternative to metals and/or metallic alloys conventionally used in aerospace applications. Here we report a detailed study on the ballistic fracturing of CNTs for different velocity ranges. Our results show that the highly energetic impacts cause bond breakage and carbon atom rehybridizations, and sometimes extensive structural reconstructions were also observed. Experimental observations show the formation of nanoribbons, nanodiamonds, and covalently interconnected nanostructures, depending on impact conditions. Fully atomistic reactive molecular dynamics simulations were also carried out in order to gain further insights into the mechanism behind the transformation of CNTs. The simulations show that the velocity and relative orientation of the multiple colliding nanotubes are critical to determine the impact outcome.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ulvestad, Andrew; Sasikumar, Kiran; Kim, Jong Woo
Multielectron transfer processes are crucially important in energy and biological science but require favorable catalysts to achieve fast kinetics. Nanostructuring catalysts can dramatically improve their properties, which can be difficult to understand due to strain- and size-dependent thermodynamics, the influence of defects, and substrate-dependent activities. Here, we report three-dimensional (3D) imaging of single gold nanoparticles during catalysis of ascorbic acid decomposition using Bragg coherent diffractive imaging (BCDI). Local strains were measured in single nanoparticles and modeled using reactive molecular dynamics (RMD) simulations and finite element analysis (FEA) simulations. RMD reveals the pathway for local strain generation in the gold lattice:more » chemisorption of hydroxyl ions. FEA reveals that the RMD results are transferable to the nanocrystal sizes studied in the experiment. Our study probes the strain-activity connection and opens a powerful avenue for theoretical and experimental studies of nanocrystal catalysis.« less
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Le, Minh-Quy
2018-05-11
Although various phosphorene allotropes have been theoretically predicted to be stable at 0 K, the mechanical properties and fracture mechanism at room temperature remain unclear for many of them. We investigate through reactive molecular dynamics simulations at room temperature the mechanical properties of phosphorene allotropes including: five sheets with hexagonal structures (β-, γ-, δ-, θ-, and α-phosphorene), one sheet with 4-8 membered rings (4-8-P), and two sheets with 5-7 membered rings. High, moderate and slight anisotropies in their mechanical properties are observed, depending on their crystal structures. Their Young's moduli and tensile strength are approximately in the range from 7.3% through 25%, and from 8.6% through 22% of those of graphene, respectively. At the early stage of fracture, eye-shaped cracks are formed by local bond breaking and perpendicular to the tensile direction in hexagonal and 4-8-P sheets. Complete fractures take place with straight cracks in these hexagonal sheets under tension along the zigzag direction and under tension along the square edge direction in the 4-8-P sheet. Crack meandering and branching are observed during the tension of α-, β-, and γ-phosphorene along the armchair direction; and along the square diagonal direction in the 4-8-P sheet. Under uniaxial tension of two phosphorene sheets with 5-7 atom rings, 12 and 10 membered rings are formed by merging two neighbor heptagons, and a heptagon and its neighbor pentagon, respectively. These 12 and 10 membered rings coalesce subsequently, causing the failure of these two sheets. The results are of great importance in the design of these novel phosphorene allotropes.
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NASA Astrophysics Data System (ADS)
Le, Minh-Quy
2018-05-01
Although various phosphorene allotropes have been theoretically predicted to be stable at 0 K, the mechanical properties and fracture mechanism at room temperature remain unclear for many of them. We investigate through reactive molecular dynamics simulations at room temperature the mechanical properties of phosphorene allotropes including: five sheets with hexagonal structures (β-, γ-, δ-, θ-, and α-phosphorene), one sheet with 4-8 membered rings (4-8-P), and two sheets with 5-7 membered rings. High, moderate and slight anisotropies in their mechanical properties are observed, depending on their crystal structures. Their Young’s moduli and tensile strength are approximately in the range from 7.3% through 25%, and from 8.6% through 22% of those of graphene, respectively. At the early stage of fracture, eye-shaped cracks are formed by local bond breaking and perpendicular to the tensile direction in hexagonal and 4-8-P sheets. Complete fractures take place with straight cracks in these hexagonal sheets under tension along the zigzag direction and under tension along the square edge direction in the 4-8-P sheet. Crack meandering and branching are observed during the tension of α-, β-, and γ-phosphorene along the armchair direction; and along the square diagonal direction in the 4-8-P sheet. Under uniaxial tension of two phosphorene sheets with 5-7 atom rings, 12 and 10 membered rings are formed by merging two neighbor heptagons, and a heptagon and its neighbor pentagon, respectively. These 12 and 10 membered rings coalesce subsequently, causing the failure of these two sheets. The results are of great importance in the design of these novel phosphorene allotropes.
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Bedrov, Dmitry; Smith, Grant D; van Duin, Adri C T
2012-03-22
We have conducted quantum chemistry calculations and gas- and solution-phase reactive molecular dynamics simulation studies of reactions involving the ethylene carbonate (EC) radical anion EC(-) using the reactive force field ReaxFF. Our studies reveal that the substantial barrier for transition from the closed (cyclic) form, denoted c-EC(-), of the radical anion to the linear (open) form, denoted o-EC(-), results in a relatively long lifetime of the c-EC(-) allowing this compound to react with other singly reduced alkyl carbonates. Using ReaxFF, we systematically investigate the fate of both c-EC(-) and o-EC(-) in the gas phase and EC solution. In the gas phase and EC solutions with a relatively low concentration of Li(+)/x-EC(-) (where x = o or c), radical termination reactions between radical pairs to form either dilithium butylene dicarbonate (CH(2)CH(2)OCO(2)Li)(2) (by reacting two Li(+)/o-EC(-)) or ester-carbonate compound (by reacting Li(+)/o-EC(-) with Li(+)/c-EC(-)) are observed. At higher concentrations of Li(+)/x-EC(-) in solution, we observe the formation of diradicals which subsequently lead to formation of longer alkyl carbonates oligomers through reaction with other radicals or, in some cases, formation of (CH(2)OCO(2)Li)(2) through elimination of C(2)H(4). We conclude that the local ionic concentration is important in determining the fate of x-EC(-) and that the reaction of c-EC(-) with o-EC(-) may compete with the formation of various alkyl carbonates from o-EC(-)/o-EC(-) reactions. © 2012 American Chemical Society
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2012-02-28
Interaction Model based on Accelerated Reactive Molecular Dynamics for Hypersonic conditions including Thermal Conduction FA9550-09-1-0157 Schwartzentruber...Dynamics for Hypersonic Conditions including Thermal Conduction Grant/Contract Number: FA9550-09-1-0157 Program Manager: Dr. John Schmisseur PI...through the boundary layer and may chemically react with the vehicle’s thermal protection system (TPS). Many TPS materials act as a catalyst for the
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Patterning of supported gold monolayers via chemical lift-off lithography
Slaughter, Liane S; Cheung, Kevin M; Kaappa, Sami; Cao, Huan H; Yang, Qing; Young, Thomas D; Serino, Andrew C; Malola, Sami; Olson, Jana M; Link, Stephan
2017-01-01
The supported monolayer of Au that accompanies alkanethiolate molecules removed by polymer stamps during chemical lift-off lithography is a scarcely studied hybrid material. We show that these Au–alkanethiolate layers on poly(dimethylsiloxane) (PDMS) are transparent, functional, hybrid interfaces that can be patterned over nanometer, micrometer, and millimeter length scales. Unlike other ultrathin Au films and nanoparticles, lifted-off Au–alkanethiolate thin films lack a measurable optical signature. We therefore devised fabrication, characterization, and simulation strategies by which to interrogate the nanoscale structure, chemical functionality, stoichiometry, and spectral signature of the supported Au–thiolate layers. The patterning of these layers laterally encodes their functionality, as demonstrated by a fluorescence-based approach that relies on dye-labeled complementary DNA hybridization. Supported thin Au films can be patterned via features on PDMS stamps (controlled contact), using patterned Au substrates prior to lift-off (e.g., selective wet etching), or by patterning alkanethiols on Au substrates to be reactive in selected regions but not others (controlled reactivity). In all cases, the regions containing Au–alkanethiolate layers have a sub-nanometer apparent height, which was found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure. PMID:29259879
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Simulation Study on Jet Formability and Damage Characteristics of a Low-Density Material Liner
Tang, Wenhui; Ran, Xianwen
2018-01-01
The shaped charge tandem warhead is an effective weapon against the ERA (explosive reactive armor). Whether the pre-warhead can reliably initiate the ERA directly determines the entire performance of the tandem warhead. The existing shaped charge pre-warhead mostly adopts a metal shaped jet, which effectively initiates the ERA, but interferes the main shaped jet. This article, on the other hand, explores the possibility of producing a pre-warhead using a low-density material as the liner. The nonlinear dynamic analysis software Autodyn-2D is used to simulate and compare three kinds of low-density shaped jets, including floatglass, Lucite, and Plexiglas, to the copper shaped jet in the effectiveness of impacting ERA. Based on the integrative criteria (including u-d initiation criterion, explosive reactive degree, explosive pressure, and particle velocity of the panels), it can be determined whether the low-density shaped jet can reliably initiate the sandwich charge. The results show that the three kinds of low-density shaped jets can not only initiate the reaction armor, but are also superior to the existing copper shaped jet in ductility, jet tip velocity, jet tip diameter, and the mass; namely, it is feasible to use the low-density material shaped jet to destroy the ERA. PMID:29300351
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Keinan, Shahar; Nocek, Judith M; Hoffman, Brian M; Beratan, David N
2012-10-28
Formation of a transient [myoglobin (Mb), cytochrome b(5) (cyt b(5))] complex is required for the reductive repair of inactive ferri-Mb to its functional ferro-Mb state. The [Mb, cyt b(5)] complex exhibits dynamic docking (DD), with its cyt b(5) partner in rapid exchange at multiple sites on the Mb surface. A triple mutant (Mb(3M)) was designed as part of efforts to shift the electron-transfer process to the simple docking (SD) regime, in which reactive binding occurs at a restricted, reactive region on the Mb surface that dominates the docked ensemble. An electrostatically-guided brownian dynamics (BD) docking protocol was used to generate an initial ensemble of reactive configurations of the complex between unrelaxed partners. This ensemble samples a broad and diverse array of heme-heme distances and orientations. These configurations seeded all-atom constrained molecular dynamics simulations (MD) to generate relaxed complexes for the calculation of electron tunneling matrix elements (T(DA)) through tunneling-pathway analysis. This procedure for generating an ensemble of relaxed complexes combines the ability of BD calculations to sample the large variety of available conformations and interprotein distances, with the ability of MD to generate the atomic level information, especially regarding the structure of water molecules at the protein-protein interface, that defines electron-tunneling pathways. We used the calculated T(DA) values to compute ET rates for the [Mb(wt), cyt b(5)] complex and for the complex with a mutant that has a binding free energy strengthened by three D/E → K charge-reversal mutations, [Mb(3M), cyt b(5)]. The calculated rate constants are in agreement with the measured values, and the mutant complex ensemble has many more geometries with higher T(DA) values than does the wild-type Mb complex. Interestingly, water plays a double role in this electron-transfer system, lowering the tunneling barrier as well as inducing protein interface remodeling that screens the repulsion between the negatively-charged propionates of the two hemes.
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PHT3D-UZF: A reactive transport model for variably-saturated porous media
Wu, Ming Zhi; Post, Vincent E. A.; Salmon, S. Ursula; Morway, Eric D.; Prommer, H.
2016-01-01
A modified version of the MODFLOW/MT3DMS-based reactive transport model PHT3D was developed to extend current reactive transport capabilities to the variably-saturated component of the subsurface system and incorporate diffusive reactive transport of gaseous species. Referred to as PHT3D-UZF, this code incorporates flux terms calculated by MODFLOW's unsaturated-zone flow (UZF1) package. A volume-averaged approach similar to the method used in UZF-MT3DMS was adopted. The PHREEQC-based computation of chemical processes within PHT3D-UZF in combination with the analytical solution method of UZF1 allows for comprehensive reactive transport investigations (i.e., biogeochemical transformations) that jointly involve saturated and unsaturated zone processes. Intended for regional-scale applications, UZF1 simulates downward-only flux within the unsaturated zone. The model was tested by comparing simulation results with those of existing numerical models. The comparison was performed for several benchmark problems that cover a range of important hydrological and reactive transport processes. A 2D simulation scenario was defined to illustrate the geochemical evolution following dewatering in a sandy acid sulfate soil environment. Other potential applications include the simulation of biogeochemical processes in variably-saturated systems that track the transport and fate of agricultural pollutants, nutrients, natural and xenobiotic organic compounds and micropollutants such as pharmaceuticals, as well as the evolution of isotope patterns.
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Measuring and monitoring KIPT Neutron Source Facility Reactivity
DOE Office of Scientific and Technical Information (OSTI.GOV)
Cao, Yan; Gohar, Yousry; Zhong, Zhaopeng
2015-08-01
Argonne National Laboratory (ANL) of USA and Kharkov Institute of Physics and Technology (KIPT) of Ukraine have been collaborating on developing and constructing a neutron source facility at Kharkov, Ukraine. The facility consists of an accelerator-driven subcritical system. The accelerator has a 100 kW electron beam using 100 MeV electrons. The subcritical assembly has k eff less than 0.98. To ensure the safe operation of this neutron source facility, the reactivity of the subcritical core has to be accurately determined and continuously monitored. A technique which combines the area-ratio method and the flux-to-current ratio method is purposed to determine themore » reactivity of the KIPT subcritical assembly at various conditions. In particular, the area-ratio method can determine the absolute reactivity of the subcritical assembly in units of dollars by performing pulsed-neutron experiments. It provides reference reactivities for the flux-to-current ratio method to track and monitor the reactivity deviations from the reference state while the facility is at other operation modes. Monte Carlo simulations are performed to simulate both methods using the numerical model of the KIPT subcritical assembly. It is found that the reactivities obtained from both the area-ratio method and the flux-to-current ratio method are spatially dependent on the neutron detector locations and types. Numerical simulations also suggest optimal neutron detector locations to minimize the spatial effects in the flux-to-current ratio method. The spatial correction factors are calculated using Monte Carlo methods for both measuring methods at the selected neutron detector locations. Monte Carlo simulations are also performed to verify the accuracy of the flux-to-current ratio method in monitoring the reactivity swing during a fuel burnup cycle.« less
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Performance evaluation of reactive and proactive routing protocol in IEEE 802.11 ad hoc network
NASA Astrophysics Data System (ADS)
Hamma, Salima; Cizeron, Eddy; Issaka, Hafiz; Guédon, Jean-Pierre
2006-10-01
Wireless technology based on the IEEE 802.11 standard is widely deployed. This technology is used to support multiple types of communication services (data, voice, image) with different QoS requirements. MANET (Mobile Adhoc NETwork) does not require a fixed infrastructure. Mobile nodes communicate through multihop paths. The wireless communication medium has variable and unpredictable characteristics. Furthermore, node mobility creates a continuously changing communication topology in which paths break and new one form dynamically. The routing table of each router in an adhoc network must be kept up-to-date. MANET uses Distance Vector or Link State algorithms which insure that the route to every host is always known. However, this approach must take into account the adhoc networks specific characteristics: dynamic topologies, limited bandwidth, energy constraints, limited physical security, ... Two main routing protocols categories are studied in this paper: proactive protocols (e.g. Optimised Link State Routing - OLSR) and reactive protocols (e.g. Ad hoc On Demand Distance Vector - AODV, Dynamic Source Routing - DSR). The proactive protocols are based on periodic exchanges that update the routing tables to all possible destinations, even if no traffic goes through. The reactive protocols are based on on-demand route discoveries that update routing tables only for the destination that has traffic going through. The present paper focuses on study and performance evaluation of these categories using NS2 simulations. We have considered qualitative and quantitative criteria. The first one concerns distributed operation, loop-freedom, security, sleep period operation. The second are used to assess performance of different routing protocols presented in this paper. We can list end-to-end data delay, jitter, packet delivery ratio, routing load, activity distribution. Comparative study will be presented with number of networking context consideration and the results show the appropriate routing protocol for two kinds of communication services (data and voice).
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Residence time revisited: The role of radiocarbon in reactive transport modeling
NASA Astrophysics Data System (ADS)
Lawrence, C. R.; Druhan, J. L.; Schulz, M. S.
2016-12-01
In recent years, our changing understanding of the dominant controls on soil carbon (C) storage and stability has cast a greater emphasis on the importance of physical and hydrological processes. These shifts in our understanding of C cycling have fostered increasingly commonplace measurements of soil physical and hydrological parameters in soil C studies (e.g. specific surface area, quantitative mineralogy, porosity) that reflect the importance of microbial accessibility to soil C. As a result, we are now poised to reassess the applicability of our approaches for conceptualizing and modeling soil C dynamics, particularly with regard to our representation of soil C pools. The goal of this work is to explore how the quantity and turnover of C, as approximated by radiocarbon measurements, is mechanistically linked to the physical and hydrologic parameters of soils. We utilize a reactive transport (RT) approach to link hydrologic transport, geochemical transformations and microbial activity influencing the magnitude and residence time of different carbon pools under variably saturated conditions. A newly developed version of the CrunchTope software is used to explicitly simulate the coupled transport, transformation, fractionation and decay of the three isotopes of carbon (12C, 13C and 14C) through a mechanistic framework. We constrain this model with a high-resolution dataset of soil carbon content, stable isotope composition and radiocarbon ages as well as physical and hydrologic data measured from a chronosequence of soils located near Santa Cruz, California. The Santa Cruz dataset is highly amenable to this task in that it demonstrates both seasonal and millennial variations in soil C distributions and associated soil properties. We present data from a series of simulations examining the sensitivity of C stocks, fluxes and mean residence times to transient processes spanning a range of temporal scales, including redox conditions, fluid flow and the distribution of reactive mineral surfaces. The results of these efforts show the promise of a modeling approach where the varied residence time of soil C emerges from the dynamic physical and hydrologic properties of the model rather than from an a priori assignment of operationally defined pools.
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Ogino, Takamichi; Ueda, Takayuki; Ogami, Koichiro; Koike, Takashi; Sakurai, Kaoru
2017-01-01
We examined how chewing rate and the extent of reactive hyperemia affect the blood flow in denture-supporting mucosa during chewing. The left palatal mucosa was loaded under conditions of simulated chewing or simulated clenching for 30s, and the blood flow during loading was recorded. We compared the relative blood flow during loading under conditions that recreated different chewing rates by combining duration of chewing cycle (DCC) and occlusal time (OT): fast chewing group, typical chewing group, slow chewing group and clenching group. The relationship between relative blood flow during simulated chewing and the extent of reactive hyperemia was also analyzed. When comparing the different chewing rate, the relative blood flow was highest in fast chewing rate, followed by typical chewing rate and slow chewing rate. Accordingly, we suggest that fast chewing increases the blood flow more than typical chewing or slow chewing. There was a significant correlation between the amount of blood flow during simulated chewing and the extent of reactive hyperemia. Within the limitations of this study, we concluded that slow chewing induced less blood flow than typical or fast chewing in denture-supporting mucosa and that people with less reactive hyperemia had less blood flow in denture-supporting mucosa during chewing. Copyright © 2016 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Srivastava, Ashish Kumar, E-mail: ashish.memech@gmail.com; Singh, Akhileshwar; Mokhalingam, A.
Atomistic simulations were conducted to estimate the effect of the carbon nanotube (CNT) reinforcement on the mechanical behavior of CNT-reinforced aluminum (Al) nanocomposite. The periodic system of CNT-Al nanocomposite was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The mechanical properties of the nanocomposite were investigated by the application of uniaxial load on one end of the representative volume element (RVE) and fixing the other end. The interactions between the atoms of Al were modeled using embedded atom method (EAM) potentials, whereas Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used for themore » interactions among carbon atoms and these pair potentials are coupled with the Lennard-Jones (LJ) potential. The results show that the incorporation of CNT into the Al matrix can increase the Young’s modulus of the nanocomposite substantially. In the present case, i.e. for approximately 9 with % reinforcement of CNT can increase the axial Young’s modulus of the Al matrix up to 77 % as compared to pure Al.« less
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Shan, Tzu-Ray; Wixom, Ryan R; Mattsson, Ann E; Thompson, Aidan P
2013-01-24
The dependence of the reaction initiation mechanism of pentaerythritol tetranitrate (PETN) on shock orientation and shock strength is investigated with molecular dynamics simulations using a reactive force field and the multiscale shock technique. In the simulations, a single crystal of PETN is shocked along the [110], [001], and [100] orientations with shock velocities in the range 3-10 km/s. Reactions occur with shock velocities of 6 km/s or stronger, and reactions initiate through the dissociation of nitro and nitrate groups from the PETN molecules. The most sensitive orientation is [110], while [100] is the most insensitive. For the [001] orientation, PETN decomposition via nitro group dissociation is the dominant reaction initiation mechanism, while for the [110] and [100] orientations the decomposition is via mixed nitro and nitrate group dissociation. For shock along the [001] orientation, we find that CO-NO(2) bonds initially acquire more kinetic energy, facilitating nitro dissociation. For the other two orientations, C-ONO(2) bonds acquire more kinetic energy, facilitating nitrate group dissociation.
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Brief analysis of Jiangsu grid security and stability based on multi-infeed DC index in power system
NASA Astrophysics Data System (ADS)
Zhang, Wenjia; Wang, Quanquan; Ge, Yi; Huang, Junhui; Chen, Zhengfang
2018-02-01
The impact of Multi-infeed HVDC has gradually increased to security and stability operating in Jiangsu power grid. In this paper, an appraisal method of Multi-infeed HVDC power grid security and stability is raised with Multi-Infeed Effective Short Circuit Ratio, Multi-Infeed Interaction Factor and Commutation Failure Immunity Index. These indices are adopted in security and stability simulating calculation of Jiangsu Multi-infeed HVDC system. The simulation results indicate that Jiangsu power grid is operating with a strong DC system. It has high level of power grid security and stability, and meet the safety running requirements. Jinpin-Suzhou DC system is located in the receiving end with huge capacity, which is easily leading to commutation failure of the transmission line. In order to resolve this problem, dynamic reactive power compensation can be applied in power grid near Jinpin-Suzhou DC system. Simulation result shows this method is feasible to commutation failure.
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Fracture Simulation of Highly Crosslinked Polymer Networks: Triglyceride-Based Adhesives
NASA Astrophysics Data System (ADS)
Lorenz, Christian; Stevens, Mark; Wool, Richard
2003-03-01
The ACRES program at the U. of Delaware has shown that triglyceride oils derived from plants are a favorable alternative to the traditional adhesives. The triglyceride networks are formed from an initial mixture of styrene monomers, free-radical initiators and triglycerides. We have performed simulations to study the effect of physical composition and physical characteristics of the triglyceride network on the strength of triglyceride network. A coarse-grained, bead-spring model of the triglyceride system is used. The average triglyceride consists of 6 beads per chain, the styrenes are represented as a single bead and the initiators are two bead chains. The polymer network is formed using an off-lattice 3D Monte Carlo simulation, in which the initiators activate the styrene and triglyceride reactive sites and then bonds are randomly formed between the styrene and active triglyceride monomers producing a highly crosslinked polymer network. Molecular dynamics simulations of the network under tensile and shear strains were performed to determine the strength as a function of the network composition. The relationship between the network structure and its strength will also be discussed.
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Lo, Rabindranath; Ganguly, Bishwajit
2014-07-29
Organophosphorus nerve agents are highly toxic compounds which strongly inhibit acetylcholinesterase (AChE) in the blood and in the central nervous system (CNS). Tabun is one of the highly toxic organophosphorus (OP) compounds and is resistant to many oxime drugs formulated for the reactivation of AChE. The reactivation mechanism of tabun-conjugated AChE with various drugs has been examined with density functional theory and ab initio quantum chemical calculations. The presence of a lone-pair located on the amidic group resists the nucleophilic attack at the phosphorus center of the tabun-conjugated AChE. We have shown that the newly designed drug candidate N-(pyridin-2-yl)hydroxylamine, at the MP2/6-31+G*//M05-2X/6-31G* level in the aqueous phase with the polarizable continuum solvation model (PCM), is more effective in reactivating the tabun-conjugated AChE than typical oxime drugs. The rate determining activation barrier with N-(pyridin-2-yl)hydroxylamine was found to be ∼1.7 kcal mol(-1), which is 7.2 kcal mol(-1) lower than the charged oxime trimedoxime (one of the most efficient reactivators in tabun poisonings). The greater nucleophilicity index (ω(-)) and higher CHelpG charge of pyridinylhydroxylamine compared to TMB4 support this observation. Furthermore, we have also examined the reactivation process of tabun-inhibited AChE with some other bis-quaternary oxime drug candidates such as methoxime (MMB4) and obidoxime. The docking analysis suggests that charged bis-quaternary pyridinium oximes have greater binding affinity inside the active-site gorge of AChE compared to the neutral pyridinylhydroxylamine. The peripheral ligand attached to the neutral pyridinylhydroxylamine enhanced the binding with the aromatic residues in the active-site gorge of AChE through effective π-π interactions. Steered molecular dynamics (SMD) simulations have also been performed with the charged oxime (TMB4) and the neutral hydroxylamine. From protein-drug interaction parameters (rupture force profiles, hydrogen bonds, hydrophobic interactions), geometry and the orientation of the drug candidates, the hydroxylamine is suggested to orchestrate the reactivation process better than TMB4. Furthermore, the calculated log P values show the effective penetration of the neutral drug candidate through the blood-brain barrier. The toxicity measurements and the IC50 values (a measure of the intrinsic affinity toward AChE) suggest that the pyridinylhydroxylamine compound could have similar toxic behavior compared to the prototype oxime antidotes used for reactivation purposes. The newly designed pyridinylhydroxylamine drug candidate can be an effective antidote both kinetically and structurally to reactivate the tabun-inhibited enzyme.
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Numerical modelling of multiphase multicomponent reactive transport in the Earth's interior
NASA Astrophysics Data System (ADS)
Oliveira, Beñat; Afonso, Juan Carlos; Zlotnik, Sergio; Diez, Pedro
2018-01-01
We present a conceptual and numerical approach to model processes in the Earth's interior that involve multiple phases that simultaneously interact thermally, mechanically and chemically. The approach is truly multiphase in the sense that each dynamic phase is explicitly modelled with an individual set of mass, momentum, energy and chemical mass balance equations coupled via interfacial interaction terms. It is also truly multicomponent in the sense that the compositions of the system and its constituent phases are expressed by a full set of fundamental chemical components (e.g. SiO2, Al2O3, MgO, etc.) rather than proxies. These chemical components evolve, react with and partition into different phases according to an internally consistent thermodynamic model. We combine concepts from Ensemble Averaging and Classical Irreversible Thermodynamics to obtain sets of macroscopic balance equations that describe the evolution of systems governed by multiphase multicomponent reactive transport (MPMCRT). Equilibrium mineral assemblages, their compositions and physical properties, and closure relations for the balance equations are obtained via a `dynamic' Gibbs free-energy minimization procedure (i.e. minimizations are performed on-the-fly as needed by the simulation). Surface tension and surface energy contributions to the dynamics and energetics of the system are taken into account. We show how complex rheologies, that is, visco-elasto-plastic, and/or different interfacial models can be incorporated into our MPMCRT ensemble-averaged formulation. The resulting model provides a reliable platform to study the dynamics and nonlinear feedbacks of MPMCRT systems of different nature and scales, as well as to make realistic comparisons with both geophysical and geochemical data sets. Several numerical examples are presented to illustrate the benefits and limitations of the model.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Schlatterer, Joerg C., E-mail: joerg.schlatterer@einstein.yu.edu; Wieder, Matthew S.; Jones, Christopher D.
2012-08-24
Highlights: Black-Right-Pointing-Pointer RNA structure is mapped by pyrite mediated {sup {center_dot}}OH footprinting. Black-Right-Pointing-Pointer Repetitive experiments can be done in a powdered pyrite filled cartridge. Black-Right-Pointing-Pointer High {sup {center_dot}}OH reactivity of nucleotides imply dynamic role in Diels-Alderase catalysis. -- Abstract: In RNA, function follows form. Mapping the surface of RNA molecules with chemical and enzymatic probes has revealed invaluable information about structure and folding. Hydroxyl radicals ({sup {center_dot}}OH) map the surface of nucleic acids by cutting the backbone where it is accessible to solvent. Recent studies showed that a microfluidic chip containing pyrite (FeS{sub 2}) can produce sufficient {sup {center_dot}}OH tomore » footprint DNA. The 49-nt Diels-Alder RNA enzyme catalyzes the C-C bond formation between a diene and a dienophile. A crystal structure, molecular dynamics simulation and atomic mutagenesis studies suggest that nucleotides of an asymmetric bulge participate in the dynamic architecture of the ribozyme's active center. Of note is that residue U42 directly interacts with the product in the crystallized RNA/product complex. Here, we use powdered pyrite held in a commercially available cartridge to footprint the Diels-Alderase ribozyme with single nucleotide resolution. Residues C39 to U42 are more reactive to {sup {center_dot}}OH than predicted by the solvent accessibility calculated from the crystal structure suggesting that this loop is dynamic in solution. The loop's flexibility may contribute to substrate recruitment and product release. Our implementation of pyrite-mediated {sup {center_dot}}OH footprinting is a readily accessible approach to gleaning information about the architecture of small RNA molecules.« less
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Unraveling the role of protein dynamics in dihydrofolate reductase catalysis
Luk, Louis Y. P.; Javier Ruiz-Pernía, J.; Dawson, William M.; Roca, Maite; Loveridge, E. Joel; Glowacki, David R.; Harvey, Jeremy N.; Mulholland, Adrian J.; Tuñón, Iñaki; Moliner, Vicent; Allemann, Rudolf K.
2013-01-01
Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy (15N, 13C, 2H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for “promoting motions” in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate. PMID:24065822
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Dang, Liem X.; Schenter, Gregory K.
To enhance our understanding of the solvent exchange mechanism in liquid methanol, we report a systematic study of this process using molecular dynamics simulations. We use transition state theory, the Impey-Madden-McDonald method, the reactive flux method, and Grote-Hynes theory to compute the rate constants for this process. Solvent coupling was found to dominate, resulting in a significantly small transmission coefficient. We predict a positive activation volume for the methanol exchange process. The essential features of the dynamics of the system as well as the pressure dependence are recovered from a Generalized Langevin Equation description of the dynamics. We find thatmore » the dynamics and response to anharmonicity can be decomposed into two time regimes, one corresponding to short time response (< 0.1 ps) and long time response (> 5 ps). An effective characterization of the process results from launching dynamics from the planar hypersurface corresponding to Grote-Hynes theory. This results in improved numerical convergence of correlation functions. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less
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Imaging dynamic fingerprints of competing E2 and SN2 reactions.
Carrascosa, Eduardo; Meyer, Jennifer; Zhang, Jiaxu; Stei, Martin; Michaelsen, Tim; Hase, William L; Yang, Li; Wester, Roland
2017-06-21
The competition between bimolecular nucleophilic substitution and base-induced elimination is of fundamental importance for the synthesis of pure samples in organic chemistry. Many factors that influence this competition have been identified over the years, but the underlying atomistic dynamics have remained difficult to observe. We present product velocity distributions for a series of reactive collisions of the type X - + RY with X and Y denoting the halogen atoms fluorine, chlorine and iodine. By increasing the size of the residue R from methyl to tert-butyl in several steps, we find that the dynamics drastically change from backward to dominant forward scattering of the leaving ion relative to the reactant RY velocity. This characteristic fingerprint is also confirmed by direct dynamics simulations for ethyl as residue and attributed to the dynamics of elimination reactions. This work opens the door to a detailed atomistic understanding of transformation reactions in even larger systems.The competition between chemical reactions critically affects our natural environment and the synthesis of new materials. Here, the authors present an approach to directly image distinct fingerprints of essential organic reactions and monitor their competition as a function of steric substitution.
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Petrov, Drazen; Zagrovic, Bojan
2011-05-11
One of the most important irreversible oxidative modifications of proteins is carbonylation, the process of introducing a carbonyl group in reaction with reactive oxygen species. Notably, carbonylation increases with the age of cells and is associated with the formation of intracellular protein aggregates and the pathogenesis of age-related disorders such as neurodegenerative diseases and cancer. However, it is still largely unclear how carbonylation affects protein structure, dynamics, and aggregability at the atomic level. Here, we use classical molecular dynamics simulations to study structure and dynamics of the carbonylated headpiece domain of villin, a key actin-organizing protein. We perform an exhaustive set of molecular dynamics simulations of a native villin headpiece together with every possible combination of carbonylated versions of its seven lysine, arginine, and proline residues, quantitatively the most important carbonylable amino acids. Surprisingly, our results suggest that high levels of carbonylation, far above those associated with cell death in vivo, may be required to destabilize and unfold protein structure through the disruption of specific stabilizing elements, such as salt bridges or proline kinks, or tampering with the hydrophobic effect. On the other hand, by using thermodynamic integration and molecular hydrophobicity potential approaches, we quantitatively show that carbonylation of hydrophilic lysine and arginine residues is equivalent to introducing hydrophobic, charge-neutral mutations in their place, and, by comparison with experimental results, we demonstrate that this by itself significantly increases the intrinsic aggregation propensity of both structured, native proteins and their unfolded states. Finally, our results provide a foundation for a novel experimental strategy to study the effects of carbonylation on protein structure, dynamics, and aggregability using site-directed mutagenesis. © 2011 American Chemical Society
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Jallu, Vincent; Poulain, Pierre; Fuchs, Patrick F J; Kaplan, Cecile; de Brevern, Alexandre G
2014-10-01
The human platelet alloantigen (HPA)-1 system, the first cause of alloimmune thrombocytopenia in Caucasians, results from leucine-to-proline substitution (alleles 1a and 1b) of residue 33 in β3 subunit of the integrin αIIbβ3. A third variant with a valine (V33) has been described. Although leucine and valine share similar physicochemical properties, sera containing alloantibodies to the HPA-1a antigen variably reacted with V33-β3, suggesting structural alterations of β3. To analyze the effect of the L33V transition, molecular dynamics simulations were performed on a 3D structural model of the V33 form of the whole β3 extracellular domain (690 residues). Dynamics of the PSI (carrying residue 33), I-EGF-1, and I-EGF-2 domains of β3 were compared to previously obtained dynamics of HPA-1a structure and HPA-1b structural model using classical and innovative developments (a structural alphabet). Clustering approach and local structure analysis showed that L33-β3 and V33-β3 mostly share common structures co-existing in different dynamic equilibria. The L33V substitution mainly displaces the equilibrium between common structures. These observations can explain the variable reactivity of anti-HPA-1a alloantibodies suggesting that molecular dynamic plays a key role in the binding of these alloantibodies. Unlike the L33P substitution, the L33V transition would not affect the structure flexibility of the β3 knee, and consequently the functions of αIIbβ3. Copyright © 2014 Elsevier Masson SAS. All rights reserved.
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Quadrature Moments Method for the Simulation of Turbulent Reactive Flows
2003-12-01
and Flame 117, 732. TSAI, K. & Fox, R. 0. 1998 The BMC/GIEM model for micromixing in non-premixed turbulent reacting flows. Industrial Engineering...L. & Fox, R. 0. 2003 Comparison of micromixing models for CFD simulation of nanoparticle formation by reactive precipitation. Submitted to AIChE
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NASA Astrophysics Data System (ADS)
Cirpka, O. A.; Loschko, M.; Wöhling, T.; Rudolph, D. L.
2017-12-01
Excess nitrate concentrations pose a threat to drinking-water production from groundwater in all regions of intensive agriculture worldwide. Natural organic matter, pyrite, and other reduced constituents of the aquifer matrix can be oxidized by aerobic and denitrifying bacteria, leading to self-cleaning of groundwater. Various studies have shown that the heterogeneity of both hydraulic and chemical aquifer properties influence the reactive behavior. Since the exact spatial distributions of these properties are not known, predictions on the temporal evolution of nitrate should be probabilistic. However, the computational effort of pde-based, spatially explicit multi-component reactive-transport simulations are so high that multiple model runs become impossible. Conversely, simplistic models that treat denitrification as first-order decay process miss important controls on denitrification. We have proposed a Lagrangian framework of nonlinear reactive transport, in which the electron-donor supply by the aquifer matrix is parameterized by a relative reactivity, that is the reaction rate relative to a standard reaction rate for identical solute concentrations (Loschko et al., 2016). We could show that reactive transport simplifies to solving a single ordinary dfferential equation in terms of the cumulative relative reactivity for a given combination of inflow concentrations. Simulating 3-D flow and reactive transport are computationally so inexpensive that Monte Carlo simulation become feasible. The original scheme did not consider a change of the relative reactivity over time, implying that the electron-donor pool in the matrix is infinite. We have modified the scheme to address the consumption of the reducing aquifer constituents upon the reactions. We also analyzed how a minimally complex model of aerobic respiration and denitrification could look like. With the revised scheme, we performed Monte Carlo simulations in 3-D domains, confirming that the uncertainty in predicting nitrate breakthrough depends on the scale of observation. Reference: M. Loschko, T. Wöhling, D.L. Rudolph, O.A. Cirpka: Cumulative relative reactivity: a concept for modeling aquifer-scale reactive transport. Water Resour. Res. 52(10): 8117-8137, 2016, doi: 10.1002/2016WR019080.
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2012-03-27
pulse- detonation engines ( PDE ), stage separation, supersonic cav- ity oscillations, hypersonic aerodynamics, detonation induced structural...ADAPTIVE UNSTRUCTURED CARTESIAN METHOD FOR LARGE-EDDY SIMULATION OF DETONATION IN MULTI-PHASE TURBULENT REACTIVE MIXTURES 5b. GRANT NUMBER FA9550...CCL Report TR-2012-03-03 Hybrid Solution-Adaptive Unstructured Cartesian Method for Large-Eddy Simulation of Detonation in Multi-Phase Turbulent
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NASA Astrophysics Data System (ADS)
Schurgers, G.; Arneth, A.; Hickler, T.
2011-11-01
Regional or global modeling studies of dynamic vegetation often represent vegetation by large functional units (plant functional types (PFTs)). For simulation of biogenic volatile organic compounds (BVOC) in these models, emission capacities, which give the emission under standardized conditions, are provided as an average value for a PFT. These emission capacities thus hide the known heterogeneity in emission characteristics that are not straightforwardly related to functional characteristics of plants. Here we study the effects of the aggregation of species-level information on emission characteristics at PFT level. The roles of temporal and spatial variability are assessed for Europe by comparing simulations that represent vegetation by dominant tree species on the one hand and by plant functional types on the other. We compare a number of time slices between the Last Glacial Maximum (21,000 years ago) and the present day to quantify the effects of dynamically changing vegetation on BVOC emissions. Spatial heterogeneity of emission factors is studied with present-day simulations. We show that isoprene and monoterpene emissions are of similar magnitude in Europe when the simulation represents dominant European tree species, which indicates that simulations applying typical global-scale emission capacities for PFTs tend to overestimate isoprene and underestimate monoterpene emissions. Moreover, both spatial and temporal variability affect emission capacities considerably, and by aggregating these to PFT level averages, one loses the information on local heterogeneity. Given the reactive nature of these compounds, accounting for spatial and temporal heterogeneity can be important for studies of their fate in the atmosphere.
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A Finite-Rate-Catalytic Model For Hypersonic Flows Informed By Molecular Dynamics
NASA Astrophysics Data System (ADS)
Schwartzentruber, T. E.; Valentini, P.; Norman, P.; Sorensen, C.
2011-05-01
The implementation of a finite-rate catalytic (FRC) wall boundary condition within a general 3D unstructured CFD solver is described. A set of one-step gas-surface chemical equations and atomistic parameters that deter- mine the reaction rates must be prescribed as input to the model. The chemical rate equations are solved at each wall face in the CFD simulation and result in a net production of species at the wall. In order for a finite- rate gas-surface reaction model to be consistent at equilibrium, it is determined that not all forward and back- ward rates can be specified arbitrarily. Provided that the forward rates for each surface recombination are as- signed, the backward rates must be determined using equilibrium constants that are consistent with the gas- phase chemistry model and thermodynamics. Reactive molecular dynamics (MD) simulations are performed us- ing the ReaxFFSiO potential to investigate oxygen-silica interactions. β-quartz and amorphous SiO2 surfaces are accommodated to a high temperature gas via MD simulation and reach a steady-state surface coverage. In addition to stable surface reconstructions a number of active sites are observed on which recombination occurs. Single collision MD simulations are performed where gas-phase oxygen atoms interact with the most dominant active site. Probabilities of recombination are found to have an exponential trend with gas-surface system temperature. The MD simulations are used to determine the activation energy for Eley-Rideal recombination of oxygen on a specific silica active site which is an important input parameter for the FRC model.
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Slush Fund: The Multiphase Nature of Oceanic Ices and Its Role in Shaping Europa's Icy Shell
NASA Astrophysics Data System (ADS)
Buffo, J.; Schmidt, B. E.; Huber, C.
2017-12-01
The role of Europa's ice shell in mediating ocean-surface interaction, constraining potential habitability of the underlying hydrosphere, and dictating the surface morphology of the moon is discussed extensively in the literature, yet the dynamics and characteristics of the shell itself remain largely unconstrained. Some of the largest unknowns arise from underrepresented physics and varying a priori assumptions built into the current ice shell models. Here we modify and apply a validated one-dimensional reactive transport model designed to simulate the formation and evolution of terrestrial sea ice to the Europa environment. The top-down freezing of sea ice due to conductive heat loss to the atmosphere is akin to the formation of the Jovian moon's outer ice shell, albeit on a different temporal and spatial scale. Nevertheless, the microscale physics that govern the formation of sea ice on Earth (heterogenous solidification leading to brine pockets and channels, multiphase reactive transport phenomena, gravity drainage) likely operate in a similar manner at the ice-ocean interface of Europa, dictating the thermal, chemical, and mechanical properties of the ice shell. Simulations of the European ice-ocean interface at different stages during the ice shell's evolution are interpolated to produce vertical profiles of temperature, salinity, solid fraction, and eutectic points throughout the entire shell. Additionally, the model is coupled to the equilibrium chemistry package FREZCHEM to investigate the impact a diverse range of putative European ocean chemistries has on ice shell properties. This method removes the need for a priori assumptions of impurity entrainment rates and ice shell properties, thus providing a first principles constraint on the stratigraphic characteristics of a simulated European ice shell. These insights have the potential to improve existing estimates for the onset of solid state convection, melt lens formation due to eutectic melting, ice shell thickness, and ocean-surface interaction rates. Moreover, this work aims to shed light on the important role microscale physics plays in determining the macroscale properties of icy worlds by highlighting and adapting successful multiphase reactive transport sea ice models utilized in large scale Earth systems science simulations.
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NASA Astrophysics Data System (ADS)
Abdellaoui, Amr
This research project presents a complete modelling process of the effects of GIC on Hydro-Quebec power system network for system planning studies. The advantage of the presented method is that it enables planning engineers to simulate the effects of geomagnetic disturbances on the Hydro-Quebec System under different conditions and contingencies within reasonable calculation time frame. This modelling method of GIC in electric power systems has been applied to the Hydro-Quebec System. An equivalent HQ DC model has been achieved. A numerical calculation method of DC sources from a non-uniform geoelectric field has been developed and implemented on HQ DC model. Harmonics and increased reactive power losses of saturated transformers have been defined as a function of GIC through a binary search algorithm using a chosen HQ magnetization curve. The evolution in time of each transformer saturation according to its effective GIC has been evaluated using analytical formulas. The reactive power losses of saturated transformers have been modeled in PSS/E[1] HQ network as constant reactive current loads assigned to the corresponding transformer buses. Finally, time domain simulations have been performed with PSS/E taking into account transformer saturation times. This has been achieved by integrating HQ DC model results and analytical calculations results of transformer saturation times into an EMTP load model. An interface has been used to link EMTP load model to HQ PSS/E network. Different aspects of GIC effects on the Hydro-Quebec system have been studied, including the influence of uniform and non-uniform geoelectric fields, the comparison of reactive power losses of the 735kV HQ system with those of Montreal network, the risks to voltage levels and the importance of reactive power dynamic reserve. This dissertation presents a new GIC modelling approach for power systems for planning and operations purposes. This methodology could be further enhanced, particularly, the aspect regarding the transformer saturation times. Hence more research remains to be pursued in this area.
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Molecular modeling studies of interfacial reactions in wet supercritical CO2.
NASA Astrophysics Data System (ADS)
Glezakou, V.; McGrail, B. P.; Windisch, C. F.; Schaef, H. T.; Martin, P.
2011-12-01
In the recent years, Carbon Capture and Sequestration (CCS) technologies have gained considerable momentum in a globally organized effort to mitigate greenhouse emissions and adverse climate change. Co-sequestration refers to the capture and geologic sequestration of carbon dioxide and minor contaminants (sulfur compounds, NOx, Hg, etc.) in subsurface formations. Cosequestration offers the potential to make carbon management more economically acceptable to industry relative to sequestration of pure CO2. This may be achieved through significant savings in plant (and retrofit) capital cost, operating cost, and energy savings as well by eliminating the need for one or more individual pollutant capture systems (such as SO2 scrubbers). The latter point is important because co-sequestration may result in a net positive impact to the environment through avoided loss of power generation capacity from parasitic loads and reduced fuel needs. This paper will discuss our research on modeling, imaging and characterization of cosequestration processes and reactivity at a fundamental level. Our work examines the interactions of CO2-rich fluids with metal and mineral surfaces, and how these are affected by the presence of other gas components (e.g. SO2, H2O or NOx) commonly present in the CO2 streams. We have found that reactivity is also affected by the composition of the surface or, less obviously, by the surface exposed, for example, (104) vs (100 )of carbonate minerals. We combine experimental techniques such as XRD and Raman spectroscopy, which can detect and follow reactive processes, with ab initio modeling methods based on density functional theory, to establish a reliable correspondence between theory and experiment with predictive capability. Analysis of our molecular dynamics simulations, reveals structural information and vibrational density of states that can directly compare with XRD measurements and vibrational spectroscopy. While reactivity in CO2-containing aqueous environments has been widely studied, the reverse, i.e. reactivity in water-bearing condensed media, is not true. Our simulations show that mechanistic details in these environments can be drastically different, and they are very important in elucidating molecular transformations relevant to CCS or carbon conversion.
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A Multi-domain Spectral Method for Supersonic Reactive Flows
NASA Technical Reports Server (NTRS)
Don, Wai-Sun; Gottlieb, David; Jung, Jae-Hun; Bushnell, Dennis M. (Technical Monitor)
2002-01-01
This paper has a dual purpose: it presents a multidomain Chebyshev method for the solution of the two-dimensional reactive compressible Navier-Stokes equations, and it reports the results of the application of this code to the numerical simulations of high Mach number reactive flows in recessed cavity. The computational method utilizes newly derived interface boundary conditions as well as an adaptive filtering technique to stabilize the computations. The results of the simulations are relevant to recessed cavity flameholders.
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NASA Astrophysics Data System (ADS)
Chojnicki, K. N.; Yoon, H.; Martinez, M. J.
2015-12-01
Understanding reactive flow in geomaterials is important for optimizing geologic carbon storage practices, such as using pore space efficiently. Flow paths can be complex in large degrees of geologic heterogeneities across scales. In addition, local heterogeneity can evolve as reactive transport processes alter the pore-scale morphology. For example, dissolved carbon dioxide may react with minerals in fractured rocks, confined aquifers, or faults, resulting in heterogeneous cementation (and/or dissolution) and evolving flow conditions. Both path and flow complexities are important and poorly characterized, making it difficult to determine their evolution with traditional 2-D transport models. Here we characterize the development of 3-D pore-scale flow with an evolving pore configuration due to calcium carbonate (CaCO3) precipitation and dissolution. A simple pattern of a microfluidic pore network is used initially and pore structures will become more complex due to precipitation and dissolution processes. At several stages of precipitation and dissolution, we directly visualize 3-D velocity vectors using micro particle image velocimetry and a laser scanning confocal microscope. Measured 3-D velocity vectors are then compared to 3-D simulated flow fields which will be used to simulate reactive transport. Our findings will highlight the importance of the 3-D flow dynamics and its impact on estimating reactive surface area over time. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114.
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Structural and functional characterization of the hazelnut allergen Cor a 8
DOE Office of Scientific and Technical Information (OSTI.GOV)
Offermann, Lesa R.; Bublin, Merima; Perdue, Makenzie L.
Nonspecific lipid transfer proteins (nsLTPs) are basic proteins, stabilized by four disulfide bonds, and are expressed throughout the plant kingdom. These proteins are also known as important allergens in fruits and tree nuts. In this study, the nsLTP from hazelnuts, Cor a 8, was purified and its crystal structure determined. The protein is stable at low pH and refolds after thermal denaturation. Molecular dynamics simulations were used to provide an insight into conformational changes of Cor a 8 upon ligand binding. When known epitope areas from Pru p 3 were compared to those of Cor a 8, differences were obvious,more » which may contribute to limited cross-reactivity between peach and hazelnut allergens. The differences in epitope regions may contribute to limited cross-reactivity between Cor a 8 and nsLTPs from other plant sources. The structure of Cor a 8 represents the first resolved structure of a hazelnut allergen.« less
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Structural and functional characterization of the hazelnut allergen Cor a 8
Offermann, Lesa R.; Bublin, Merima; Perdue, Makenzie L.; ...
2015-09-28
Nonspecific lipid transfer proteins (nsLTPs) are basic proteins, stabilized by four disulfide bonds, and are expressed throughout the plant kingdom. These proteins are also known as important allergens in fruits and tree nuts. In this study, the nsLTP from hazelnuts, Cor a 8, was purified and its crystal structure determined. The protein is stable at low pH and refolds after thermal denaturation. Molecular dynamics simulations were used to provide an insight into conformational changes of Cor a 8 upon ligand binding. When known epitope areas from Pru p 3 were compared to those of Cor a 8, differences were obvious,more » which may contribute to limited cross-reactivity between peach and hazelnut allergens. The differences in epitope regions may contribute to limited cross-reactivity between Cor a 8 and nsLTPs from other plant sources. The structure of Cor a 8 represents the first resolved structure of a hazelnut allergen.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wang, Chao; Xu, Zhijie; Lai, Kevin
Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO2) capture. To generate data for WWC model validation, CO2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO2 in MEA. In addition, the overall mass transfer coefficient predictedmore » using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO2 reaction rate constants after using the N2O/CO2 analogy method. The calibrated model can be used to predict the CO2 mass transfer in a WWC for a wider range of operating conditions.« less
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Wang, Chao; Xu, Zhijie; Lai, Kevin; ...
2017-10-24
Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO2) capture. To generate data for WWC model validation, CO2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO2 in MEA. In addition, the overall mass transfer coefficient predictedmore » using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO2 reaction rate constants after using the N2O/CO2 analogy method. The calibrated model can be used to predict the CO2 mass transfer in a WWC for a wider range of operating conditions.« less
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Hybrid finite-volume/transported PDF method for the simulation of turbulent reactive flows
NASA Astrophysics Data System (ADS)
Raman, Venkatramanan
A novel computational scheme is formulated for simulating turbulent reactive flows in complex geometries with detailed chemical kinetics. A Probability Density Function (PDF) based method that handles the scalar transport equation is coupled with an existing Finite Volume (FV) Reynolds-Averaged Navier-Stokes (RANS) flow solver. The PDF formulation leads to closed chemical source terms and facilitates the use of detailed chemical mechanisms without approximations. The particle-based PDF scheme is modified to handle complex geometries and grid structures. Grid-independent particle evolution schemes that scale linearly with the problem size are implemented in the Monte-Carlo PDF solver. A novel algorithm, in situ adaptive tabulation (ISAT) is employed to ensure tractability of complex chemistry involving a multitude of species. Several non-reacting test cases are performed to ascertain the efficiency and accuracy of the method. Simulation results from a turbulent jet-diffusion flame case are compared against experimental data. The effect of micromixing model, turbulence model and reaction scheme on flame predictions are discussed extensively. Finally, the method is used to analyze the Dow Chlorination Reactor. Detailed kinetics involving 37 species and 158 reactions as well as a reduced form with 16 species and 21 reactions are used. The effect of inlet configuration on reactor behavior and product distribution is analyzed. Plant-scale reactors exhibit quenching phenomena that cannot be reproduced by conventional simulation methods. The FV-PDF method predicts quenching accurately and provides insight into the dynamics of the reactor near extinction. The accuracy of the fractional time-stepping technique in discussed in the context of apparent multiple-steady states observed in a non-premixed feed configuration of the chlorination reactor.
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NASA Astrophysics Data System (ADS)
Gigan, Olivier; Chen, Hua; Robert, Olivier; Renard, Stephane; Marty, Frederic
2002-11-01
This paper is dedicated to the fabrication and technological aspect of a silicon microresonator sensor. The entire project includes the fabrication processes, the system modelling/simulation, and the electronic interface. The mechanical model of such resonator is presented including description of frequency stability and Hysterises behaviour of the electrostatically driven resonator. Numeric model and FEM simulations are used to simulate the system dynamic behaviour. The complete fabrication process is based on standard microelectronics technology with specific MEMS technological steps. The key steps are described: micromachining on SOI by Deep Reactive Ion Etching (DRIE), specific release processes to prevent sticking (resist and HF-vapour release process) and collective vacuum encapsulation by Silicon Direct Bonding (SDB). The complete process has been validated and prototypes have been fabricated. The ASIC was designed to interface the sensor and to control the vibration amplitude. This electronic was simulated and designed to work up to 200°C and implemented in a standard 0.6μ CMOS technology. Characterizations of sensor prototypes are done both mechanically and electrostatically. These measurements showed good agreements with theory and FEM simulations.
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Zero dimensional model of atmospheric SMD discharge and afterglow in humid air
NASA Astrophysics Data System (ADS)
Smith, Ryan; Kemaneci, Efe; Offerhaus, Bjoern; Stapelmann, Katharina; Peter Brinkmann, Ralph
2016-09-01
A novel mesh-like Surface Micro Discharge (SMD) device designed for surface wound treatment is simulated by multiple time-scaled zero-dimensional models. The chemical dynamics of the discharge are resolved in time at atmospheric pressure in humid conditions. Simulated are the particle densities of electrons, 26 ionic species, and 26 reactive neutral species including: O3, NO, and HNO3. The total of 53 described species are constrained by 624 reactions within the simulated plasma discharge volume. The neutral species are allowed to diffuse into a diffusive gas regime which is of primary interest. Two interdependent zero-dimensional models separated by nine orders of magnitude in temporal resolution are used to accomplish this; thereby reducing the computational load. Through variation of control parameters such as: ignition frequency, deposited power density, duty cycle, humidity level, and N2 content, the ideal operation conditions for the SMD device can be predicted. The described model has been verified by matching simulation parameters and comparing results to that of previous works. Current operating conditions of the experimental mesh-like SMD were matched and results are compared to the simulations. Work supported by SFB TR 87.
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Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kerisit, Sebastien N.; Liu, Chongxuan
2013-08-20
Molecular simulation techniques are employed to gain insights into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO22+) in aqueous solution. The simulations make use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff (Guilbaud, P.; Wipff, G. J. Mol. Struct. (THEOCHEM) 1996, 366, 55-63). Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficientmore » are also calculated and discussed. Finally, a combination of metadynamics and transition path sampling simulations is employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states are also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.« less
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Ray, Dhiman; Ghosh, Smita; Tiwari, Ashwani Kumar
2018-06-07
Copper-Nickel bimetallic alloys are emerging heterogeneous catalysts for water dissociation which is the rate determining step of industrially important Water Gas Shift (WGS) reaction. Yet, the detailed quantum dynamics studies of water-surface scattering in literature are limited to pure metal surfaces. We present here, a three dimensional wave-packet dynamics study of water dissociation on Cu-Ni alloy surfaces, using a pseudo diatomic model of water on a London-Eyring-Polanyi-Sato (LEPS) potential energy surface in order to study the effect of initial vibration, rotation and orientation of water molecule on reactivity. For all the chosen surfaces reactivity increases significantly with vibrational excitation. In general, for lower vibrational states the reactivity increases with increasing rotational excitation but it decreases in higher vibrational states. Molecular orientation strongly affects reactivity by helping the molecule to align along the reaction path at higher vibrational states. For different alloys, the reaction probability follows the trend of barrier heights and the surfaces having all Ni atoms in the uppermost layer are much more reactive than the ones with Cu atoms. Hence the nature of the alloy surface and initial quantum state of the incoming molecule significantly influence the reactivity in surface catalyzed water dissociation.
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Shi, Zongbo; Krom, Michael D; Bonneville, Steeve; Baker, Alex R; Jickells, Timothy D; Benning, Liane G
2009-09-01
The formation of iron (Fe) nanoperticles and increase in Fe reactivity in mineral dust during simulated cloud processing was investigated using high-resolution microscopy and chemical extraction methods. Cloud processing of dust was experimentally simulated via an alternation of acidic (pH 2) and circumneutral conditions (pH 5-6) over periods of 24 h each on presieved (<20 microm) Saharan soil and goethite suspensions. Microscopic analyses of the processed soil and goethite samples reveal the neo-formation of Fe-rich nanoparticle aggregates, which were not found initially. Similar Fe-rich nanoparticles were also observed in wet-deposited Saharen dusts from the western Mediterranean but not in dry-deposited dust from the eastern Mediterranean. Sequential Fe extraction of the soil samples indicated an increase in the proportion of chemically reactive Fe extractable by an ascorbate solution after simulated cloud processing. In addition, the sequential extractions on the Mediterranean dust samples revealed a higher content of reactive Fe in the wet-deposited dust compared to that of the dry-deposited dust These results suggestthat large variations of pH commonly reported in aerosol and cloud waters can trigger neo-formation of nanosize Fe particles and an increase in Fe reactivity in the dust
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NASA Astrophysics Data System (ADS)
Hunter, Kendall; Zhang, Yanhang; Lanning, Craig
2005-11-01
Insight into the progression of pulmonary hypertension may be obtained from thorough study of vascular flow during reactivity testing, an invasive diagnostic procedure which can dramatically alter vascular hemodynamics. Diagnostic imaging methods, however, are limited in their ability to provide extensive data. Here we present detailed flow and wall deformation results from simulations of pulmonary arteries undergoing this procedure. Patient-specific 3-D geometric reconstructions of the first four branches of the pulmonary vasculature were obtained clinically and meshed for use with computational software. Transient simulations in normal and reactive states were obtained from four such models were completed with patient-specific velocity inlet conditions and flow impedance exit conditions. A microstructurally based orthotropic hyperelastic model that simulates pulmonary artery mechanics under normotensive and hypoxic hypertensive conditions treated wall constitutive changes due to pressure reactivity and arterial remodeling. Pressure gradients, velocity fields, arterial deformation, and complete topography of shear stress were obtained. These models provide richer detail of hemodynamics than can be obtained from current imaging techniques, and should allow maximum characterization of vascular function in the clinical situation.
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Indirect dynamics in SN2@N: insight into the influence of central atoms.
Liu, Xu; Zhao, Chenyang; Yang, Li; Zhang, Jiaxu; Sun, Rui
2017-08-30
Central atoms have a significant influence on the reaction kinetics and dynamics of nucleophilic substitution (S N 2). Herein, atomistic dynamics of a prototype S N 2@N reaction F - + NH 2 Cl is uncovered employing direct dynamics simulations that show strikingly distinct features from those determined for a S N 2@C congener F - + CH 3 Cl. Indirect scattering is found to prevail, which proceeds predominantly through a hydrogen-bonded F - -HNHCl complex in the reactant entrance channel. This unexpected finding of a pronounced contribution of indirect reaction dynamics, even at a high collision energy, is in strong contrast to a general evolution from indirect to direct dynamics with enhanced energy that characterizes S N 2@C. This result suggests that the relative importance of different atomic-level mechanisms may depend essentially on the interaction potential of reactive encounters and the coupling between inter- and intramolecular modes of the pre-reaction complex. For F - + NH 2 Cl the proton transfer pathway is less competitive than S N 2. A remarkable finding is that the more favorable energetics for NH 2 Cl proton transfer, as compared to that for CH 3 Cl, does not manifest itself in the reaction dynamics. The present work sheds light on the underlying reaction dynamics of S N 2@N, which remain largely unclear compared to well-studied S N 2@C.
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Reactive Flow Modeling of Liquid Explosives via ALE3D/Cheetah Simulations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kuo, I W; Bastea, S; Fried, L E
2010-03-10
We carried out reactive flow simulations of liquid explosives such as nitromethane using the hydrodynamic code ALE3D coupled with equations of state and reaction kinetics modeled by the thermochemical code Cheetah. The simulation set-up was chosen to mimic cylinder experiments. For pure unconfined nitromethane we find that the failure diameter and detonation velocity dependence on charge diameter are in agreement with available experimental results. Such simulations are likely to be useful for determining detonability and failure behavior for a wide range of experimental conditions and explosive compounds.
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ReaxFF molecular dynamics simulation of thermal stability of a Cu3(BTC)2 metal-organic framework.
Huang, Liangliang; Joshi, Kaushik L; van Duin, Adri C T; Bandosz, Teresa J; Gubbins, Keith E
2012-08-28
The thermal stability of a dehydrated Cu(3)(BTC)(2) (copper(II) benzene 1,3,5-tricarboxylate) metal-organic framework was studied by molecular dynamics simulation with a ReaxFF reactive force field. The results show that Cu(3)(BTC)(2) is thermally stable up to 565 K. When the temperature increases between 600 K and 700 K, the framework starts to partially collapse. The RDF analysis shows that the long range correlations between Cu dimers disappear, indicating the loss of the main channels of Cu(3)(BTC)(2). When the temperature is above 800 K, we find the decomposition of the Cu(3)(BTC)(2) framework. CO is the major product, and we also observe the release of CO(2), O(2), 1,3,5-benzenetricarboxylate (C(6)H(3)(CO(2))(3), BTC) and glassy carbon. The Cu dimer is stable up to 1100 K, but we find the formation of new copper oxide clusters at 1100 K. These results are consistent with experimental findings, and provide valuable information for future theoretical investigations of Cu(3)(BTC)(2) and its application in adsorption, separation and catalytic processes.
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Li, Wenjin
2018-02-28
Transition path ensemble consists of reactive trajectories and possesses all the information necessary for the understanding of the mechanism and dynamics of important condensed phase processes. However, quantitative description of the properties of the transition path ensemble is far from being established. Here, with numerical calculations on a model system, the equipartition terms defined in thermal equilibrium were for the first time estimated in the transition path ensemble. It was not surprising to observe that the energy was not equally distributed among all the coordinates. However, the energies distributed on a pair of conjugated coordinates remained equal. Higher energies were observed to be distributed on several coordinates, which are highly coupled to the reaction coordinate, while the rest were almost equally distributed. In addition, the ensemble-averaged energy on each coordinate as a function of time was also quantified. These quantitative analyses on energy distributions provided new insights into the transition path ensemble.
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Epidemics in Adaptive Social Networks with Temporary Link Deactivation
NASA Astrophysics Data System (ADS)
Tunc, Ilker; Shkarayev, Maxim S.; Shaw, Leah B.
2013-04-01
Disease spread in a society depends on the topology of the network of social contacts. Moreover, individuals may respond to the epidemic by adapting their contacts to reduce the risk of infection, thus changing the network structure and affecting future disease spread. We propose an adaptation mechanism where healthy individuals may choose to temporarily deactivate their contacts with sick individuals, allowing reactivation once both individuals are healthy. We develop a mean-field description of this system and find two distinct regimes: slow network dynamics, where the adaptation mechanism simply reduces the effective number of contacts per individual, and fast network dynamics, where more efficient adaptation reduces the spread of disease by targeting dangerous connections. Analysis of the bifurcation structure is supported by numerical simulations of disease spread on an adaptive network. The system displays a single parameter-dependent stable steady state and non-monotonic dependence of connectivity on link deactivation rate.
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The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies.
Hawelek, L; Brodka, A; Dore, J C; Honkimaki, V; Burian, A
2013-11-13
The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.
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Understanding the Reactivity of Lunar Dust for Future Lunar Missions
NASA Technical Reports Server (NTRS)
Wallace, William; Taylor, L. A.; Jeevarajan, Antony
2009-01-01
During the Apollo missions, dust was found to cause numerous problems for various instruments and systems. Additionally, the dust may have caused momentary health issues for some of the astronauts. Therefore, the plan to resume robotic and manned missions to the Moon in the next decade has led to a renewed interest in the properties of lunar dust, ranging from geological to chemical to toxicological. An important property to understand is the reactivity of the dust particles. Due to the lack of an atmosphere on the Moon, there is nothing to protect the lunar soil from ultraviolet radiation, solar wind, and meteorite impacts. These processes could all serve to activate the soil, or produce reactive surface species. On the Moon, these species can be maintained for millennia without oxygen or water vapor present to satisfy the broken bonds. Unfortunately, the Apollo dust samples that were returned to Earth were inadvertently exposed to the atmosphere, causing them to lose their reactive characteristics. In order to aid in the preparation of mitigation techniques prior to returning to the Moon, we measured the ability of lunar dust, lunar dust simulant, and quartz samples to produce hydroxyl radicals in solution[1]. As a first approximation of meteorite impacts on the lunar surface, we ground samples using a mortar and pestle. Our initial studies showed that all three test materials (lunar dust (62241), lunar dust simulant (JSC-1Avf), and quartz) produced hydroxyl radicals after grinding and mixing with water. However, the radical production of the ground lunar dust was approximately 10-fold and 3-fold greater than quartz and JSC-1 Avf, respectively. These reactivity differences between the different samples did not correlate with differences in specific surface area. The increased reactivity produced for the quartz by grinding was attributed to the presence of silicon- or oxygen-based radicals on the surface, as had been seen previously[2]. These radicals may also play a part in the reactivity of the lunar dust and lunar simulant. However, other factors would seem to be required to account for the greatly increased reactivity of the lunar soil. It was proposed that nanometer-size Fe 0 (zero valent) particles in the lunar soil might play a role, as they are not present in quartz or lunar dust simulant. The present work has been performed with the aim of understanding the origin of the considerable reactivity of lunar dust[3]. We have ground 8 lunar soils of varying maturity and source (highland or mare) and measured the hydroxyl-radical production and decay of the reactivity. It was determined that there is a direct correlation between the reactivity and the amount of nanophase metallic iron particles (as a function of soil maturity, I s/FeO, in which Is is the amount of iron present as nanophase iron particles present and FeO is the total iron content) in the samples; thus, the highland soils, with their lesser total FeO content, are less reactive than ground mare soils. Additionally, grinding of nanophase iron simulant [4] showed reactivity in line with the lunar soils and much greater than lunar dust simulant or quartz. Studies aimed at determining the time required to deactivate the reactive soils in a habitable environment showed that the average time to reach 50% of the initial reactivity was approximately 3.5 hours. However, even after one week, none of the soils had returned completely to its unground level of reactivity. In contrast to the reactivity results, there was no obvious correlation between the maturity of the soil and its deactivation time. These results provide the first chemical reactivity and persistence values as an important property of lunar soils, data that is paramount as mankind prepares to return to the Moon.
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Initial Comparison of Direct and Legacy Modeling Approaches for Radial Core Expansion Analysis
DOE Office of Scientific and Technical Information (OSTI.GOV)
Shemon, Emily R.
2016-10-10
Radial core expansion in sodium-cooled fast reactors provides an important reactivity feedback effect. As the reactor power increases due to normal start up conditions or accident scenarios, the core and surrounding materials heat up, causing both grid plate expansion and bowing of the assembly ducts. When the core restraint system is designed correctly, the resulting structural deformations introduce negative reactivity which decreases the reactor power. Historically, an indirect procedure has been used to estimate the reactivity feedback due to structural deformation which relies upon perturbation theory and coupling legacy physics codes with limited geometry capabilities. With advancements in modeling andmore » simulation, radial core expansion phenomena can now be modeled directly, providing an assessment of the accuracy of the reactivity feedback coefficients generated by indirect legacy methods. Recently a new capability was added to the PROTEUS-SN unstructured geometry neutron transport solver to analyze deformed meshes quickly and directly. By supplying the deformed mesh in addition to the base configuration input files, PROTEUS-SN automatically processes material adjustments including calculation of region densities to conserve mass, calculation of isotopic densities according to material models (for example, sodium density as a function of temperature), and subsequent re-homogenization of materials. To verify the new capability of directly simulating deformed meshes, PROTEUS-SN was used to compute reactivity feedback for a series of contrived yet representative deformed configurations for the Advanced Burner Test Reactor design. The indirect legacy procedure was also performed to generate reactivity feedback coefficients for the same deformed configurations. Interestingly, the legacy procedure consistently overestimated reactivity feedbacks by 35% compared to direct simulations by PROTEUS-SN. This overestimation indicates that the legacy procedures are in fact not conservative and could be overestimating reactivity feedback effects that are closely tied to reactor safety. We conclude that there is indeed value in performing direct simulation of deformed meshes despite the increased computational expense. PROTEUS-SN is already part of the SHARP multi-physics toolkit where both thermal hydraulics and structural mechanical feedback modeling can be applied but this is the first comparison of direct simulation to legacy techniques for radial core expansion.« less
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NASA Astrophysics Data System (ADS)
Jacques, Diederik
2017-04-01
As soil functions are governed by a multitude of interacting hydrological, geochemical and biological processes, simulation tools coupling mathematical models for interacting processes are needed. Coupled reactive transport models are a typical example of such coupled tools mainly focusing on hydrological and geochemical coupling (see e.g. Steefel et al., 2015). Mathematical and numerical complexity for both the tool itself or of the specific conceptual model can increase rapidly. Therefore, numerical verification of such type of models is a prerequisite for guaranteeing reliability and confidence and qualifying simulation tools and approaches for any further model application. In 2011, a first SeSBench -Subsurface Environmental Simulation Benchmarking- workshop was held in Berkeley (USA) followed by four other ones. The objective is to benchmark subsurface environmental simulation models and methods with a current focus on reactive transport processes. The final outcome was a special issue in Computational Geosciences (2015, issue 3 - Reactive transport benchmarks for subsurface environmental simulation) with a collection of 11 benchmarks. Benchmarks, proposed by the participants of the workshops, should be relevant for environmental or geo-engineering applications; the latter were mostly related to radioactive waste disposal issues - excluding benchmarks defined for pure mathematical reasons. Another important feature is the tiered approach within a benchmark with the definition of a single principle problem and different sub problems. The latter typically benchmarked individual or simplified processes (e.g. inert solute transport, simplified geochemical conceptual model) or geometries (e.g. batch or one-dimensional, homogeneous). Finally, three codes should be involved into a benchmark. The SeSBench initiative contributes to confidence building for applying reactive transport codes. Furthermore, it illustrates the use of those type of models for different environmental and geo-engineering applications. SeSBench will organize new workshops to add new benchmarks in a new special issue. Steefel, C. I., et al. (2015). "Reactive transport codes for subsurface environmental simulation." Computational Geosciences 19: 445-478.
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NASA Astrophysics Data System (ADS)
Wu, Y.; Blodau, C.
2013-08-01
Elevated nitrogen deposition and climate change alter the vegetation communities and carbon (C) and nitrogen (N) cycling in peatlands. To address this issue we developed a new process-oriented biogeochemical model (PEATBOG) for analyzing coupled carbon and nitrogen dynamics in northern peatlands. The model consists of four submodels, which simulate: (1) daily water table depth and depth profiles of soil moisture, temperature and oxygen levels; (2) competition among three plants functional types (PFTs), production and litter production of plants; (3) decomposition of peat; and (4) production, consumption, diffusion and export of dissolved C and N species in soil water. The model is novel in the integration of the C and N cycles, the explicit spatial resolution belowground, the consistent conceptualization of movement of water and solutes, the incorporation of stoichiometric controls on elemental fluxes and a consistent conceptualization of C and N reactivity in vegetation and soil organic matter. The model was evaluated for the Mer Bleue Bog, near Ottawa, Ontario, with regards to simulation of soil moisture and temperature and the most important processes in the C and N cycles. Model sensitivity was tested for nitrogen input, precipitation, and temperature, and the choices of the most uncertain parameters were justified. A simulation of nitrogen deposition over 40 yr demonstrates the advantages of the PEATBOG model in tracking biogeochemical effects and vegetation change in the ecosystem.
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NASA Astrophysics Data System (ADS)
Wu, Y.; Blodau, C.
2013-03-01
Elevated nitrogen deposition and climate change alter the vegetation communities and carbon (C) and nitrogen (N) cycling in peatlands. To address this issue we developed a new process-oriented biogeochemical model (PEATBOG) for analyzing coupled carbon and nitrogen dynamics in northern peatlands. The model consists of four submodels, which simulate: (1) daily water table depth and depth profiles of soil moisture, temperature and oxygen levels; (2) competition among three plants functional types (PFTs), production and litter production of plants; (3) decomposition of peat; and (4) production, consumption, diffusion and export of dissolved C and N species in soil water. The model is novel in the integration of the C and N cycles, the explicit spatial resolution belowground, the consistent conceptualization of movement of water and solutes, the incorporation of stoichiometric controls on elemental fluxes and a consistent conceptualization of C and N reactivity in vegetation and soil organic matter. The model was evaluated for the Mer Bleue Bog, near Ottawa, Ontario, with regards to simulation of soil moisture and temperature and the most important processes in the C and N cycles. Model sensitivity was tested for nitrogen input, precipitation, and temperature, and the choices of the most uncertain parameters were justified. A simulation of nitrogen deposition over 40 yr demonstrates the advantages of the PEATBOG model in tracking biogeochemical effects and vegetation change in the ecosystem.
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Reactive strategies in indirect reciprocity.
Ohtsuki, Hisashi
2004-04-07
Evolution of reactive strategy of indirect reciprocity is discussed, where individuals interact with others through the one-shot Prisoner's Dilemma game, changing their partners in every round. We investigate all of the reactive strategies that are stochastic, including deterministic ones as special cases. First we study adaptive dynamics of reactive strategies by assuming monomorphic population. Results are very similar to the corresponding evolutionary dynamics of direct reciprocity. The discriminating strategy, which prescribes cooperation only with those who cooperated in the previous round, cannot be an outcome of the evolution. Next we examine the case where the population includes a diversity of strategies. We find that only the mean 'discriminatoriness' in the population is the parameter that affects the evolutionary dynamics. The discriminating strategy works as a promoter of cooperation there. However, it is again not the end point of the evolution. This is because retaliatory defection, which was prescribed by the discriminating strategy, is regarded as another defection toward the society. These results caution that we have to reconsider the role of retaliatory defection much more carefully.
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NASA Astrophysics Data System (ADS)
Keller, Tobias; Katz, Richard F.
2015-04-01
Laboratory experiments indicate that even small concentrations volatiles (H2O or CO2) in the upper mantle significantly affect the silicate melting behavior [HK96,DH06]. The presence of volatiles stabilizes volatile-rich melt at high pressure, thus vastly increasing the volume of the upper mantle expected to be partially molten [H10,DH10]. These small-degree melts have important consequences for chemical differentiation and could affect the dynamics of mantle flow. We have developed theory and numerical implementation to simulate thermo-chemically coupled magma/mantle dynamics in terms of a two-phase (rock+melt), three component (dunite+MORB+volatilized MORB) physical model. The fluid dynamics is based on McKenzie's equations [McK84], while the thermo-chemical formulation of the system is represented by a novel disequilibrium multi-component melting model based on thermo-dynamic theory [RBS11]. This physical model is implemented as a parallel, two-dimensional, finite-volume code that leverages tools from the PETSc toolkit. Application of this simulation code to a mid-ocean ridge system suggests that the methodology captures the leading-order features of both hydrated and carbonated mantle melting, including deep, low-degree, volatile-rich melt formation. Melt segregation leads to continuous dynamic thermo-chemical dis-equilibration, while phenomenological reaction rates are applied to continually move the system towards re-equilibration. The simulations will be used first to characterize volatile extraction from the MOR system assuming a chemically homogeneous mantle. Subsequently, simulations will be extended to investigate the consequences of heterogeneity in lithology [KW12] and volatile content. These studies will advance our understanding of the role of volatiles in the dynamic and chemical evolution of the upper mantle. Moreover, they will help to gauge the significance of the coupling between the deep carbon cycle and the ocean/atmosphere system. REFERENCES HK96 Hirth & Kohlstedt (1996), Earth Planet Sci Lett DH06 Dasgupta & Hirschmann (2006), doi:10.1038/nature04612. H10 Hirschmann (2010), doi:10.1016/j.pepi.2009.12.003. DH10 Dasgupta & Hirschmann (2010), doi:10.1016/j.epsl.2010.06.039. McK84 McKenzie (1984), J Pet KW12 Katz & Weatherley (2012), doi: 10.1016/j.epsl.2012.04.042. RBS11 Rudge, Bercovici & Spiegelman (2011), doi: 10.1111/j.1365-246X.2010.04870.x
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NASA Astrophysics Data System (ADS)
Stolpovsky, Konstantin; Dale, Andrew W.; Wallmann, Klaus
2018-06-01
The kinetics of particulate organic carbon (POC) mineralization in marine surface sediments is not well constrained. This creates considerable uncertainties when benthic processes are considered in global biogeochemical or Earth system circulation models to simulate climate-ocean interactions and biogeochemical tracer distributions in the ocean. In an attempt to improve our understanding of the rate and depth distribution of organic carbon mineralization in bioturbated (0-20 cm) sediments at the global scale, we parameterized a 1-D diagenetic model that simulates the mineralization of three discrete POC pools (a
multi-G
model). The rate constants of the three reactive classes (highly reactive, reactive, refractory) are fixed and determined to be 70, 0.5 and ˜ 0.001 yr-1, respectively, based on the Martin curve model for pelagic POC degradation. In contrast to previous approaches, however, the reactivity of the organic material degraded in the seafloor is continuous with, and set by, the apparent reactivity of material sinking through the water column. Despite the simplifications of describing POC remineralization using G-type approaches, the model is able to simulate a global database (185 stations) of benthic oxygen and nitrate fluxes across the sediment-water interface in addition to porewater oxygen and nitrate distributions and organic carbon burial efficiencies. It is further consistent with degradation experiments using fresh phytoplankton reported in a previous study. We propose that an important yet mostly overlooked consideration in upscaling approaches is the proportion of the reactive POC classes reaching the seafloor in addition to their reactivity. The approach presented is applicable to both steady-state and non-steady state scenarios, and links POC degradation kinetics in sedimentary environments to water depth and the POC rain rate to the seafloor. -
NASA Astrophysics Data System (ADS)
Wang, Wu; Huang, Wei; Zhang, Yongjun
2018-03-01
The grid-integration of Photovoltaic-Storage System brings some undefined factors to the network. In order to make full use of the adjusting ability of Photovoltaic-Storage System (PSS), this paper puts forward a reactive power optimization model, which are used to construct the objective function based on power loss and the device adjusting cost, including energy storage adjusting cost. By using Cataclysmic Genetic Algorithm to solve this optimization problem, and comparing with other optimization method, the result proved that: the method of dynamic extended reactive power optimization this article puts forward, can enhance the effect of reactive power optimization, including reducing power loss and device adjusting cost, meanwhile, it gives consideration to the safety of voltage.
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Discrete meso-element simulation of chemical reactions in shear bands
NASA Astrophysics Data System (ADS)
Tamura, S.; Horie, Y.
1998-07-01
A meso-dynamic simulation technique is used to investigate the chemical reactions in high speed shearing of reactive porous mixtures. The reaction speed is assumed to be a function of temperature, pressure and mixing of materials. To gain a theoretical insight into the experiments reported by Nesterenko et al., a parametric study of material flow and local temperature was carried out using a Nb and Si mixture. In the model calculation, a heterogeneous shear region of 5 μm width, consisting of alternating layers of Nb and Si, was created first in a mixture and then sheared at the rate of 8.0×107s-1. Results show that the material flow is mostly homogeneous, but contains a local agglomeration and circulatory flow. This behavior accelerates mass mixing and causes a significant temperature increase. To evaluate the mixing of material, average minimum distance of materials separation was calculated. Voids effect were also investigated.
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Simulations of Fluid Nitromethane Under Extreme Conditions
DOE Office of Scientific and Technical Information (OSTI.GOV)
Fried, L E; Reed, E J; Manaa, M R
2003-07-15
We report density functional molecular dynamics simulations to determine the early chemical events of hot (T = 3000 K) and dense (1.97 g/cm{sup 3}, V/V{sub 0} = 0.68) nitromethane (CH{sub 3}NO{sub 2}). The first step in the decomposition process is an intermolecular proton abstraction mechanism that leads to the formation of CH{sub 3}NO{sub 2}H and the aci ion H{sub 2}CNO{sub 2}{sup -}, in support of evidence from static high-pressure and shock experiments. An intramolecular hydrogen transfer that transforms nitromethane into the aci acid form, CH{sub 2}NO{sub 2}H, accompanies this event. This is the first confirmation of chemical reactivity with bondmore » selectivity for an energetic material near the condition of fully reacted specimen. We also report the decomposition mechanism followed up to the formation of H{sub 2}O as the first stable product.« less
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NEAMS Update. Quarterly Report for January - March 2014
DOE Office of Scientific and Technical Information (OSTI.GOV)
Stan, Marius
2014-08-01
This quarterly report covers the following points: A fully three-dimensional smeared cracking model has been implemented and tested in BISON; DAKOTA-BISON was used to study the parameters that govern heat transfer across the fuel-cladding; Calculations of grain boundary mobility in UO 2 have been extended to high temperatures; Mesh adaptivity is being employed in MARMOT simulations to increase computational efficiency; Molecular dynamics simulations have shown correlation between atomic displacements and the anisotropic thermal conductivity in UO 2; The SHARP team continues to address the application of the toolkit to assembly deformations driven by reactivity feedback; The Nek5000 team has extendedmore » the low-Machnumber capability to mixtures with multiple species; The generalized cross section library has been tested for various fuel assemblies and reactor types; and The subgroup cross-section interface was successfully implemented in PROTEUS-SN (page 6).« less
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NASA Technical Reports Server (NTRS)
Desai, Tapan G.; Lawson, John W.; Keblinski, Pawel
2010-01-01
Reactive molecular dynamics simulations are used to study initial stage of pyrolysis of ablation materials and their composites with carbon nanotubes and carbon fibers. The products formed during pyrolysis are characterized and water is found as the primary product in all cases. The water formation mechanisms are analyzed and the value of the activation energy for water formation is estimated. A detailed study on graphitic precursor formation reveals the presence of two temperature zones. In the lower temperature zone (less than 2000 K) polymerization occurs resulting in formation of large, stable graphitic precursors, and in the high temperature zone (greater than 2000 K) polymer scission results in formation of short polymer chains/molecules. Simulations performed in the high temperature zone on the phenolic resin composites (with carbon nanotubes and carbon fibers) shows that the presence of interfaces had no substantial effect on the chain scission rate or the activation energy value for water formation.
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Characterization of Impact Initiation of Aluminum-Based Intermetallic-Forming Reactive Materials
2011-12-01
compressed intermetallic-forming aluminum-based reactive materials upon impact initiation, consisting of equi-volumetric tantalum-aluminum, tungsten-aluminum...18 2.3.4 Dynamic Energy Release Characterization using Pig Test . . . . . . 21 2.3.5 Shock Compression of Reactive Powder Mixtures...is to evaluate the reaction initiation characteristics of quasi-statically compressed intermetallic-forming aluminum-based reactive materials upon
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Reduced Order Models for Reactions of Energetic Materials
NASA Astrophysics Data System (ADS)
Kober, Edward
The formulation of reduced order models for the reaction chemistry of energetic materials under high pressures is needed for the development of mesoscale models in the areas of initiation, deflagration and detonation. Phenomenologically, 4-8 step models have been formulated from the analysis of cook-off data by analyzing the temperature rise of heated samples. Reactive molecular dynamics simulations have been used to simulate many of these processes, but reducing the results of those simulations to simple models has not been achieved. Typically, these efforts have focused on identifying molecular species and detailing specific chemical reactions. An alternative approach is presented here that is based on identifying the coordination geometries of each atom in the simulation and tracking classes of reactions by correlated changes in these geometries. Here, every atom and type of reaction is documented for every time step; no information is lost from unsuccessful molecular identification. Principal Component Analysis methods can then be used to map out the effective chemical reaction steps. For HMX and TATB decompositions simulated with ReaxFF, 90% of the data can be explained by 4-6 steps, generating models similar to those from the cook-off analysis. By performing these simulations at a variety of temperatures and pressures, both the activation and reaction energies and volumes can then be extracted.
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Kodavasal, Janardhan; Kolodziej, Christopher P.; Ciatti, Stephen A.; ...
2016-11-03
In this study, we study the effects of injector nozzle inclusion angle, injection pressure, boost, and swirl ratio on gasoline compression ignition combustion. Closed-cycle computational fluid dynamics simulations using a 1/7th sector mesh representing a single cylinder of a four-cylinder 1.9 L diesel engine, operated in gasoline compression ignition mode with 87 anti-knock index (AKI) gasoline, were performed. Two different operating conditions were studied—the first is representative of idle operation (4 mg fuel/cylinder/cycle, 850 r/min), and the second is representative of a low-load condition (10 mg fuel/cylinder/cycle, 1500 r/min). The mixture preparation and reaction space from the simulations were analyzedmore » to gain insights into the effects of injection pressure, nozzle inclusion angle, boost, and swirl ratio on achieving stable low-load to idle gasoline compression ignition operation. It was found that narrower nozzle inclusion angles allow for more reactivity or propensity to ignition (determined qualitatively by computing constant volume ignition delays) and are suitable over a wider range of injection timings. Under idle conditions, it was found that lower injection pressures helped to reduce overmixing of the fuel, resulting in greater reactivity and ignitability (ease with which ignition can be achieved) of the gasoline. However, under the low-load condition, lower injection pressures did not increase ignitability, and it is hypothesized that this is because of reduced chemical residence time resulting from longer injection durations. Reduced swirl was found to maintain higher in-cylinder temperatures through compression, resulting in better ignitability. It was found that boosting the charge also helped to increase reactivity and advanced ignition timing.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kodavasal, Janardhan; Kolodziej, Christopher P.; Ciatti, Stephen A.
In this study, we study the effects of injector nozzle inclusion angle, injection pressure, boost, and swirl ratio on gasoline compression ignition combustion. Closed-cycle computational fluid dynamics simulations using a 1/7th sector mesh representing a single cylinder of a four-cylinder 1.9 L diesel engine, operated in gasoline compression ignition mode with 87 anti-knock index (AKI) gasoline, were performed. Two different operating conditions were studied—the first is representative of idle operation (4 mg fuel/cylinder/cycle, 850 r/min), and the second is representative of a low-load condition (10 mg fuel/cylinder/cycle, 1500 r/min). The mixture preparation and reaction space from the simulations were analyzedmore » to gain insights into the effects of injection pressure, nozzle inclusion angle, boost, and swirl ratio on achieving stable low-load to idle gasoline compression ignition operation. It was found that narrower nozzle inclusion angles allow for more reactivity or propensity to ignition (determined qualitatively by computing constant volume ignition delays) and are suitable over a wider range of injection timings. Under idle conditions, it was found that lower injection pressures helped to reduce overmixing of the fuel, resulting in greater reactivity and ignitability (ease with which ignition can be achieved) of the gasoline. However, under the low-load condition, lower injection pressures did not increase ignitability, and it is hypothesized that this is because of reduced chemical residence time resulting from longer injection durations. Reduced swirl was found to maintain higher in-cylinder temperatures through compression, resulting in better ignitability. It was found that boosting the charge also helped to increase reactivity and advanced ignition timing.« less
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Cera, Luca; Schalley, Christoph A
2014-03-21
The high vacuum inside a mass spectrometer offers unique conditions to broaden our view on the reactivity of supramolecules. Because dynamic exchange processes between complexes are efficiently suppressed, the intrinsic and intramolecular reactivity of the complexes of interest is observed. Besides this, the significantly higher strength of non-covalent interactions in the absence of competing solvent allows processes to occur that are unable to compete in solution. The present review highlights a series of examples illustrating different aspects of supramolecular gas-phase reactivity ranging from the dissociation and formation of covalent bonds in non-covalent complexes through the reactivity in the restricted inner phase of container molecules and step-by-step mechanistic studies of organocatalytic reaction cycles to cage contraction reactions, processes induced by electron capture, and finally dynamic molecular motion within non-covalent complexes as unravelled by hydrogen-deuterium exchange processes performed in the gas phase.
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Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C; Brooks, Scott C; Pace, Molly N; Kim, Young-Jin; Jardine, Philip M; Watson, David B
2007-06-16
This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.
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NASA Astrophysics Data System (ADS)
Jöckel, Patrick; Tost, Holger; Pozzer, Andrea; Kunze, Markus; Kirner, Oliver; Brenninkmeijer, Carl A. M.; Brinkop, Sabine; Cai, Duy S.; Dyroff, Christoph; Eckstein, Johannes; Frank, Franziska; Garny, Hella; Gottschaldt, Klaus-Dirk; Graf, Phoebe; Grewe, Volker; Kerkweg, Astrid; Kern, Bastian; Matthes, Sigrun; Mertens, Mariano; Meul, Stefanie; Neumaier, Marco; Nützel, Matthias; Oberländer-Hayn, Sophie; Ruhnke, Roland; Runde, Theresa; Sander, Rolf; Scharffe, Dieter; Zahn, Andreas
2016-03-01
Three types of reference simulations, as recommended by the Chemistry-Climate Model Initiative (CCMI), have been performed with version 2.51 of the European Centre for Medium-Range Weather Forecasts - Hamburg (ECHAM)/Modular Earth Submodel System (MESSy) Atmospheric Chemistry (EMAC) model: hindcast simulations (1950-2011), hindcast simulations with specified dynamics (1979-2013), i.e. nudged towards ERA-Interim reanalysis data, and combined hindcast and projection simulations (1950-2100). The manuscript summarizes the updates of the model system and details the different model set-ups used, including the on-line calculated diagnostics. Simulations have been performed with two different nudging set-ups, with and without interactive tropospheric aerosol, and with and without a coupled ocean model. Two different vertical resolutions have been applied. The on-line calculated sources and sinks of reactive species are quantified and a first evaluation of the simulation results from a global perspective is provided as a quality check of the data. The focus is on the intercomparison of the different model set-ups. The simulation data will become publicly available via CCMI and the Climate and Environmental Retrieval and Archive (CERA) database of the German Climate Computing Centre (DKRZ). This manuscript is intended to serve as an extensive reference for further analyses of the Earth System Chemistry integrated Modelling (ESCiMo) simulations.
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Simulations of the modified gap experiment
NASA Astrophysics Data System (ADS)
Sutherland, Gerrit T.; Benjamin, Richard; Kooker, Douglas
2017-01-01
Modified gap experiment (test) hydrocode simulations predict the trends seen in experimental excess free surface velocity versus input pressure curves for explosives with both large and modest failure diameters. Simulations were conducted for explosive "A", an explosive with a large failure diameter, and for cast TNT, which has a modest failure diameter. Using the best available reactive rate models, the simulations predicted sustained ignition thresholds similar to experiment. This is a threshold where detonation is likely given a long enough run distance. For input pressures greater than the sustained ignition threshold pressure, the simulations predicted too little velocity for explosive "A" and too much velocity for TNT. It was found that a better comparison of experiment and simulation requires additional experimental data for both explosives. It was observed that the choice of reactive rate model for cast TNT can lead to large differences in the predicted modified gap experiment result. The cause of the difference is that the same data was not used to parameterize both models; one set of data was more shock reactive than the other.
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Implementing fluid dynamics obtained from GeoPET in reactive transport models
NASA Astrophysics Data System (ADS)
Lippmann-Pipke, Johanna; Eichelbaum, Sebastian; Kulenkampff, Johannes
2016-04-01
Flow and transport simulations in geomaterials are commonly conducted on high-resolution tomograms (μCT) of the pore structure or stochastic models that are calibrated with measured integral quantities, like break through curves (BTC). Yet, there existed virtually no method for experimental verification of the simulated velocity distribution results. Positron emission tomography (PET) has unrivaled sensitivity and robustness for non-destructive, quantitative, spatio-temporal measurement of tracer concentrations in body tissue. In the past decade, we empowered PET for its applicability in opaque/geological media - GeoPET (Kulenkampff et al.; Kulenkampff et al., 2008; Zakhnini et al., 2013) and have developed detailed correction schemes to bring the images into sharp focus. Thereby it is the appropriate method for experimental verification and calibration of computer simulations of pore-scale transport by means of the observed propagation of a tracer pulse, c_PET(x,y,z,t). In parallel, we aimed at deriving velocity and porosity distributions directly from our concentration time series of fluid flow processes in geomaterials. This would allow us to directly benefit from lab scale observations and to parameterize respective numerical transport models. For this we have developed a robust spatiotemporal (3D+t) parameter extraction algorithm. Here, we will present its functionality, and demonstrate the use of obtained velocity distributions in finite element simulations of reactive transport processes on drill core scale. Kulenkampff, J., Gruendig, M., Zakhnini, A., Gerasch, R., and Lippmann-Pipke, J.: Process tomography of diffusion with PET for evaluating anisotropy and heterogeneity, Clay Minerals, in press. Kulenkampff, J., Gründig, M., Richter, M., and Enzmann, F.: Evaluation of positron emission tomography for visualisation of migration processes in geomaterials, Physics and Chemistry of the Earth, 33, 937-942, 2008. Zakhnini, A., Kulenkampff, J., Sauerzapf, S., Pietrzyk, U., and Lippmann-Pipke, J.: Monte Carlo simulations of GeoPET experiments: 3D images of tracer distributions (18-F, 124-I and 58-Co) in Opalinus Clay, anhydrite and quartz, Computers and Geosciences, 57 183-196, 2013.
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NASA Astrophysics Data System (ADS)
Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.
2015-12-01
Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined with genome-enabled reactive flow and transport we simulated the importance of pore network properties including connectivity in regulating metabolic interdependencies between microbial functional guilds.
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NASA Technical Reports Server (NTRS)
Bragg-Sitton, Shannon M.; Forsbacka, Matthew
2004-01-01
For a compact, fast-spectrum reactor, reactivity feedback is dominated by core deformation at elevated temperature. Given the use of accurate deformation measurement techniques, it is possible to simulate nuclear feedback in non-nuclear electrically heated reactor tests. Implementation of simulated reactivity feedback in response to measured deflection is being tested at the NASA Marshall Space Flight Center Early Flight Fission Test Facility (EFF-TF). During tests of the SAFE-100 reactor prototype, core deflection was monitored using a high resolution camera. "virtual" reactivity feedback was accomplished by applying the results of Monte Carlo calculations (MCNPX) to core deflection measurements; the computational analysis was used to establish the reactivity worth of van'ous core deformations. The power delivered to the SAFE-100 prototype was then dusted accordingly via kinetics calculations, The work presented in this paper will demonstrate virtual reactivity feedback as core power was increased from 1 kilowatt(sub t), to 10 kilowatts(sub t), held approximately constant at 10 kilowatts (sub t), and then allowed to decrease based on the negative thermal reactivity coefficient.
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Developmental metaplasticity in neural circuit codes of firing and structure.
Baram, Yoram
2017-01-01
Firing-rate dynamics have been hypothesized to mediate inter-neural information transfer in the brain. While the Hebbian paradigm, relating learning and memory to firing activity, has put synaptic efficacy variation at the center of cortical plasticity, we suggest that the external expression of plasticity by changes in the firing-rate dynamics represents a more general notion of plasticity. Hypothesizing that time constants of plasticity and firing dynamics increase with age, and employing the filtering property of the neuron, we obtain the elementary code of global attractors associated with the firing-rate dynamics in each developmental stage. We define a neural circuit connectivity code as an indivisible set of circuit structures generated by membrane and synapse activation and silencing. Synchronous firing patterns under parameter uniformity, and asynchronous circuit firing are shown to be driven, respectively, by membrane and synapse silencing and reactivation, and maintained by the neuronal filtering property. Analytic, graphical and simulation representation of the discrete iteration maps and of the global attractor codes of neural firing rate are found to be consistent with previous empirical neurobiological findings, which have lacked, however, a specific correspondence between firing modes, time constants, circuit connectivity and cortical developmental stages. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Dephasing dynamics in confined myoglobin
NASA Astrophysics Data System (ADS)
Goj, Anne; Loring, Roger F.
2007-11-01
Confinement of a solution can slow solvent dynamics and in turn influence the reactivity and structure of the solute. Encapsulating a protein in an aqueous pore affects its binding properties, stability to degradation, interconversion between conformational states, and energy relaxation. We perform molecular dynamics simulations of H64V-CO mutant myoglobin solvated by varying amounts of liquid water, and in turn enclosed by a matrix of immobilized solvent, to mimic differing degrees of confinement of H64V-CO in a glass. We calculate the three-pulse vibrational echo signal of the CO ligand from the autocorrelation function of fluctuations in the CO vibrational frequency. When the first solvation layer alone is free to relax, the correlation function displays only fast relaxation reminiscent of the case of a protein in a fixed, immobilized solvent matrix. However the vibrational echo signal in this case decays significantly more rapidly than for a static solvent. With two solvation layers mobile, the correlation function displays long time relaxation characteristic of the unconfined protein and the echo signal decays rapidly. The echo signal of the protein with two mobile solvation layers is nearly identical to that of the unconfined protein, despite the substantially constrained solvent dynamics in the confined case.
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The global nonmethane reactive organic carbon budget: A modeling perspective
NASA Astrophysics Data System (ADS)
Safieddine, Sarah A.; Heald, Colette L.; Henderson, Barron H.
2017-04-01
The cycling of reactive organic carbon (ROC) is central to tropospheric chemistry. We characterize the global tropospheric ROC budget as simulated with the GEOS-Chem model. We expand the standard simulation by including new emissions and gas-phase chemistry, an expansion of dry and wet removal, and a mass tracking of all ROC species to achieve carbon closure. The resulting global annual mean ROC burden is 16 Tg C, with sources from methane oxidation and direct emissions contributing 415 and 935 Tg C yr-1. ROC is lost from the atmosphere via physical deposition (460 Tg C yr-1), and oxidation to CO/CO2 (875 Tg C yr-1). Ketones, alkanes, alkenes, and aromatic hydrocarbons dominate the ROC burden, whereas aldehydes and isoprene dominate the ROC global mean surface OH reactivity. Simulated OH reactivities are between 0.8-1 s-1, 3-14 s-1, and 12-34 s-1 over selected regions in the remote ocean, continental midlatitudes, and the tropics, respectively, and are consistent with observational constraints.
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Manner, Virginia W.; Cawkwell, Marc; Kober, Edward M.; ...
2018-03-09
The sensitivity of explosives is controlled by factors that span from intrinsic chemical reactivity and chemical intramolecular effects to mesoscale structure and defects, and has been a topic of extensive study for over 50 years. Due to these complex competing chemical and physical elements, a unifying relationship between molecular framework, crystal structure, and sensitivity has yet to be developed. In order to move towards this goal, ideally experimental studies should be performed on systems with small, systematic structural modifications, with modeling utilized to interpret experimental results. Pentaerythritol tetranitrate (PETN) is a common nitrate ester explosive that has been widely studiedmore » due to its use in military and commercial explosives. We have synthesized PETN derivatives with modified sensitivity characteristics by substituting the CCH 2ONO 2 moiety with other substituents, including CH, CNH 2, CNH3X, CCH 3, and PO. We relate the handling sensitivity properties of each PETN derivative to its structural properties, and discuss the potential roles of thermodynamic properties such as heat capacity and heat of formation, thermal stability, crystal structure, compressibility, and inter- and intramolecular hydrogen bonding on impact sensitivity. Reactive molecular dynamics (MD) simulations of the C/H/N/O-based PETN-derivatives have been performed under cook-off conditions that mimic those accessed in impact tests. These simulations infer how changes in chemistry affect the subsequent decomposition pathways.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Manner, Virginia W.; Cawkwell, Marc; Kober, Edward M.
The sensitivity of explosives is controlled by factors that span from intrinsic chemical reactivity and chemical intramolecular effects to mesoscale structure and defects, and has been a topic of extensive study for over 50 years. Due to these complex competing chemical and physical elements, a unifying relationship between molecular framework, crystal structure, and sensitivity has yet to be developed. In order to move towards this goal, ideally experimental studies should be performed on systems with small, systematic structural modifications, with modeling utilized to interpret experimental results. Pentaerythritol tetranitrate (PETN) is a common nitrate ester explosive that has been widely studiedmore » due to its use in military and commercial explosives. We have synthesized PETN derivatives with modified sensitivity characteristics by substituting the CCH 2ONO 2 moiety with other substituents, including CH, CNH 2, CNH3X, CCH 3, and PO. We relate the handling sensitivity properties of each PETN derivative to its structural properties, and discuss the potential roles of thermodynamic properties such as heat capacity and heat of formation, thermal stability, crystal structure, compressibility, and inter- and intramolecular hydrogen bonding on impact sensitivity. Reactive molecular dynamics (MD) simulations of the C/H/N/O-based PETN-derivatives have been performed under cook-off conditions that mimic those accessed in impact tests. These simulations infer how changes in chemistry affect the subsequent decomposition pathways.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Corley, Richard A; Minard, Kevin R; Kabilan, Senthil
The percentages of total airflows over the nasal respiratory and olfactory epithelium of female rabbits were calculated from computational fluid dynamics (CFD) simulations of steady-state inhalation. These airflows calculations, along with nasal airway geometry determinations, are critical parameters for hybrid CFD/physiologically based pharmacokinetic models that describe the nasal dosimetry of water-soluble or reactive gases and vapors in rabbits. CFD simulations were based upon three-dimensional computational meshes derived from magnetic resonance images of three adult female New Zealand White (NZW) rabbits. In the anterior portion of the nose, the maxillary turbinates of rabbits are considerably more complex than comparable regions inmore » rats, mice, monkeys, or humans. This leads to a greater surface area to volume ratio in this region and thus the potential for increased extraction of water soluble or reactive gases and vapors in the anterior portion of the nose compared to many other species. Although there was considerable interanimal variability in the fine structures of the nasal turbinates and airflows in the anterior portions of the nose, there was remarkable consistency between rabbits in the percentage of total inspired airflows that reached the ethmoid turbinate region (~50%) that is presumably lined with olfactory epithelium. These latter results (airflows reaching the ethmoid turbinate region) were higher than previous published estimates for the male F344 rat (19%) and human (7%). These differences in regional airflows can have significant implications in interspecies extrapolations of nasal dosimetry.« less
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Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.
Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E
2016-08-09
Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.
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Combined spectroscopic, DFT, TD-DFT and MD study of newly synthesized thiourea derivative
NASA Astrophysics Data System (ADS)
Menon, Vidya V.; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Bielenica, Anna; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian
2018-03-01
A novel thiourea derivative, 1-(3-bromophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (ANF-22) is synthesized and characterized by FTIR, FT-Raman and NMR spectroscopy experimentally and theoretically. A detailed conformational analysis of the title molecule has been conducted in order to locate the lowest energy geometry, which was further subjected to the detailed investigation of spectroscopic, reactive, degradation and docking studies by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Time dependent DFT (TD-DFT) calculations have been used also in order to simulate UV spectra and investigate charge transfer within molecule. Natural bond orbital analysis has been performed analyzing the charge delocalization and using HOMO and LUMO energies the electronic properties are analyzed. Molecular electrostatic potential map is used for the quantitative measurement of active sites in the molecule. In order to determine the locations possibly prone to electrophilic attacks we have calculated average local ionization energies and mapped them to the electron density surface. Further insight into the local reactivity properties have been obtained by calculation of Fukui functions, also mapped to the electron density surface. Possible degradation properties by the autoxidation mechanism have been assessed by calculations of bond dissociation energies for hydrogen abstraction. Atoms of title molecule with significant interactions with water molecules have been determined by calculations of radial distribution functions. The title compound can be a lead compound for developing new analgesic drug.
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NASA Astrophysics Data System (ADS)
Woo, Dong K.; Kumar, Praveen
2017-10-01
How does the variability of topography structure the spatial heterogeneity of nutrient dynamics? In particular, what role does micro-topographic depression play in the spatial and temporal dynamics of nitrate, ammonia, and ammonium? We explore these questions using the 3-D simulation of their joint dynamics of concentration and age. To explicitly resolve micro-topographic variability and its control on moisture, vegetation, and carbon-nitrogen dynamics, we use a high-resolution LiDAR data over an agricultural site under a corn-soybean rotation in the Intensively Managed landscapes Critical Zone Observatory in the U.S. Midwest. We utilize a hybrid CPU-GPU parallel computing architecture to reduce the computational cost associated with such high-resolution simulations. Our results show that in areas that present closed topographic depressions, relatively lower nitrate concentration and age are observed compared to elsewhere. The periodic ponding in depressions increases the downward flux of water that carries more dissolved nitrate to the deeper soil layer. However, the variability in the depressions is relatively higher as a result of the episodic ponding pattern. When aggregate efflux from the soil domain at the bottom of the soil is considered, we find a gradual decrease in the age on the rising limb of nitrate efflux and a gradual increase on the falling limb. In addition, the age of the nitrate efflux ranges from 4 to 7 years. These are significantly higher as compared to the ages associated with a nonreactive tracer indicating that they provide an inaccurate estimate of residence time of a reactive constituent through the soil column.
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NASA Astrophysics Data System (ADS)
Morrison, Christopher
Nuclear fuels with similar aggregate material composition, but with different millimeter and micrometer spatial configurations of the component materials can have very different safety and performance characteristics. This research focuses on modeling and attempting to engineer heterogeneous combinations of nuclear fuels to improve negative prompt temperature feedback in response to reactivity insertion accidents. Improvements in negative prompt temperature feedback are proposed by developing a tailored thermal resistance in the nuclear fuel. In the event of a large reactivity insertion, the thermal resistance allows for a faster negative Doppler feedback by temporarily trapping heat in material zones with strong absorption resonances. A multi-physics simulation framework was created that could model large reactivity insertions. The framework was then used to model a comparison of a heterogeneous fuel with a tailored thermal resistance and a homogeneous fuel without the tailored thermal resistance. The results from the analysis confirmed the fundamental premise of prompt temperature feedback and provide insights into the neutron spectrum dynamics throughout the transient process. A trade study was conducted on infinite lattice fuels to help map a design space to study and improve prompt temperature feedback with many results. A multi-scale fuel pin analysis was also completed to study more realistic geometries. The results of this research could someday allow for novel nuclear fuels that would behave differently than current fuels. The idea of having a thermal barrier coating in the fuel is contrary to most current thinking. Inherent resistance to reactivity insertion accidents could enable certain reactor types once considered vulnerable to reactivity insertion accidents to be reevaluated in light of improved negative prompt temperature feedback.
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Horitani, Masaki; Offenbacher, Adam R; Carr, Cody A Marcus; Yu, Tao; Hoeke, Veronika; Cutsail, George E; Hammes-Schiffer, Sharon; Klinman, Judith P; Hoffman, Brian M
2017-02-08
In enzymatic C-H activation by hydrogen tunneling, reduced barrier width is important for efficient hydrogen wave function overlap during catalysis. For native enzymes displaying nonadiabatic tunneling, the dominant reactive hydrogen donor-acceptor distance (DAD) is typically ca. 2.7 Å, considerably shorter than normal van der Waals distances. Without a ground state substrate-bound structure for the prototypical nonadiabatic tunneling system, soybean lipoxygenase (SLO), it has remained unclear whether the requisite close tunneling distance occurs through an unusual ground state active site arrangement or by thermally sampling conformational substates. Herein, we introduce Mn 2+ as a spin-probe surrogate for the SLO Fe ion; X-ray diffraction shows Mn-SLO is structurally faithful to the native enzyme. 13 C ENDOR then reveals the locations of 13 C10 and reactive 13 C11 of linoleic acid relative to the metal; 1 H ENDOR and molecular dynamics simulations of the fully solvated SLO model using ENDOR-derived restraints give additional metrical information. The resulting three-dimensional representation of the SLO active site ground state contains a reactive (a) conformer with hydrogen DAD of ∼3.1 Å, approximately van der Waals contact, plus an inactive (b) conformer with even longer DAD, establishing that stochastic conformational sampling is required to achieve reactive tunneling geometries. Tunneling-impaired SLO variants show increased DADs and variations in substrate positioning and rigidity, confirming previous kinetic and theoretical predictions of such behavior. Overall, this investigation highlights the (i) predictive power of nonadiabatic quantum treatments of proton-coupled electron transfer in SLO and (ii) sensitivity of ENDOR probes to test, detect, and corroborate kinetically predicted trends in active site reactivity and to reveal unexpected features of active site architecture.
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Dynamics of polymerization induced phase separation in reactive polymer blends
NASA Astrophysics Data System (ADS)
Lee, Jaehyung
Mechanisms and dynamics of phase decomposition following polymerization induced phase separation (PIPS) of reactive polymer blends have been investigated experimentally and theoretically. The phenomenon of PIPS is a non-equilibrium and non-linear dynamic process. The mechanism of PIPS has been thought to be a nucleation and growth (NG) type originally, however, newer results indicate spinodal decomposition (SD). In PIPS, the coexistence curve generally passes through the reaction temperature at off-critical compositions, thus phase separation has to be initiated first in the metastable region where nucleation occurs. When the system farther drifts from the metastable to unstable region, the NG structure transforms to the SD bicontinuous morphology. The crossover behavior of PIPS may be called nucleation initiated spinodal decomposition (NISD). The formation of newer domains between the existing ones is responsible for the early stage of PIPS. Since PIPS is non- equilibrium kinetic process, it would not be surprising to discern either or both structures. The phase separation dynamics of DGEBA/CTBN mixtures having various kinds of curing agents from low reactivity to high reactivity and various amount of curing agents were examined at various reaction temperatures. The phase separation behavior was monitored by a quantity of scattered light intensity experimentally and by a quantity of collective structure factor numerically. Prior to the study of phase separation dynamics, a preliminary investigation on the isothermal cure behavior of the mixtures were executed in order to determine reaction kinetics parameters. The cure behavior followed the overall second order reaction kinetics. Next, based on the knowledge obtained from the phase separation dynamics study of DGEBA/CTBN mixtures, the phase separation dynamics of various composition of DGEBA/R45EPI mixtures having MDA as a curing agent were investigated. The phase separation behavior was quite dependent upon the composition variation. R45EPI itself can react with itself or with DGEBA without curing, therefore three-component system was considered in this mixture. For the numerical studies of this three- component mixture, a system that is composed of a reactive component-1 that is miscible with its growing molecules and another reactive component-2 that is not miscible with its growing molecules was considered with crosslinking reaction kinetics of the each component.
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Reactive power management and voltage control in deregulated power markets
NASA Astrophysics Data System (ADS)
Spangler, Robert G.
The research that is the subject of this dissertation is about the management of reactive power and voltage support in the wholesale open access power markets in the United States (US). The purpose of this research is to place decisions about open access market structures, as they relate to reactive power and voltage control, on a logical and consistent economic basis, given the engineering needs of a commercial electric power system. An examination of the electricity markets operating in the US today reveals that current approaches to reactive power management and voltage support are extensions of those based on historical, regulated monopoly electric service. A case for change is built by first looking at the subject of reactive power from an engineering viewpoint and then from an economic perspective. Ultimately, a set of market rules for managing reactive power and voltage support is proposed. The proposal suggests that cost recovery for static and dynamic VARs is appropriately accomplished through the regulated transmission cost of service. Static VAR cost recovery should follow traditional rate recovery methodologies. In the case of dynamic VARs, this work provides a methodology based on the microeconomic theory of the firm for determining such cost. It further suggests that an operational strategy that reduces and limits the use of dynamic VARs, during normal operations, is appropriate. This latter point leads to an increase in the fixed cost of the transmission network but prevents price spikes and short supply situations from affecting, or being affected by, the reactive capability limitations associated with dynamic VARs supplied from synchronous generators. The rules are consistent with a market structure that includes competitive generation and their application will result in the communication of a clear understanding of the responsibilities, related to voltage control, of each type of market entity. In this sense, their application will contribute to the efficient functioning of the wholesale open access markets.
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LES-ODT Simulations of Turbulent Reacting Shear Layers
NASA Astrophysics Data System (ADS)
Hoffie, Andreas; Echekki, Tarek
2012-11-01
Large-eddy simulations (LES) combined with the one-dimensional turbulence (ODT) simulations of a spatially developing turbulent reacting shear layer with heat release and high Reynolds numbers were conducted and compared to results from direct numerical simulations (DNS) of the same configuration. The LES-ODT approach is based on LES solutions for momentum on a coarse grid and solutions for momentum and reactive scalars on a fine ODT grid, which is embedded in the LES computational domain. The shear layer is simulated with a single-step, second-order reaction with an Arrhenius reaction rate. The transport equations are solved using a low Mach number approximation. The LES-ODT simulations yield reasonably accurate predictions of turbulence and passive/reactive scalars' statistics compared to DNS results.
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Dynamics starting at a conical intersection: Application to the photochemistry of pyrrole
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sellner, Bernhard; Barbatti, Mario; Lischka, Hans
The photochemical ring opening process in pyrrole has been investigated by performing classical on-the-fly dynamics using the multiconfiguration self-consistent field method for the computation of energies and energy gradients. As starting point for the dynamics the conical intersection corresponding to the ring-puckered ring-opened structure, determined previously [Barbatti et al., J. Chem. Phys. 125, 164323 (2006)], has been chosen. Two sets of initial conditions for the nuclear velocities were constructed: (i) nuclear velocities in the branching (g,h) plane of the conical intersection and (ii) statistical distribution for all atoms. Both sets of initial conditions show very similar results. Reactive trajectories aremore » only found in a very limited sector in the (g,h) plane and reaction products are very similar. Within the simulation time of 1 ps, ring opening of pyrrole to the biradical NH=CH-CH-CH=CH chain followed by ring closure to a substituted cyclopropene structure (NH=CH-C{sub 3}H{sub 3}) is observed. The computed structural data correlate well with the experimentally observed dissociation products.« less
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Chemotactic and hydrodynamic effects on collective dynamics of self-diffusiophoretic Janus motors
NASA Astrophysics Data System (ADS)
Huang, Mu-Jie; Schofield, Jeremy; Kapral, Raymond
2017-12-01
Collective motion in nonequilibrium steady state suspensions of self-propelled Janus motors driven by chemical reactions can arise due to interactions coming from direct intermolecular forces, hydrodynamic flow effects, or chemotactic effects mediated by chemical gradients. The relative importance of these interactions depends on the reactive characteristics of the motors, the way in which the system is maintained in a steady state, and properties of the suspension, such as the volume fraction. From simulations of a microscopic hard collision model for the interaction of fluid particles with the Janus motor we show that dynamic cluster states exist and determine the interaction mechanisms that are responsible for their formation. The relative importance of chemotactic and hydrodynamic effects is identified by considering a microscopic model in which chemotactic effects are turned off while the full hydrodynamic interactions are retained. The system is maintained in a steady state by means of a bulk reaction in which product particles are reconverted into fuel particles. The influence of the bulk reaction rate on the collective dynamics is also studied.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wang, Chao; Xu, Zhijie; Lai, Kevin
The first part of this paper (Part 1) presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO2) capture. To generate data for WWC model validation, CO2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work has the ability to account for both chemical absorption and desorption of CO2 in MEA. In addition,more » the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry’s constant and gas diffusivity in the non-reacting nitrous oxide (N2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO2 reaction rate constants after using the N2O/CO2 analogy method. The calibrated model can be used to predict the CO2 mass transfer in a WWC for a wider range of operating conditions.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wang, Chao; Xu, Zhijie; Lai, Kevin
Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO 2) capture. In this study, to generate data for WWC model validation, CO 2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO 2 in MEA. In addition,more » the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO 2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N 2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO 2 reaction rate constants after using the N 2O/CO 2 analogy method. Finally, the calibrated model can be used to predict the CO 2 mass transfer in a WWC for a wider range of operating conditions.« less
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Gabba, Matteo; Poblete, Simón; Rosenkranz, Tobias; Katranidis, Alexandros; Kempe, Daryan; Züchner, Tina; Winkler, Roland G.; Gompper, Gerhard; Fitter, Jörg
2014-01-01
Over the last few decades, a view has emerged showing that multidomain enzymes are biological machines evolved to harness stochastic kicks of solvent particles into highly directional functional motions. These intrinsic motions are structurally encoded, and Nature makes use of them to catalyze chemical reactions by means of ligand-induced conformational changes and states redistribution. Such mechanisms align reactive groups for efficient chemistry and stabilize conformers most proficient for catalysis. By combining single-molecule Förster resonance energy transfer measurements with normal mode analysis and coarse-grained mesoscopic simulations, we obtained results for a hinge-bending enzyme, namely phosphoglycerate kinase (PGK), which support and extend these ideas. From single-molecule Förster resonance energy transfer, we obtained insight into the distribution of conformational states and the dynamical properties of the domains. The simulations allowed for the characterization of interdomain motions of a compact state of PGK. The data show that PGK is intrinsically a highly dynamic system sampling a wealth of conformations on timescales ranging from nanoseconds to milliseconds and above. Functional motions encoded in the fold are performed by the PGK domains already in its ligand-free form, and substrate binding is not required to enable them. Compared to other multidomain proteins, these motions are rather fast and presumably not rate-limiting in the enzymatic reaction. Ligand binding slightly readjusts the orientation of the domains and feasibly locks the protein motions along a preferential direction. In addition, the functionally relevant compact state is stabilized by the substrates, and acts as a prestate to reach active conformations by means of Brownian motions. PMID:25418172
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Wang, Chao; Xu, Zhijie; Lai, Kevin; ...
2017-10-24
Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO 2) capture. In this study, to generate data for WWC model validation, CO 2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO 2 in MEA. In addition,more » the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO 2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N 2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO 2 reaction rate constants after using the N 2O/CO 2 analogy method. Finally, the calibrated model can be used to predict the CO 2 mass transfer in a WWC for a wider range of operating conditions.« less