Path finding methods accounting for stoichiometry in metabolic networks

PubMed Central

2011-01-01

Graph-based methods have been widely used for the analysis of biological networks. Their application to metabolic networks has been much discussed, in particular noting that an important weakness in such methods is that reaction stoichiometry is neglected. In this study, we show that reaction stoichiometry can be incorporated into path-finding approaches via mixed-integer linear programming. This major advance at the modeling level results in improved prediction of topological and functional properties in metabolic networks. PMID:21619601

An adaptive multi-level simulation algorithm for stochastic biological systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lester, C., E-mail: lesterc@maths.ox.ac.uk; Giles, M. B.; Baker, R. E.

2015-01-14

Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Montemore » Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10(1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.« less

Predictions of hydrothermal alteration within near-ridge oceanic crust from coordinated geochemical and fluid flow models

USGS Publications Warehouse

Wetzel, L.R.; Raffensperger, Jeff P.; Shock, E.L.

2001-01-01

Coordinated geochemical and hydrological calculations guide our understanding of the composition, fluid flow patterns, and thermal structure of near-ridge oceanic crust. The case study presented here illustrates geochemical and thermal changes taking place as oceanic crust ages from 0.2 to 1.0 Myr. Using a finite element code, we model fluid flow and heat transport through the upper few hundred meters of an abyssal hill created at an intermediate spreading rate. We use a reaction path model with a customized database to calculate equilibrium fluid compositions and mineral assemblages of basalt and seawater at 500 bars and temperatures ranging from 150 to 400??C. In one scenario, reaction path calculations suggest that volume increases on the order of 10% may occur within portions of the basaltic basement. If this change in volume occurred, it would be sufficient to fill all primary porosity in some locations, effectively sealing off portions of the oceanic crust. Thermal profiles resulting from fluid flow simulations indicate that volume changes along this possible reaction path occur primarily within the first 0.4 Myr of crustal aging. ?? 2001 Elsevier Science B.V. All rights reserved.

Comparison Of Reaction Barriers In Energy And Free Energy For Enzyme Catalysis

NASA Astrophysics Data System (ADS)

Andrés Cisneros, G.; Yang, Weitao

Reaction paths on potential energy surfaces obtained from QM/MM calculations of enzymatic or solution reactions depend on the starting structure employed for the path calculations. The free energies associated with these paths should be more reliable for studying reaction mechanisms, because statistical averages are used. To investigate this, the role of enzyme environment fluctuations on reaction paths has been studied with an ab initio QM/MM method for the first step of the reaction catalyzed by 4-oxalocrotonate tautomerase (4OT). Four minimum energy paths (MEPs) are compared, which have been determined with two different methods. The first path (path A) has been determined with a procedure that combines the nudged elastic band (NEB) method and a second order parallel path optimizer recently developed in our group. The second path (path B) has also been determined by the combined procedure, however, the enzyme environment has been relaxed by molecular dynamics (MD) simulations. The third path (path C) has been determined with the coordinate driving (CD) method, using the enzyme environment from path B. We compare these three paths to a previously determined path (path D) determined with the CD method. In all four cases the QM/MM-FE method (Y. Zhang et al., JCP, 112, 3483) was employed to obtain the free energy barriers for all four paths. In the case of the combined procedure, the reaction path is approximated by a small number of images which are optimized to the MEP in parallel, which results in a reduced computational cost. However, this does not allow the FEP calculation on the MEP. In order to perform FEP calculations on these paths, we introduce a modification to the NEB method that enables the addition of as many extra images to the path as needed for the FEP calculations. The calculated potential energy barriers show differences in the activation barrier between the calculated paths of as much as 5.17 kcal/mol. However, the largest free energy barrier difference is 1.58 kcal/mol. These results show the importance of the inclusion of the environment fluctuation in the calculation of enzymatic activation barriers

Porosity development in coastal carbonate aquifers

USGS Publications Warehouse

Sanford, W.E.; Konikow, Leonard F.

1989-01-01

Combines geochemical mixing theory with the hydrodynamics of fresh-water-salt-water mixing zones in a coupled reaction-transport model. Results from the reaction-path model PHREEQE are used with a variable-density groundwater flow and solute-transport model to simulate an idealized cross section of a coastal carbonate aquifer. The dissolution process is sensitive to fresh-water chemistry, groundwater velocities, and sea-level movement. -from Authors

A theory-based dual-focus alcohol intervention for preadolescents: the Strong African American Families Program.

PubMed

Gerrard, Meg; Gibbons, Frederick X; Brody, Gene H; Murry, Velma McBride; Cleveland, Michael J; Wills, Thomas A

2006-06-01

This study examined mediators of the Strong African American Families Program, a randomized, dual-focus prevention trial intended to delay the onset of alcohol use and reduce alcohol consumption among rural African American youths. More specifically, it demonstrated that changes in consumption 2 yrs after the intervention were mediated through 2 different paths, a social reaction path and a reasoned/intention path. The social reaction path provided evidence that relative to the control condition, the intervention decreased children's willingness to drink by making their images of drinkers less favorable. The reasoned/intention path provided evidence that the intervention influenced the children's intentions to drink by increasing targeted parenting behaviors related to alcohol. Furthermore, the data demonstrate that these changes in willingness and intentions were independently associated with alcohol consumption at the follow-up, and they suggest that a dual-process model approach that targets both intentions and willingness can be more successful than either approach alone.

An optimization model for metabolic pathways.

PubMed

Planes, F J; Beasley, J E

2009-10-15

Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner.

Atmospheric reaction of Cl + methacrolein: a theoretical study on the mechanism, and pressure- and temperature-dependent rate constants.

PubMed

Sun, Cuihong; Xu, Baoen; Zhang, Shaowen

2014-05-22

Methacrolein is a major degradation product of isoprene, the reaction of methacrolein with Cl atoms may play some roles in the degradation of isoprene where these species are relatively abundant. However, the energetics and kinetics of this reaction, which govern the reaction branching, are still not well understood so far. In the present study, two-dimensional potential energy surfaces were constructed to analyze the minimum energy path of the barrierless addition process between Cl and the C═C double bond of methacrolein, which reveals that the terminal addition intermediate is directly formed from the addition reaction. The terminal addition intermediate can further yield different products among which the reaction paths abstracting the aldehyde hydrogen atom and the methyl hydrogen atom are dominant reaction exits. The minimum reaction path for the direct aldehydic hydrogen atom abstraction is also obtained. The reaction kinetics was calculated by the variational transition state theory in conjunction with the master equation method. From the theoretical model we predicted that the overall rate constant of the Cl + methacrolein reaction at 297 K and atmospheric pressure is koverall = 2.3× 10(-10) cm(3) molecule(-1) s(-1), and the branching ratio of the aldehydic hydrogen abstraction is about 12%. The reaction is pressure dependent at P < 10 Torr with the high pressure limit at about 100 Torr. The calculated results could well account for the experimental observations.

Unusual reaction paths of SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-: Quantum chemical calculations

NASA Astrophysics Data System (ADS)

Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.

2013-11-01

Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.

Cumulative Significance of Hyporheic Exchange and Biogeochemical Processing in River Networks

NASA Astrophysics Data System (ADS)

Harvey, J. W.; Gomez-Velez, J. D.

2014-12-01

Biogeochemical reactions in rivers that decrease excessive loads of nutrients, metals, organic compounds, etc. are enhanced by hydrologic interactions with microbially and geochemically active sediments of the hyporheic zone. The significance of reactions in individual hyporheic flow paths has been shown to be controlled by the contact time between river water and sediment and the intrinsic reaction rate in the sediment. However, little is known about how the cumulative effects of hyporheic processing in large river basins. We used the river network model NEXSS (Gomez-Velez and Harvey, submitted) to simulate hyporheic exchange through synthetic river networks based on the best available models of network topology, hydraulic geometry and scaling of geomorphic features, grain size, hydraulic conductivity, and intrinsic reaction rates of nutrients and metals in river sediment. The dimensionless reaction significance factor, RSF (Harvey et al., 2013) was used to quantify the cumulative removal fraction of a reactive solute by hyporheic processing. SF scales reaction progress in a single pass through the hyporheic zone with the proportion of stream discharge passing through the hyporheic zone for a specified distance. Reaction progress is optimal where the intrinsic reaction timescale in sediment matches the residence time of hyporheic flow and is less efficient in longer residence time hyporheic flow as a result of the decreasing proportion of river flow that is processed by longer residence time hyporheic flow paths. In contrast, higher fluxes through short residence time hyporheic flow paths may be inefficient because of the repeated surface-subsurface exchanges required to complete the reaction. Using NEXSS we found that reaction efficiency may be high in both small streams and large rivers, although for different reasons. In small streams reaction progress generally is dominated by faster pathways of vertical exchange beneath submerged bedforms. Slower exchange beneath meandering river banks mainly has importance only in large rivers. For solutes entering networks in proportion to water inputs it is the lower order streams that tend to dominate cumulative reaction progress.

Sputtering, Plasma Chemistry, and RF Sheath Effects in Low-Temperature and Fusion Plasma Modeling

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Kruger, Scott E.; McGugan, James M.; Pankin, Alexei Y.; Roark, Christine M.; Smithe, David N.; Stoltz, Peter H.

2016-09-01

A new sheath boundary condition has been implemented in VSim, a plasma modeling code which makes use of both PIC/MCC and fluid FDTD representations. It enables physics effects associated with DC and RF sheath formation - local sheath potential evolution, heat/particle fluxes, and sputtering effects on complex plasma-facing components - to be included in macroscopic-scale plasma simulations that need not resolve sheath scale lengths. We model these effects in typical ICRF antenna operation scenarios on the Alcator C-Mod fusion device, and present comparisons of our simulation results with experimental data together with detailed 3D animations of antenna operation. Complex low-temperature plasma chemistry modeling in VSim is facilitated by MUNCHKIN, a standalone python/C++/SQL code that identifies possible reaction paths for a given set of input species, solves 1D rate equations for the ensuing system's chemical evolution, and generates VSim input blocks with appropriate cross-sections/reaction rates. These features, as well as principal path analysis (to reduce the number of simulated chemical reactions while retaining accuracy) and reaction rate calculations from user-specified distribution functions, will also be demonstrated. Supported by the U.S. Department of Energy's SBIR program, Award DE-SC0009501.

A Detailed Chemical Kinetic Model for TNT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pitz, W J; Westbrook, C K

2005-01-13

A detailed chemical kinetic mechanism for 2,4,6-tri-nitrotoluene (TNT) has been developed to explore problems of explosive performance and soot formation during the destruction of munitions. The TNT mechanism treats only gas-phase reactions. Reactions for the decomposition of TNT and for the consumption of intermediate products formed from TNT are assembled based on information from the literature and on current understanding of aromatic chemistry. Thermodynamic properties of intermediate and radical species are estimated by group additivity. Reaction paths are developed based on similar paths for aromatic hydrocarbons. Reaction-rate constant expressions are estimated from the literature and from analogous reactions where themore » rate constants are available. The detailed reaction mechanism for TNT is added to existing reaction mechanisms for RDX and for hydrocarbons. Computed results show the effect of oxygen concentration on the amount of soot precursors that are formed in the combustion of RDX and TNT mixtures in N{sub 2}/O{sub 2} mixtures.« less

Changes at work and employee reactions: organizational elements, job insecurity, and short-term stress as predictors for employee health and safety.

PubMed

Størseth, Fred

2006-12-01

The objective was to identify focus areas for possible reduction of job insecurity and its outcomes. A model was specified and tested as a prediction model for health and safety. First, a parsimonious model was specified. The model consisted of perceived job insecurity (as a stressor), organizational factors (information quality, leadership style, work task administration), and short-term stress reactions (job dissatisfaction, reduced work motivation). Second, the model was tested as a prediction model in three separate path analyses, in order to examine the model's contribution in explaining (1) physical health complaints, (2) mental health complaints, and (3) risk taking behavior. A quota sample of Norwegian employees (N= 1,002) was obtained by means of a self-completion questionnaire survey. The results of the structural equation modeling (path analyses) supported the hypothesized model. Mental health complaints and employee risk taking behavior were significantly predicted (not physical health complaints).

Exploring the full catalytic cycle of rhodium(i)–BINAP-catalysed isomerisation of allylic amines: a graph theory approach for path optimisation† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00401j Click here for additional data file.

PubMed Central

Yoshimura, Takayoshi; Taketsugu, Tetsuya; Sawamura, Masaya

2017-01-01

We explored the reaction mechanism of the cationic rhodium(i)–BINAP complex catalysed isomerisation of allylic amines using the artificial force induced reaction method with the global reaction route mapping strategy, which enabled us to search for various reaction paths without assumption of transition states. The entire reaction network was reproduced in the form of a graph, and reasonable paths were selected from the complicated network using Prim’s algorithm. As a result, a new dissociative reaction mechanism was proposed. Our comprehensive reaction path search provided rationales for the E/Z and S/R selectivities of the stereoselective reaction. PMID:28970877

A new network representation of the metabolism to detect chemical transformation modules.

PubMed

Sorokina, Maria; Medigue, Claudine; Vallenet, David

2015-11-14

Metabolism is generally modeled by directed networks where nodes represent reactions and/or metabolites. In order to explore metabolic pathway conservation and divergence among organisms, previous studies were based on graph alignment to find similar pathways. Few years ago, the concept of chemical transformation modules, also called reaction modules, was introduced and correspond to sequences of chemical transformations which are conserved in metabolism. We propose here a novel graph representation of the metabolic network where reactions sharing a same chemical transformation type are grouped in Reaction Molecular Signatures (RMS). RMS were automatically computed for all reactions and encode changes in atoms and bonds. A reaction network containing all available metabolic knowledge was then reduced by an aggregation of reaction nodes and edges to obtain a RMS network. Paths in this network were explored and a substantial number of conserved chemical transformation modules was detected. Furthermore, this graph-based formalism allows us to define several path scores reflecting different biological conservation meanings. These scores are significantly higher for paths corresponding to known metabolic pathways and were used conjointly to build association rules that should predict metabolic pathway types like biosynthesis or degradation. This representation of metabolism in a RMS network offers new insights to capture relevant metabolic contexts. Furthermore, along with genomic context methods, it should improve the detection of gene clusters corresponding to new metabolic pathways.

Mixed quantum-classical studies of energy partitioning in unimolecular chemical reactions

NASA Astrophysics Data System (ADS)

Bladow, Landon Lowell

A mixed quantum-classical reaction path Hamiltonian method is utilized to study the dynamics of unimolecular reactions. The method treats motion along the reaction path classically and treats the transverse vibrations quantum mechanically. The theory leads to equations that predict the disposai of the exit-channel potential energy to product translation and vibration. In addition, vibrational state distributions are obtained for the product normal modes. Vibrational excitation results from the curvature of the minimum energy reaction path. The method is applied to six unimolecular reactions: HF elimination from fluoroethane, 1,1-difluoroethane, 1,1-difluoroethene, and trifluoromethane; and HCl elimination from chloroethane and acetyl chloride. The minimum energy paths were calculated at either the MP2 or B3LYP level of theory. In all cases, the majority of the vibrational excitation of the products occurs in the HX fragment. The results are compared to experimental data and other theoretical results, where available. The best agreement between the experimental and calculated HX vibrational distributions is found for the halogenated ethanes, and the experimental deduction that the majority of the HX vibrational excitation arises from the potential energy release is supported. It is believed that the excess energy provided in experiments contributes to the poorer agreement between experiment and theory observed for HF elimination from 1,1-difluoroethene and trifluoromethane. An attempt is described to incorporate a treatment of the excess energy into the present method. However, the sign of the curvature coupling elements is then found to affect the dynamics. Overall, the method appears to be an efficient dynamical tool for modeling the disposal of the exit-channel potential energy in unimolecular reactions.

Reactions and reaction rates in the regional aquifer beneath the Pajarito Plateau, north-central New Mexico, USA

NASA Astrophysics Data System (ADS)

Hereford, Anne G.; Keating, Elizabeth H.; Guthrie, George D.; Zhu, Chen

2007-05-01

Reactions and reaction rates within aquifers are fundamental components of critical hydrological processes. However, reactions simulated in laboratory experiments typically demonstrate rates that are much faster than those observed in the field. Therefore, it is necessary to conduct more reaction rate analyses in natural settings. This study of geochemical reactions in the regional aquifer in the Pajarito Plateau near Los Alamos, New Mexico combines modeling with petrographic assessment to further knowledge and understanding of complex natural hydrologic systems. Groundwater geochemistry shows marked evolution along assumed flow paths. The flow path chosen for this study was evaluated using inverse mass balance modeling to calculate the mass transfer. X-ray diffraction and field emission gun scanning electron microscopy were used to identify possible reactants and products. Considering the mineralogy of the aquifer and saturation indices for the regional water refined initial interpretations. Calculations yielded dissolution rates for plagioclase on the order of 10-15 mol s-1 m-2 and for K-feldspar on the order of 10-17 mol s-1 m-2, orders of magnitude slower than laboratory rates. While these rates agree with other aquifer studies, they must be considered in the light of the uncertainty associated with geometric surface area estimates, 14C ages, and aquifer properties.

A benchmark for reaction coordinates in the transition path ensemble

PubMed Central

2016-01-01

The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems. PMID:27059559

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

PubMed Central

Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

2013-01-01

Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008

Developing Chemistry and Kinetic Modeling Tools for Low-Temperature Plasma Simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas; Beckwith, Kris; Davidson, Bradley; Kruger, Scott; Pankin, Alexei; Roark, Christine; Stoltz, Peter

2015-09-01

We discuss the use of proper orthogonal decomposition (POD) methods in VSim, a FDTD plasma simulation code capable of both PIC/MCC and fluid modeling. POD methods efficiently generate smooth representations of noisy self-consistent or test-particle PIC data, and are thus advantageous in computing macroscopic fluid quantities from large PIC datasets (e.g. for particle-based closure computations) and in constructing optimal visual representations of the underlying physics. They may also confer performance advantages for massively parallel simulations, due to the significant reduction in dataset sizes conferred by truncated singular-value decompositions of the PIC data. We also demonstrate how complex LTP chemistry scenarios can be modeled in VSim via an interface with MUNCHKIN, a developing standalone python/C++/SQL code that identifies reaction paths for given input species, solves 1D rate equations for the time-dependent chemical evolution of the system, and generates corresponding VSim input blocks with appropriate cross-sections/reaction rates. MUNCHKIN also computes reaction rates from user-specified distribution functions, and conducts principal path analyses to reduce the number of simulated chemical reactions. Supported by U.S. Department of Energy SBIR program, Award DE-SC0009501.

Computational study on the aminolysis of beta-hydroxy-alpha,beta-unsaturated ester via the favorable path including the formation of alpha-oxo ketene intermediate.

PubMed

Jin, Lu; Xue, Ying; Zhang, Hui; Kim, Chan Kyung; Xie, Dai Qian; Yan, Guo Sen

2008-05-15

The possible mechanisms of the aminolysis of N-methyl-3-(methoxycarbonyl)-4-hydroxy-2-pyridone (beta-hydroxy-alpha,beta-unsaturated ester) with dimethylamine are investigated at the hybrid density functional theory B3LYP/6-31G(d,p) level in the gas phase. Single-point computations at the B3LYP/6-311++G(d,p) and the Becke88-Becke95 1-parameter model BB1K/6-311++G(d,p) levels are performed for more precise energy predictions. Solvent effects are also assessed by single-point calculations at the integral equation formalism polarized continuum model IEFPCM-B3LYP/6-311++G(d,p) and IEFPCM-BB1K/6-311++G(d,p) levels on the gas-phase optimized geometries. Three possible pathways, the concerted pathway (path A), the stepwise pathway involving tetrahedral intermediates (path B), and the stepwise pathway via alpha-oxo ketene intermediate due to the participation of beta-hydroxy (path C), are taken into account for the title reaction. Moreover, path C includes two sequential processes. The first process is to generate alpha-oxo ketene intermediate via the decomposition of N-methyl-3-(methoxycarbonyl)-4-hydroxy-2-pyridone; the second process is the addition of dimethylamine to alpha-oxo ketene intermediate. Our results indicate that path C is more favorable than paths A and B both in the gas phase and in solvent (heptane). In path C, the first process is the rate-determining step, and the second process is revealed to be a [4+2] pseudopericyclic reaction without the energy barrier. Being independent of the concentration of amine, the first process obeys the first-order rate law.

Quantum optimal control of isomerization dynamics of a one-dimensional reaction-path model dominated by a competing dissociation channel

NASA Astrophysics Data System (ADS)

Kurosaki, Yuzuru; Artamonov, Maxim; Ho, Tak-San; Rabitz, Herschel

2009-07-01

Quantum wave packet optimal control simulations with intense laser pulses have been carried out for studying molecular isomerization dynamics of a one-dimensional (1D) reaction-path model involving a dominant competing dissociation channel. The 1D intrinsic reaction coordinate model mimics the ozone open→cyclic ring isomerization along the minimum energy path that successively connects the ozone cyclic ring minimum, the transition state (TS), the open (global) minimum, and the dissociative O2+O asymptote on the O3 ground-state A1' potential energy surface. Energetically, the cyclic ring isomer, the TS barrier, and the O2+O dissociation channel lie at ˜0.05, ˜0.086, and ˜0.037 hartree above the open isomer, respectively. The molecular orientation of the modeled ozone is held constant with respect to the laser-field polarization and several optimal fields are found that all produce nearly perfect isomerization. The optimal control fields are characterized by distinctive high temporal peaks as well as low frequency components, thereby enabling abrupt transfer of the time-dependent wave packet over the TS from the open minimum to the targeted ring minimum. The quick transition of the ozone wave packet avoids detrimental leakage into the competing O2+O channel. It is possible to obtain weaker optimal laser fields, resulting in slower transfer of the wave packets over the TS, when a reduced level of isomerization is satisfactory.

Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in the QM/MM scheme.

PubMed

Asada, Toshio; Ando, Kanta; Sakurai, Koji; Koseki, Shiro; Nagaoka, Masataka

2015-10-28

An efficient approach to evaluate free energy gradients (FEGs) within the quantum mechanical/molecular mechanical (QM/MM) framework has been proposed to clarify reaction processes on the free energy surface (FES) in molecular assemblies. The method is based on response kernel approximations denoted as the charge and the atom dipole response kernel (CDRK) model that include explicitly induced atom dipoles. The CDRK model was able to reproduce polarization effects for both electrostatic interactions between QM and MM regions and internal energies in the QM region obtained by conventional QM/MM methods. In contrast to charge response kernel (CRK) models, CDRK models could be applied to various kinds of molecules, even linear or planer molecules, without using imaginary interaction sites. Use of the CDRK model enabled us to obtain FEGs on QM atoms in significantly reduced computational time. It was also clearly demonstrated that the time development of QM forces of the solvated propylene carbonate radical cation (PC˙(+)) provided reliable results for 1 ns molecular dynamics (MD) simulation, which were quantitatively in good agreement with expensive QM/MM results. Using FEG and nudged elastic band (NEB) methods, we found two optimized reaction paths on the FES for decomposition reactions to generate CO2 molecules from PC˙(+), whose reaction is known as one of the degradation mechanisms in the lithium-ion battery. Two of these reactions proceed through an identical intermediate structure whose molecular dipole moment is larger than that of the reactant to be stabilized in the solvent, which has a high relative dielectric constant. Thus, in order to prevent decomposition reactions, PC˙(+) should be modified to have a smaller dipole moment along two reaction paths.

Chemical reaction path modeling of hydrothermal processes on Mars: Preliminary results

NASA Technical Reports Server (NTRS)

Plumlee, Geoffrey S.; Ridley, W. Ian

1992-01-01

Hydrothermal processes are thought to have had significant roles in the development of surficial mineralogies and morphological features on Mars. For example, a significant proportion of the Martian soil could consist of the erosional products of hydrothermally altered impact melt sheets. In this model, impact-driven, vapor-dominated hydrothermal systems hydrothermally altered the surrounding rocks and transported volatiles such as S and Cl to the surface. Further support for impact-driven hydrothermal alteration on Mars was provided by studies of the Ries crater, Germany, where suevite deposits were extensively altered to montmorillonite clays by inferred low-temperature (100-130 C) hydrothermal fluids. It was also suggested that surface outflow from both impact-driven and volcano-driven hydrothermal systems could generate the valley networks, thereby eliminating the need for an early warm wet climate. We use computer-driven chemical reaction path calculation to model chemical processes which were likely associated with postulated Martian hydrothermal systems.

A Networks Approach to Modeling Enzymatic Reactions.

PubMed

Imhof, P

2016-01-01

Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.

Modeling of hydrogen evolution reaction on the surface of GaInP2

NASA Astrophysics Data System (ADS)

Choi, Woon Ih; Wood, Brandon; Schwegler, Eric; Ogitsu, Tadashi

2012-02-01

GaInP2 is promising candidate material for hydrogen production using sunlight. It reduces solvated proton into hydrogen molecule using light-induced excited electrons in the photoelectrochemical cell. However, it is challenging to model hydrogen evolution reaction (HER) using first-principles molecular dynamics. Instead, we use Anderson-Newns model and generalized solvent coordinate in Marcus-Hush theory to describe adiabatic free energy surface of HER. Model parameters are fitted from the DFT calculations. We model Volmer-Heyrovsky reaction path on the surfaces of CuPt phase of GaInP2. We also discuss effects of surface oxide and catalyst atoms that exist on top of bare surfaces in experimental circumstances.

Modeling the mechanism of glycosylation reactions between ethanol, 1,2-ethanediol and methoxymethanol.

PubMed

Azofra, Luis Miguel; Alkorta, Ibon; Toro-Labbé, Alejandro; Elguero, José

2013-09-07

The mechanism of the S(N)2 model glycosylation reaction between ethanol, 1,2-ethanediol and methoxymethanol has been studied theoretically at the B3LYP/6-311+G(d,p) computational level. Three different types of reactions have been explored: (i) the exchange of hydroxyl groups between these model systems; (ii) the basic catalysis reactions by combination of the substrates as glycosyl donors (neutral species) and acceptors (enolate species); and (iii) the effect on the reaction profile of an explicit H2O molecule in the reactions considered in (ii). The reaction force, the electronic chemical potential and the reaction electronic flux have been characterized for the reaction path in each case. Energy calculations show that methoxymethanol is the worst glycosyl donor model among the ones studied here, while 1,2-ethanediol is the best, having the lowest activation barrier of 74.7 kJ mol(-1) for the reaction between this one and the ethanolate as the glycosyl acceptor model. In general, the presence of direct interactions between the atoms involved in the penta-coordinated TS increases the activation energies of the processes.

Reaction path modelling of in-situ mineralisation of CO2 at the CarbFix site at Hellisheidi, SW-Iceland

NASA Astrophysics Data System (ADS)

Snæbjörnsdóttir, Sandra Ó.; Gislason, Sigurdur R.; Galeczka, Iwona M.; Oelkers, Eric H.

2018-01-01

Results from injection of 175 tonnes of CO2 into the basaltic subsurface rocks at the CarbFix site in SW-Iceland in 2012 show almost complete mineralisation of the injected carbon in less than two years (Matter et al., 2016; Snæbjörnsdóttir et al., 2017). Reaction path modelling was performed to illuminate the rate and extent of CO2-water-rock reactions during and after the injection. The modelling calculations were constrained by the compositions of fluids sampled prior to, during, and after the injection, as reported by Alfredsson et al. (2013) and Snæbjörnsdóttir et al. (2017). The pH of the injected fluid, prior to CO2 dissolution was ∼9.5, whereas the pH of the background waters in the first monitoring well prior to the injections was ∼9.4. The pH of the sampled fluids used in the modelling ranged from ∼3.7 at the injection well to as high as 8.2 in the first monitoring well. Modelling results suggest that CO2-rich water-basalt interaction is dominated by crystalline basalt dissolution along a faster, high permeability flow path, but by basaltic glass dissolution along a slower, pervasive flow path through which the bulk of the injected fluid flows. Dissolution of pre-existing calcite at the onset of the injection does not have a net effect on the carbonation, but does contribute to a rapid early pH rise during the injection, and influences which carbonate minerals precipitate. At low pH, Mg, and Fe are preferentially released from crystalline basalts due to the higher dissolution rates of olivine, and to lesser extent pyroxene, compared to plagioclase and glass (Gudbrandsson et al., 2011). This favours the formation of siderite and Fe-Mg carbonates over calcite during early mineralisation. The model suggests the formation of the following carbonate mineral sequences: siderite at pH < 5, Mg-Fe-carbonates and Ca-Mg-Fe-carbonates at pH > 5, and calcite at higher pH. Other minerals forming with the carbonates are Al- and Fe-hydroxides and chalcedony, and zeolites and smectites at elevated pH. The most efficient carbonate formation is when the pH is high enough for formation of carbonates, but not so high that zeolites and smectites start to form, which compete with carbonates over both cations and pore space. The results of reaction path modelling at the CarbFix site in SW-Iceland indicate that this ;sweet spot; for mineralisation of CO2 is at pH from ∼5.2 to 6.5 in basalts at low temperature (20-50 °C).

Enzymatic reaction paths as determined by transition path sampling

NASA Astrophysics Data System (ADS)

Masterson, Jean Emily

Enzymes are biological catalysts capable of enhancing the rates of chemical reactions by many orders of magnitude as compared to solution chemistry. Since the catalytic power of enzymes routinely exceeds that of the best artificial catalysts available, there is much interest in understanding the complete nature of chemical barrier crossing in enzymatic reactions. Two specific questions pertaining to the source of enzymatic rate enhancements are investigated in this work. The first is the issue of how fast protein motions of an enzyme contribute to chemical barrier crossing. Our group has previously identified sub-picosecond protein motions, termed promoting vibrations (PVs), that dynamically modulate chemical transformation in several enzymes. In the case of human heart lactate dehydrogenase (hhLDH), prior studies have shown that a specific axis of residues undergoes a compressional fluctuation towards the active site, decreasing a hydride and a proton donor--acceptor distance on a sub-picosecond timescale to promote particle transfer. To more thoroughly understand the contribution of this dynamic motion to the enzymatic reaction coordinate of hhLDH, we conducted transition path sampling (TPS) using four versions of the enzymatic system: a wild type enzyme with natural isotopic abundance; a heavy enzyme where all the carbons, nitrogens, and non-exchangeable hydrogens were replaced with heavy isotopes; and two versions of the enzyme with mutations in the axis of PV residues. We generated four separate ensembles of reaction paths and analyzed each in terms of the reaction mechanism, time of barrier crossing, dynamics of the PV, and residues involved in the enzymatic reaction coordinate. We found that heavy isotopic substitution of hhLDH altered the sub-picosecond dynamics of the PV, changed the favored reaction mechanism, dramatically increased the time of barrier crossing, but did not have an effect on the specific residues involved in the PV. In the mutant systems, we observed changes in the reaction mechanism and altered contributions of the mutated residues to the enzymatic reaction coordinate, but we did not detect a substantial change in the time of barrier crossing. These results confirm the importance of maintaining the dynamics and structural scaffolding of the hhLDH PV in order to facilitate facile barrier passage. We also utilized TPS to investigate the possible role of fast protein dynamics in the enzymatic reaction coordinate of human dihydrofolate reductase (hsDHFR). We found that sub-picosecond dynamics of hsDHFR do contribute to the reaction coordinate, whereas this is not the case in the E. coli version of the enzyme. This result indicates a shift in the DHFR family to a more dynamic version of catalysis. The second inquiry we addressed in this thesis regarding enzymatic barrier passage concerns the variability of paths through reactive phase space for a given enzymatic reaction. We further investigated the hhLDH-catalyzed reaction using a high-perturbation TPS algorithm. Though we saw that alternate reaction paths were possible, the dominant reaction path we observed corresponded to that previously elucidated in prior hhLDH TPS studies. Since the additional reaction paths we observed were likely high-energy, these results indicate that only the dominant reaction path contributes significantly to the overall reaction rate. In conclusion, we show that the enzymes hhLDH and hsDHFR exhibit paths through reactive phase space where fast protein motions are involved in the enzymatic reaction coordinate and exhibit a non-negligible contribution to chemical barrier crossing.

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

PubMed Central

2015-01-01

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys.2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled. PMID:25516726

Variational nature, integration, and properties of Newton reaction path

NASA Astrophysics Data System (ADS)

Bofill, Josep Maria; Quapp, Wolfgang

2011-02-01

The distinguished coordinate path and the reduced gradient following path or its equivalent formulation, the Newton trajectory, are analyzed and unified using the theory of calculus of variations. It is shown that their minimum character is related to the fact that the curve is located in a valley region. In this case, we say that the Newton trajectory is a reaction path with the category of minimum energy path. In addition to these findings a Runge-Kutta-Fehlberg algorithm to integrate these curves is also proposed.

Variational nature, integration, and properties of Newton reaction path.

PubMed

Bofill, Josep Maria; Quapp, Wolfgang

2011-02-21

The distinguished coordinate path and the reduced gradient following path or its equivalent formulation, the Newton trajectory, are analyzed and unified using the theory of calculus of variations. It is shown that their minimum character is related to the fact that the curve is located in a valley region. In this case, we say that the Newton trajectory is a reaction path with the category of minimum energy path. In addition to these findings a Runge-Kutta-Fehlberg algorithm to integrate these curves is also proposed.

A theoretical study of three gas-phase reactions involving the production or loss of methane cations.

PubMed

Baptista, Leonardo; da Silveira, Enio F

2014-10-21

Hydrocarbon ions are important species in flames, spectroscopy and the interstellar medium. Their importance is reflected in the extensive body of literature on the structure and reactivity of carbocations. However, the geometry, electronic structure and reactivity of carbocations are difficult to assess. This study aims to contribute to the current knowledge of this subject by presenting a quantum mechanics description of methane cation dissociation using multiconfigurational methods. The geometric and electronic parameters of the minimum structure were determined for three main reaction paths: the dissociation CH4(+)→ CH2(+) + H2 and the dissociation-recombination processes CH4(+)↔ CH3(+) + H. The electronic and energetic effects of these reactions were analyzed, and it was found that each reaction path has a strong dependence on the methodology used as well as a strong multiconfigurational character during dissociation. The first doublet excited states are inner-shell excited states and may correspond to the ions that are expected to be formed after electron detachment. The rate coefficient for each reaction path was determined using variational transition state theory and RRKM/master equation calculations. The major dissociation paths, with their rate coefficients at the high-pressure limit, are CH4(+)(X(~)(2)B1) → CH3(+)(A(2)A1') + H((2)S) (k∞(T) = 1.42 × 10(+14) s(-1) exp(-37.12/RT)) and CH4(+)(X(~)(2)B1) → CH2(+)(A(2)A1) + H2((2)Σg(+)) (k∞(T) = 9.18 × 10(+14) s(-1) exp(-55.77/RT)). Our findings help to explain the abundance of ions formed from CH4 in the interstellar medium and to build models of chemical evolution.

Development of Bicarbonate-Activated Peroxide as a Chemical and Biological Warfare Agent Decontaminant

DTIC Science & Technology

2006-06-30

may operate for certain substrates. The reaction of equation 1 proceeds with the intermediacy of CO2 as shown in Figure 1. Although it is well...competition between paths 5 and 6 will depend on the conditions and the nature of the substrate S. Note that figures, equations , etc. in the...1 shows the complete reaction scheme used to model the equilibration reaction at low temperature. Table 1 Kinetic equations and their

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salloum, Maher; Robinson, David B.

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

DOE PAGES

Salloum, Maher; Robinson, David B.

2018-01-30

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

Dry (CO2) reforming of methane over Pt catalysts studied by DFT and kinetic modeling

NASA Astrophysics Data System (ADS)

Niu, Juntian; Du, Xuesen; Ran, Jingyu; Wang, Ruirui

2016-07-01

Dry reforming of methane (DRM) is a well-studied reaction that is of both scientific and industrial importance. In order to design catalysts that minimize the deactivation and improve the selectivity and activity for a high H2/CO yield, it is necessary to understand the elementary reaction steps involved in activation and conversion of CO2 and CH4. In our present work, a microkinetic model based on density functional theory (DFT) calculations is applied to explore the reaction mechanism for methane dry reforming on Pt catalysts. The adsorption energies of the reactants, intermediates and products, and the activation barriers for the elementary reactions involved in the DRM process are calculated over the Pt(1 1 1) surface. In the process of CH4 direct dissociation, the kinetic results show that CH dissociative adsorption on Pt(1 1 1) surface is the rate-determining step. CH appears to be the most abundant species on the Pt(1 1 1) surface, suggesting that carbon deposition is not easy to form in CH4 dehydrogenation on Pt(1 1 1) surface. In the process of CO2 activation, three possible reaction pathways are considered to contribute to the CO2 decomposition: (I) CO2* + * → CO* + O*; (II) CO2* + H* → COOH* + * → CO* + OH*; (III) CO2* + H* → mono-HCOO* + * → bi-HCOO* + * [CO2* + H* → bi-HCOO* + *] → CHO* + O*. Path I requires process to overcome the activation barrier of 1.809 eV and the forward reaction is calculated to be strongly endothermic by 1.430 eV. In addition, the kinetic results also indicate this process is not easy to proceed on Pt(1 1 1) surface. While the CO2 activation by H adsorbed over the catalyst surface to form COOH intermediate (Path II) is much easier to be carried out with the lower activation barrier of 0.746 eV. The Csbnd O bond scission is the rate-determining step along this pathway and the process needs to overcome the activation barrier of 1.522 eV. Path III reveals the CO2 activation through H adsorbed over the catalyst surface to form HCOO intermediate firstly. This reaction requires a quite high activation barrier and is a strongly endothermic process leading to a very low forward rate constant. In conclusion, Path II is the dominant reaction pathway in CO2 activation. Additionally, there are two pathways of CH oxidation by O: (A) CH* + O* → CHO* + * → CO* + H*; (B) CH* + O* → COH* + * → CO* + H*. Both the activation barriers and kinetic results demonstrate that Path A is the prior reaction pathway. Furthermore, in the two pathways of CH oxidation by OH: (C) CH* + OH* → CHOH* + * → CHO* + H*; (D) CH* + OH* → CHOH* + * → COH* + H*. Path C is easier to proceed. In conclusion, the main reaction pathway in CH oxidation according to the mechanism: CH* + OH* → CHOH* + * → CHO* + H* → CO* + 2H*. These results could provide some useful information for the operation of DRM over Pt catalysts, and are helpful to understand the mechanisms of DRM from the atomic scale.

Amoeba-Inspired Heuristic Search Dynamics for Exploring Chemical Reaction Paths.

PubMed

Aono, Masashi; Wakabayashi, Masamitsu

2015-09-01

We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called "AmoebaSAT [Aono et al. 2013]," which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al. 2013]. AmoebaSAT is used for solving an NP-complete combinatorial optimization problem [Garey and Johnson 1979], "the satisfiability problem," and finds a constraint-satisfying solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods [Iwama and Tamaki 2004] for a class of randomly generated problem instances [ http://www.cs.ubc.ca/~hoos/5/benchm.html ]. In cases where the problem has more than one solution, AmoebaSAT exhibits dynamic transition behavior among a variety of the solutions. Inheriting these features of AmoebaSAT, we formulate "AmoebaChem," which explores a variety of metastable molecules in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules. AmoebaChem and its developed forms will be applied to the study of the origins of life, to discover reaction paths for which expected or unexpected organic compounds may be formed via unknown unstable intermediates and to estimate the likelihood of each of the discovered paths.

Ab initio study of C + H3+ reactions

NASA Technical Reports Server (NTRS)

Talbi, D.; DeFrees, D. J.

1991-01-01

The reaction C + H3+ --> CH(+) + H2 is frequently used in models of dense interstellar cloud chemistry with the assumption that it is fast, i.e. there are no potential energy barriers inhibiting it. Ab initio molecular orbital study of the triplet CH3+ potential energy surface (triplet because the reactant carbon atom is a ground state triplet) supports this hypothesis. The reaction product is 3 pi CH+; the reaction is to exothermic even though the product is not in its electronic ground state. No path has been found on the potential energy surface for C + H3+ --> CH2(+) + H reaction.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

NASA Astrophysics Data System (ADS)

Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

2016-06-01

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations.

PubMed

Varga, Matthew J; Schwartz, Steven D

2016-04-12

In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems.

Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems.

PubMed

Suzuki, Kimichi; Morokuma, Keiji; Maeda, Satoshi

2017-10-05

We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non-reaction-center (surrounding) part is optimized by fixing atoms in the reaction-center part before displacements of the reaction-center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized. Then, geometric displacements of the reaction-center atoms are performed in the mean field generated by the weighted sum of the surrounding parts. MSM was combined with the QM/MM-ONIOM method and applied to chemical reactions in aqueous solution or enzyme. In all three cases, MSM gave lower reaction energy profiles than the QM/MM-ONIOM-microiteration method over the entire reaction paths with comparable computational costs. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A FMO-controlled reaction path in the benzil-benzilic acid rearrangement.

PubMed

Yamabe, Shinichi; Tsuchida, Noriko; Yamazaki, Shoko

2006-03-03

Reaction paths for the title rearrangement along with its methyl analogue were investigated by density functional theory calculations. The reaction model is R-CO-CO-R + OH(-)(H2O)4 --> R2C(OH)-COO- + (H2O)4 (R = Me and Ph), where the water tetramer is employed both for solvation to OH- and for the proton relay along hydrogen bonds. The reaction is composed of OH- addition, C-C rotation, carbanion [1,2] migration, and proton relay toward the product anions. The rate-determining step was calculated to be the carbanion migration. Apparently, carbanion [1,2] migration is unlikely relative to the carbonium ion one. However, LUMOs of the 1,2-diketones have large and nodeless lobes at the reaction center, the C1-C2 bond. The specific LUMO character is reflected both in the [2+1]-like one-center nucleophilic addition and in the carbanion [1,2] shift. The proton relay involved in the isomerization from the oxo intermediate to the carboxylate was calculated to take place via the water tetramer.

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

DOE PAGES

Kale, Seyit; Sode, Olaseni; Weare, Jonathan; ...

2014-11-07

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum undermore » DFT by several fold. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.« less

Guiding brine shrimp through mazes by solving reaction diffusion equations

NASA Astrophysics Data System (ADS)

Singal, Krishma; Fenton, Flavio

Excitable systems driven by reaction diffusion equations have been shown to not only find solutions to mazes but to also to find the shortest path between the beginning and the end of the maze. In this talk we describe how we can use the Fitzhugh-Nagumo model, a generic model for excitable media, to solve a maze by varying the basin of attraction of its two fixed points. We demonstrate how two dimensional mazes are solved numerically using a Java Applet and then accelerated to run in real time by using graphic processors (GPUs). An application of this work is shown by guiding phototactic brine shrimp through a maze solved by the algorithm. Once the path is obtained, an Arduino directs the shrimp through the maze using lights from LEDs placed at the floor of the Maze. This method running in real time could be eventually used for guiding robots and cars through traffic.

Detecting reactive islands using Lagrangian descriptors and the relevance to transition path sampling.

PubMed

Patra, Sarbani; Keshavamurthy, Srihari

2018-02-14

It has been known for sometime now that isomerization reactions, classically, are mediated by phase space structures called reactive islands (RI). RIs provide one possible route to correct for the nonstatistical effects in the reaction dynamics. In this work, we map out the reactive islands for the two dimensional Müller-Brown model potential and show that the reactive islands are intimately linked to the issue of rare event sampling. In particular, we establish the sensitivity of the so called committor probabilities, useful quantities in the transition path sampling technique, to the hierarchical RI structures. Mapping out the RI structure for high dimensional systems, however, is a challenging task. Here, we show that the technique of Lagrangian descriptors is able to effectively identify the RI hierarchy in the model system. Based on our results, we suggest that the Lagrangian descriptors can be useful for detecting RIs in high dimensional systems.

Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

PubMed

Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

2008-01-01

A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

Experimental Study of Serpentinization Reactions

NASA Technical Reports Server (NTRS)

Cohen, B. A.; Brearley, A. J.; Ganguly, J.; Liermann, H.-P.; Keil, K.

2004-01-01

Current carbonaceous chondrite parent-body thermal models [1-3] produce scenarios that are inconsistent with constraints on aqueous alteration conditions based on meteorite mineralogical evidence, such as phase stability relationships within the meteorite matrix minerals [4] and isotope equilibration arguments [5, 6]. This discrepancy arises principally because of the thermal runaway effect produced by silicate hydration reactions (here loosely called serpentinization, as the principal products are serpentine minerals), which are so exothermic as to produce more than enough heat to melt more ice and provide a self-sustaining chain reaction. One possible way to dissipate the heat of reaction is to use a very small parent body [e.g., 2] or possibly a rubble pile model. Another possibility is to release this heat more slowly, which depends on the alteration reaction path and kinetics.

Modeling the maneuvering of a vehicle

NASA Astrophysics Data System (ADS)

Antonyuk, E. Ya.; Zabuga, A. T.

2012-07-01

A kinematic model of one- and two-link robotic vehicles with two or three steerable wheels is considered. A nonsmooth path in the form of an astroid enveloping the positions of the robot is planned. The motion of a two-link vehicle with such a trajectory is modeled. A numerical analysis of the dynamic of robots is performed determining the reactions of nonholonomic constraints

Communication: Coordinate-dependent diffusivity from single molecule trajectories

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Makarov, Dmitrii E.

2017-11-01

Single-molecule observations of biomolecular folding are commonly interpreted using the model of one-dimensional diffusion along a reaction coordinate, with a coordinate-independent diffusion coefficient. Recent analysis, however, suggests that more general models are required to account for single-molecule measurements performed with high temporal resolution. Here, we consider one such generalization: a model where the diffusion coefficient can be an arbitrary function of the reaction coordinate. Assuming Brownian dynamics along this coordinate, we derive an exact expression for the coordinate-dependent diffusivity in terms of the splitting probability within an arbitrarily chosen interval and the mean transition path time between the interval boundaries. This formula can be used to estimate the effective diffusion coefficient along a reaction coordinate directly from single-molecule trajectories.

Quasi-Monte Carlo Methods Applied to Tau-Leaping in Stochastic Biological Systems.

PubMed

Beentjes, Casper H L; Baker, Ruth E

2018-05-25

Quasi-Monte Carlo methods have proven to be effective extensions of traditional Monte Carlo methods in, amongst others, problems of quadrature and the sample path simulation of stochastic differential equations. By replacing the random number input stream in a simulation procedure by a low-discrepancy number input stream, variance reductions of several orders have been observed in financial applications. Analysis of stochastic effects in well-mixed chemical reaction networks often relies on sample path simulation using Monte Carlo methods, even though these methods suffer from typical slow [Formula: see text] convergence rates as a function of the number of sample paths N. This paper investigates the combination of (randomised) quasi-Monte Carlo methods with an efficient sample path simulation procedure, namely [Formula: see text]-leaping. We show that this combination is often more effective than traditional Monte Carlo simulation in terms of the decay of statistical errors. The observed convergence rate behaviour is, however, non-trivial due to the discrete nature of the models of chemical reactions. We explain how this affects the performance of quasi-Monte Carlo methods by looking at a test problem in standard quadrature.

Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide.

PubMed

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.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

DOE PAGES

Gao, Connie W.; Allen, Joshua W.; Green, William H.; ...

2016-02-24

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involvingmore » carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.« less

Reaction path of energetic materials using THOR code

NASA Astrophysics Data System (ADS)

Durães, L.; Campos, J.; Portugal, A.

1998-07-01

The method of predicting reaction path, using THOR code, allows for isobar and isochor adiabatic combustion and CJ detonation regimes, the calculation of the composition and thermodynamic properties of reaction products of energetic materials. THOR code assumes the thermodynamic equilibria of all possible products, for the minimum Gibbs free energy, using HL EoS. The code allows the possibility of estimating various sets of reaction products, obtained successively by the decomposition of the original reacting compound, as a function of the released energy. Two case studies of thermal decomposition procedure were selected, calculated and discussed—pure Ammonium Nitrate and its based explosive ANFO, and Nitromethane—because their equivalence ratio is respectively lower, near and greater than the stoicheiometry. Predictions of reaction path are in good correlation with experimental values, proving the validity of proposed method.

Chemical Evolution of Groundwater Near a Sinkhole Lake, Northern Florida: 2. Chemical Patterns, Mass Transfer Modeling, and Rates of Mass Transfer Reactions

NASA Astrophysics Data System (ADS)

Katz, Brian G.; Plummer, L. Niel; Busenberg, Eurybiades; Revesz, Kinga M.; Jones, Blair F.; Lee, Terrie M.

1995-06-01

Chemical patterns along evolutionary groundwater flow paths in silicate and carbonate aquifers were interpreted using solute tracers, carbon and sulfur isotopes, and mass balance reaction modeling for a complex hydrologic system involving groundwater inflow to and outflow from a sinkhole lake in northern Florida. Rates of dominant reactions along defined flow paths were estimated from modeled mass transfer and ages obtained from CFC-modeled recharge dates. Groundwater upgradient from Lake Barco remains oxic as it moves downward, reacting with silicate minerals in a system open to carbon dioxide (CO2), producing only small increases in dissolved species. Beneath and downgradient of Lake Barco the oxic groundwater mixes with lake water leakage in a highly reducing, silicate-carbonate mineral environment. A mixing model, developed for anoxic groundwater downgradient from the lake, accounted for the observed chemical and isotopic composition by combining different proportions of lake water leakage and infiltrating meteoric water. The evolution of major ion chemistry and the 13C isotopic composition of dissolved carbon species in groundwater downgradient from the lake can be explained by the aerobic oxidation of organic matter in the lake, anaerobic microbial oxidation of organic carbon, and incongruent dissolution of smectite minerals to kaolinite. The dominant process for the generation of methane was by the CO2 reduction pathway based on the isotopic composition of hydrogen (δ2H(CH4) = -186 to -234‰) and carbon (δ13C(CH4) = -65.7 to -72.3‰). Rates of microbial metabolism of organic matter, estimated from the mass transfer reaction models, ranged from 0.0047 to 0.039 mmol L-1 yr-1 for groundwater downgradient from the lake.

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2008-01-01

We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the protein maintains its compact configuration, while a (de)increase of secondary structure is observed. The calculated folding rate agrees reasonably with experiment, while the unfolding rate is 10 times higher. We discuss possible origins for this mismatch. We recomputed the rates with the forward flux sampling method, and found a discrepancy of four orders of magnitude, probably caused by the method's higher sensitivity to the choice of order parameter with respect to transition interface sampling. Finally, we used the previously computed transition path-sampling ensemble to screen combinations of many order parameters for the best model of the reaction coordinate by employing likelihood maximization. We found that a combination of the root mean-square deviation of the helix and of the entire protein was, of the set of tried order parameters, the one that best describes the reaction coordination. PMID:18676648

Unraveling the role of water in the stereoselective step of aqueous proline-catalyzed aldol reactions.

PubMed

Ribas-Arino, Jordi; Carvajal, Maria Angels; Chaumont, Alain; Masia, Marco

2012-12-03

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self-condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First-principles molecular dynamics simulations were used to study the free-energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high-level static first-principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An integrated experimental and theoretical reaction path search: analyses of the multistage reaction of an ionized diethylether dimer involving isomerization, proton transfer, and dissociation.

PubMed

Matsuda, Yoshiyuki; Xie, Min; Fujii, Asuka

2018-05-30

An ionization-induced multistage reaction of an ionized diethylether (DEE) dimer involving isomerization, proton transfer, and dissociation is investigated by combining infrared (IR) spectroscopy, tandem mass spectrometry, and a theoretical reaction path search. The vertically-ionized DEE dimer isomerizes to a hydrogen-bonded cluster of protonated DEE and the [DEE-H] radical through barrierless intermolecular proton transfer from the CH bond of the ionized moiety. This isomerization process is confirmed by IR spectroscopy and the theoretical reaction path search. The multiple dissociation pathways following the isomerization are analyzed by tandem mass spectrometry. The isomerized cluster dissociates stepwise into a [protonated DEE-acetaldehyde (AA)] cluster, protonated DEE, and protonated AA. The structure of the fragment ion is also analyzed by IR spectroscopy. The reaction map of the multistage processes is revealed through a harmony of these experimental and theoretical methods.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

NASA Astrophysics Data System (ADS)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method.

PubMed

Perdih, Andrej; Hodoscek, Milan; Solmajer, Tom

2009-02-15

MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase), a three-domain bacterial protein, catalyses a highly specific incorporation of D-glutamate to the cytoplasmic intermediate UDP-N-acetyl-muramoyl-L-alanine (UMA) utilizing ATP hydrolysis to ADP and P(i). This reaction is part of a biosynthetic path yielding bacterial peptidoglycan. On the basis of structural studies of MurD complexes, a stepwise catalytic mechanism was proposed that commences with a formation of the acyl-phosphate intermediate, followed by a nucleophilic attack of D-glutamate that, through the formation of a tetrahedral reaction intermediate and subsequent phosphate dissociation, affords the final product, UDP-N-acetyl-muramoyl-L-alanine-D-glutamate (UMAG). A hybrid quantum mechanical/molecular mechanical (QM/MM) molecular modeling approach was utilized, combining the B3LYP QM level of theory with empirical force field simulations to evaluate three possible reaction pathways leading to tetrahedral intermediate formation. Geometries of the starting structures based on crystallographic experimental data and tetrahedral intermediates were carefully examined together with a role of crucial amino acids and water molecules. The replica path method was used to generate the reaction pathways between the starting structures and the corresponding tetrahedral reaction intermediates, offering direct comparisons with a sequential kinetic mechanism and the available structural data for this enzyme. The acquired knowledge represents new and valuable information to assist in the ongoing efforts leading toward novel inhibitors of MurD as potential antibacterial drugs. (c) 2008 Wiley-Liss, Inc.

Modeling the exhumation path of partially melted ultrahigh-pressure metapelites, North-East Greenland Caledonides

NASA Astrophysics Data System (ADS)

Lang, Helen M.; Gilotti, Jane A.

2015-06-01

Pseudosection modeling constrains the pressure-temperature (P-T) exhumation path of partially melted ultrahigh-pressure (UHP) metapelites exposed in the North-East Greenland UHP terrane. A robust peak P and T estimate of 3.6 GPa and 970 °C based on mineral assemblages in nearby kyanite eclogites is the starting point for the P-T path. Although the peak assemblage for the metapelite is not preserved, the calculated modeled peak assemblage contained substantial clinopyroxene, garnet, phengite, K-feldspar and coesite with minor kyanite and rutile. Combining the pseudosection and observed textures, the decompression path crosses the coesite-quartz transition before reaching the dry phengite dehydration melting reaction where phengite is abruptly consumed. In the range of 2.5 to 2.2 GPa, clinopyroxene is completely consumed and garnet grows to its maximum volume and grossular content, matching the high grossular rims of relict megacrysts. Plagioclase joins the assemblage and the pseudosection predicts up to 12-13 vol.% melt in the supersolidus assemblage, which contained garnet, liquid, K-feldspar, plagioclase, kyanite, quartz and rutile. At this stage, the steep decompression path flattened out and became nearly isobaric. The melt crystallization assemblage that formed when the path crossed the solidus with decreasing temperature contains phengite, garnet, biotite, 2 feldspars, kyanite, quartz and rutile. Therefore, the path must have intersected the solidus at approximately 1.2 GPa, 825 °C. The pseudosection predicts that garnet is consumed on the cooling path, but little evidence of late garnet consumption or other retrograde effects is observed. This may be due to partial melt loss from the rock. Isochemical PT-n and PT-X sections calculated along the P-T path display changes in mineral assemblage and composition that are consistent with preserved assemblages.

CMPF: class-switching minimized pathfinding in metabolic networks.

PubMed

Lim, Kevin; Wong, Limsoon

2012-01-01

The metabolic network is an aggregation of enzyme catalyzed reactions that converts one compound to another. Paths in a metabolic network are a sequence of enzymes that describe how a chemical compound of interest can be produced in a biological system. As the number of such paths is quite large, many methods have been developed to score paths so that the k-shortest paths represent the set of paths that are biologically meaningful or efficient. However, these approaches do not consider whether the sequence of enzymes can be manufactured in the same pathway/species/localization. As a result, a predicted sequence might consist of groups of enzymes that operate in distinct pathway/species/localization and may not truly reflect the events occurring within cell. We propose a path weighting method CMPF (Class-switching Minimized Pathfinder) to search for routes in a metabolic network which minimizes pathway switching. In biological terms, a pathway is a series of chemical reactions which define a specific function (e.g. glycolysis). We conjecture that routes that cross many pathways are inefficient since different pathways define different metabolic functions. In addition, native routes are also well characterized within pathways, suggesting that reasonable paths should not involve too many pathway switches. Our method can be generalized when reactions participate in a class set (e.g., pathways, species or cellular localization) so that the paths predicted have minimal class crossings. We show that our method generates k-paths that involve the least number of class switching. In addition, we also show that native paths are recoverable and alternative paths deviates less from native paths compared to other methods. This suggests that paths ranked by our method could be a way to predict paths that are likely to occur in biological systems.

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.

PubMed

Khavrutskii, Ilja V; Smith, Jason B; Wallqvist, Anders

2013-10-28

Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Hang, E-mail: hangchen@mit.edu; Thill, Peter; Cao, Jianshu

In biochemical systems, intrinsic noise may drive the system switch from one stable state to another. We investigate how kinetic switching between stable states in a bistable network is influenced by dynamic disorder, i.e., fluctuations in the rate coefficients. Using the geometric minimum action method, we first investigate the optimal transition paths and the corresponding minimum actions based on a genetic toggle switch model in which reaction coefficients draw from a discrete probability distribution. For the continuous probability distribution of the rate coefficient, we then consider two models of dynamic disorder in which reaction coefficients undergo different stochastic processes withmore » the same stationary distribution. In one, the kinetic parameters follow a discrete Markov process and in the other they follow continuous Langevin dynamics. We find that regulation of the parameters modulating the dynamic disorder, as has been demonstrated to occur through allosteric control in bistable networks in the immune system, can be crucial in shaping the statistics of optimal transition paths, transition probabilities, and the stationary probability distribution of the network.« less

User's guide to PHREEQC, a computer program for speciation, reaction-path, advective-transport, and inverse geochemical calculations

USGS Publications Warehouse

Parkhurst, D.L.

1995-01-01

PHREEQC is a computer program written in the C pwgranuning language that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations, (2) reaction-path and advective-transport calculations involving specified irreversible reactions, mixing of solutions, mineral and gas equilibria surface-complex-ation reactions, and ion-exchange reactions, and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for composition differences between waters, within specified compositional uncertainties. PHREEQC is derived from the Fortran program PHREEQE, but it has been completely rewritten in C with the addition many new capabilities. New features include the capabilities to use redox couples to distribute redox elements among their valence states in speciation calculations; to model ion-exchange and surface-compiexation reactions; to model reactions with a fixed-pressure, multicomponent gas phase (that is, a gas bubble); to calculate the mass of water in the aqueous phase during reaction and transport calculations; to keep track of the moles of minerals present in the solid phases and determine antomaticaHy the thermodynamically stable phase assemblage; to simulate advective transport in combination with PHREEQC's reaction-modeling capability; and to make inverse modeling calculations that allow for uncertainties in the analytical data. The user interface is improved through the use of a simplified approach to redox reactions, which includes explicit mole-balance equations for hydrogen and oxygen; the use of a revised input that is modular and completely free format; and the use of mineral names and standard chemical symbolism rather than index numbers. The use of (2 eliminates nearly all limitations on army sizes, including numbers of elements, aqueous species, solutions, phases, and lengths of character strings. A new equation solver that optimizes a set of equalities subject to both equality and inequality constraints is used to determine the thermodynamically stable set of phases in equilibrium with a solution. A more complete Newton-Raphson formulation, master-species switching, and scaling of the algebraic equations reduce the number of failures of the nunmrical method in PHREEQC relative to PHREEQE. This report presents the equations that are the basis for chemical equilibrium and inverse-modeling calculations in PHREEQC, describes the input for the program, and presents twelve examples that demonstrate most of the program's capabilities.

New Development on Modelling Fluctuations and Fragmentation in Heavy-Ion Collisions

NASA Astrophysics Data System (ADS)

Lin, Hao; Danielewicz, Pawel

2017-09-01

During heavy-ion collisions (HIC), colliding nuclei form an excited composite system. Instabilities present in the system may deform the shape of the system exotically, leading to a break-up into fragments. Many experimental efforts have been devoted to the nuclear multifragmentation phenomenon, while traditional HIC models, lacking in proper treatment of fluctuations, fall short in explaining it. In view of this, we are developing a new model to implement realistic fluctuations into transport simulation. The new model is motivated by the Brownian motion description of colliding particles. The effects of two-body collisions are recast in one-body diffusion processes. Vastly different dynamical paths are sampled by solving Langevin equations in momentum space. It is the stochastic sampling of dynamical paths that leads to a wide spread of exit channels. In addition, the nucleon degree of freedom is used to enhance the fluctuations. The model has been tested in reactions such as 112Sn + 112Sn and 58Ni + 58Ni, where reasonable results are yielded. An exploratory comparison on the 112Sn + 112Sn reaction at 50 MeV/nucleon with two other models, the stochastic mean-field (SMF) and the antisymmetrized molecular dynamics (AMD) models, has also been conducted. Work supported by the NSF Grant No. PHY-1403906.

Capture reactions on C-14 in nonstandard big bang nucleosynthesis

NASA Technical Reports Server (NTRS)

Wiescher, Michael; Gorres, Joachim; Thielemann, Friedrich-Karl

1990-01-01

Nonstandard big bang nucleosynthesis leads to the production of C-14. The further reaction path depends on the depletion of C-14 by either photon, alpha, or neutron capture reactions. The nucleus C-14 is of particular importance in these scenarios because it forms a bottleneck for the production of heavier nuclei A greater than 14. The reaction rates of all three capture reactions at big bang conditions are discussed, and it is shown that the resulting reaction path, leading to the production of heavier elements, is dominated by the (p, gamma) and (n, gamma) rates, contrary to earlier suggestions.

Application of a new model for groundwater age distributions: Modeling and isotopic analysis of artificial recharge in the Rialto-Colton basin, California

USGS Publications Warehouse

Ginn, T.R.; Woolfenden, L.

2002-01-01

A project for modeling and isotopic analysis of artificial recharge in the Rialto-Colton basin aquifer in California, is discussed. The Rialto-Colton aquifer has been divided into four primary and significant flowpaths following the general direction of groundwater flow from NW to SE. The introductory investigation include sophisticated chemical reaction modeling, with highly simplified flow path simulation. A comprehensive reactive transport model with the established set of geochemical reactions over the whole aquifer will also be developed for treating both reactions and transport realistically. This will be completed by making use of HBGC123D implemented with isotopic calculation step to compute Carbon-14 (C14) and stable Carbon-13 (C13) contents of the water. Computed carbon contents will also be calibrated with the measured carbon contents for assessment of the amount of imported recharge into the Linden pond.

Multi-path variational transition state theory for chemical reaction rates of complex polyatomic species: ethanol + OH reactions.

PubMed

Zheng, Jingjing; Truhlar, Donald G

2012-01-01

Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.

Applicability of DFT model in reactive distillation

NASA Astrophysics Data System (ADS)

Staszak, Maciej

2017-11-01

The density functional theory (DFT) applicability to reactive distillation is discussed. Brief modeling techniques description of distillation and rectification with chemical reaction is provided as a background for quantum method usage description. The equilibrium and nonequilibrium distillation models are described for that purpose. The DFT quantum theory is concisely described. The usage of DFT in the modeling of reactive distillation is described in two parts. One of the fundamental and very important component of distillation modeling is vapor-liquid equilibrium description for which the DFT quantum approach can be used. The representative DFT models, namely COSMO-RS (Conductor like Screening Model for Real Solvents), COSMOSPACE (COSMO Surface Pair Activity Coefficient) and COSMO-SAC (SAC - segment activity coefficient) approaches are described. The second part treats the way in which the chemical reaction is described by means of quantum DFT method. The intrinsic reaction coordinate (IRC) method is described which is used to find minimum energy path of substrates to products transition. The DFT is one of the methods which can be used for that purpose. The literature data examples are provided which proves that IRC method is applicable for chemical reaction kinetics description.

Insights into the Hydrogen-Atom Transfer of the Blue Aroxyl.

PubMed

Bächle, Josua; Marković, Marijana; Kelterer, Anne-Marie; Grampp, Günter

2017-10-19

An experimental and theoretical study on hydrogen-atom transfer dynamics in the hydrogen-bonded substituted phenol/phenoxyl complex of the blue aroxyl (2,4,6-tri-tert-butylphenoxyl) is presented. The experimental exchange dynamics is determined in different organic solvents from the temperature-dependent alternating line-width effect in the continuous-wave ESR spectrum. From bent Arrhenius plots, effective tunnelling contributions with parallel heavy-atom motion are concluded. To clarify the transfer mechanism, reaction paths for different conformers of the substituted phenol/phenoxyl complex are modelled theoretically. Various DFT and post-Hartree-Fock methods including multireference methods are applied. From the comparison of experimental and theoretical data it is concluded that the system favours concerted hydrogen-atom transfer along a parabolic reaction path caused by heavy-atom motion. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermochemical and Kinetics of Hydrazine Dehydrogenation by an Oxygen Atom in Hydrazine-Rich Systems: A Dimer Model.

PubMed

Spada, Rene F K; Ferrão, Luiz F A; Roberto-Neto, Orlando; Lischka, Hans; Machado, Francisco B C

2015-12-24

The kinetics of the reaction of N2H4 with oxygen depends sensitively on the initial conditions used. In oxygen-rich systems, the rate constant shows a conventional positive temperature dependence, while in hydrazine-rich setups the dependence is negative in certain temperature ranges. In this study, a theoretical model is presented that adequately reproduces the experimental results trend and values for hydrazine-rich environment, consisting of the hydrogen abstraction from the hydrazine (N2H4) dimer by an oxygen atom. The thermochemical properties of the reaction were computed using two quantum chemical approaches, the coupled cluster theory with single, double, and noniterative triple excitations (CCSD(T)) and the M06-2X DFT approach with the aug-cc-pVTZ and the maug-cc-pVTZ basis sets, respectively. The kinetic data were calculated with the improved canonical variational theory (ICVT) using a dual-level methodology to build the reaction path. The tunneling effects were considered by means of the small curvature tunneling (SCT) approximation. Potential wells on both sides of the reaction ((N2H4)2 + O → N2H4···N2H3 + OH) were determined. A reaction path with a negative activation energy was found leading, in the temperature range of 250-423 K, to a negative dependence of the rate constant on the temperature, which is in good agreement with the experimental measurements. Therefore, the consideration of the hydrazine dimer model provides significantly improved agreement with the experimental data and should be included in the mechanism of the global N2H4 combustion process, as it can be particularly important in hydrazine-rich systems.

Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways

PubMed Central

Wu, Dongsheng; Fajer, Mikolai I.; Cao, Liaoran; Cheng, Xiaolin; Yang, Wei

2016-01-01

Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this mini presentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study. PMID:27498634

Chemical Memory Reactions Induced Bursting Dynamics in Gene Expression

PubMed Central

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems. PMID:23349679

Chemical memory reactions induced bursting dynamics in gene expression.

PubMed

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.

Kinetics of enzymatic trans-esterification of glycerides for biodiesel production.

PubMed

Calabrò, Vincenza; Ricca, Emanuele; De Paola, Maria Gabriela; Curcio, Stefano; Iorio, Gabriele

2010-08-01

In this paper, the reaction of enzymatic trans-esterification of glycerides with ethanol in a reaction medium containing hexane at a temperature of 37 degrees C has been studied. The enzyme was Lipase from Mucor miehei, immobilized on ionic exchange resin, aimed at achieving high catalytic specific surface and recovering, regenerating and reusing the biocatalyst. A kinetic analysis has been carried out to identify the reaction path; the rate equation and kinetic parameters have been also calculated. The kinetic model has been validated by comparison between predicted and experimental results. Mass transport resistances estimation was undertaken in order to verify that the kinetics found was intrinsic. Model potentialities in terms of reactors design and optimization are also shown.

Theoretical investigation on the mechanism and dynamics of oxo exchange of neptunyl(VI) hydroxide in aqueous solution.

PubMed

Yang, Xia; Chai, Zhifang; Wang, Dongqi

2015-03-21

Four types of reaction mechanisms for the oxo ligand exchange of monomeric and dimeric neptunyl(VI) hydroxide in aqueous solution were explored computationally using density functional theory (DFT) and ab initio classical molecular dynamics. The obtained results were compared with previous studies on the oxo exchange of uranyl hydroxide, as well as with experiments. It is found that the stable T-shaped [NpO3(OH)3](3-) intermediate is a key species for oxo exchange in the proton transfer in mononuclear Path I and binuclear Path IV, similar to the case of uranyl(VI) hydroxide. Path I is thought to be the preferred oxo exchange mechanism for neptunyl(VI) hydroxide in our calculations, due to the lower activation energy (22.7 and 13.1 kcal mol(-1) for ΔG(‡) and ΔH(‡), respectively) of the overall reaction. Path II via a cis-neptunyl structure assisted by a water molecule might be a competitive channel against Path I with a mononuclear mechanism, owing to a rapid dynamical process occurring in Path II. In Path IV with the binuclear mechanism, oxo exchange is accomplished via the interaction between [NpO2(OH)4](2-) and T-shaped [NpO3(OH)3](3-) with a low activation energy for the rate-determining step, however, the overall energy required to fulfill the reaction is slightly higher than that in mononuclear Path I, suggesting a possible binuclear process in the higher energy region. The chemical bonding evolution along the reaction pathways was discussed by using topological methodologies of the electron localization function (ELF).

Studies of ion kinetic effects in OMEGA shock-driven implosions using fusion burn imaging

NASA Astrophysics Data System (ADS)

Rosenberg, M. J.; Seguin, F. H.; Rinderknecht, H. G.; Sio, H.; Zylstra, A. B.; Gatu Johnson, M.; Frenje, J. A.; Li, C. K.; Petrasso, R. D.; Amendt, P. A.; Wilks, S. C.; Zimmerman, G.; Hoffman, N. M.; Kagan, G.; Molvig, K.; Glebov, V. Yu.; Stoeckl, C.; Marshall, F. J.; Seka, W.; Delettrez, J. A.; Sangster, T. C.; Betti, R.; Meyerhofer, D. D.; Atzeni, S.; Nikroo, A.

2014-10-01

Ion kinetic effects have been inferred in a series of shock-driven implosions at OMEGA from an increasing yield discrepancy between observations and hydrodynamic simulations as the ion-ion mean free path increases. To more precisely identify the nature and impact of ion kinetic effects, spatial burn profile measurements of DD and D3He reactions in these D3He-filled shock-driven implosions are presented and contrasted to both purely hydrodynamic models and models that include ion kinetic effects. It is shown that in implosions where the ion mean free path is equal to or greater than the size of the fuel region, purely hydrodynamic models fail to capture the observed burn profiles, while a model that includes ion diffusion is able to recover the observed burn profile shape. These results further elucidate the ion kinetic mechanisms that are present under long mean-free-path conditions after shock convergence in both shock-driven and ablatively-driven implosions. This work was supported in part by the U.S. DOE, NLUF, LLE, and LLNL.

A new intermediate in the Prins reaction

PubMed Central

Fukuda, Takeshi; Yamazaki, Shoko

2013-01-01

Summary Two Prins reactions were investigated by the use of DFT calculations. A model composed of R–CH=CH2 + H3O+(H2O)13 + (H2C=O)2, R = Me and Ph, was adopted to trace reaction paths. For both alkenes, the concerted path forming 1,3-diols was obtained as the rate determining step (TS1). TS stands for a transition state. From the 1,3-diol, a bimolecular elimination (TS2) leads to the allylic alcohol as the first channel. In the second channel, the 1,3-diol was converted via TS3 into an unprecedented hemiacetal intermediate, HO–CH2–O–CH(R)–CH2–CH2–OH. This intermediate undergoes ring closure (TS4), affording the 1,3-dioxane product. The intermediate is of almost the same stability as the product, and two species were suggested to be in a state of equilibrium. While the geometry of TS1 appears to be forwarded to that of a carbocation intermediate, the cation disappeared through the enlargement of the water cluster. Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them. PMID:23532354

Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations

DOE PAGES

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

Exposure Time Distributions reveal Denitrification Rates along Groundwater Flow Path of an Agricultural Unconfined Aquifer

NASA Astrophysics Data System (ADS)

Kolbe, T.; Abbott, B. W.; Thomas, Z.; Labasque, T.; Aquilina, L.; Laverman, A.; Babey, T.; Marçais, J.; Fleckenstein, J. H.; Peiffer, S.; De Dreuzy, J. R.; Pinay, G.

2016-12-01

Groundwater contamination by nitrate is nearly ubiquitous in agricultural regions. Nitrate is highly mobile in groundwater and though it can be denitrified in the aquifer (reduced to inert N2 gas), this process requires the simultaneous occurrence of anoxia, an electron donor (e.g. organic carbon, pyrite), nitrate, and microorganisms capable of denitrification. In addition to this the ratio of the time groundwater spent in a denitrifying environment (exposure time) to the characteristic denitrification reaction time plays an important role, because denitrification can only occur if the exposure time is longer than the characteristic reaction time. Despite a long history of field studies and numerical models, it remains exceedingly difficult to measure or model exposure times in the subsurface at the catchment scale. To approach this problem, we developed a unified modelling approach combining measured environmental proxies with an exposure time based reactive transport model. We measured groundwater age, nitrogen and sulfur isotopes, and water chemistry from agricultural wells in an unconfined aquifer in Brittany, France, to quantify changes in nitrate concentration due to dilution and denitrification. Field data showed large differences in nitrate concentrations among wells, associated with differences in the exposure time distributions. By constraining a catchment-scale characteristic reaction time for denitrification with water chemistry proxies and exposure times, we were able to assess rates of denitrification along groundwater flow paths. This unified modeling approach is transferable to other catchments and could be further used to investigate how catchment structure and flow dynamics interact with biogeochemical processes such as denitrification.

Quantum Entanglement and Chemical Reactivity.

PubMed

Molina-Espíritu, M; Esquivel, R O; López-Rosa, S; Dehesa, J S

2015-11-10

The water molecule and a hydrogenic abstraction reaction are used to explore in detail some quantum entanglement features of chemical interest. We illustrate that the energetic and quantum-information approaches are necessary for a full understanding of both the geometry of the quantum probability density of molecular systems and the evolution of a chemical reaction. The energy and entanglement hypersurfaces and contour maps of these two models show different phenomena. The energy ones reveal the well-known stable geometry of the models, whereas the entanglement ones grasp the chemical capability to transform from one state system to a new one. In the water molecule the chemical reactivity is witnessed through quantum entanglement as a local minimum indicating the bond cleavage in the dissociation process of the molecule. Finally, quantum entanglement is also useful as a chemical reactivity descriptor by detecting the transition state along the intrinsic reaction path in the hypersurface of the hydrogenic abstraction reaction corresponding to a maximally entangled state.

Geochemical Impacts to Groundwater from Geologic Carbon Sequestration: Controls on pH and Inorganic Carbon Concentrations from Reaction Path and Kinetic Modeling

EPA Science Inventory

Geologic carbon sequestration has the potential to cause long-term reductions in global emissions of carbon dioxide to the atmosphere. Safe and effective application of carbon sequestration technology requires an understanding of the potential risks to the quality of underground...

Motion of an Articulated Vehicle with Two-Dimensional Sections Subject to Lateral Obstacles

NASA Astrophysics Data System (ADS)

Antonyuk, E. Ya.; Zabuga, A. T.

2016-07-01

Some aspects of the geometry, kinematics, and dynamics of a three-section robotic vehicle with a front steerable wheel are studied. The constraints between the wheels and the flat ground are assumed nonholonomic. The vehicle moves in a narrow L-shaped corridor. A path for the characteristic points of the sections of the robot is designed. A dynamic model of the system is developed. The maximum possible dimensions of the robot that allow its unimpeded and non-stop motion are determined. The kinetostatic analysis of the load on a three-section vehicle moving along a planned path is modeled. The holonomic and nonholonomic constraint reactions between the wheels and the ground and in the joints between the sections are determined

Kinetics of the BrO + NO2 Association Reaction. Temperature and Pressure Dependence in the Falloff Regime

NASA Technical Reports Server (NTRS)

Thron, R. P.; Daykin, E. P.; Wine, P.H.

1997-01-01

A laser flash photolysis-long path absorption technique has been employed to study the kinetics of the reaction BrO + NO2 + M yields (k1) products as a function of temperature (248-346 K), pressure (16-800 torr), and buffer gas identity (N2,CF4) The reaction is found to be in the falloff regime between third and second-order over the entire range of conditions investigated This is the first study where temperature-dependent measurements of k1(P,T) have been reported at pressures greater than 12 torr; hence, our results help constrain choices of k1(P,T) for use in models of lower stratospheric BrO(x) chemistry. Approximate falloff parameters in a convenient form for atmospheric modeling are derived.

Generating functionals and Gaussian approximations for interruptible delay reactions

NASA Astrophysics Data System (ADS)

Brett, Tobias; Galla, Tobias

2015-10-01

We develop a generating functional description of the dynamics of non-Markovian individual-based systems in which delay reactions can be terminated before completion. This generalizes previous work in which a path-integral approach was applied to dynamics in which delay reactions complete with certainty. We construct a more widely applicable theory, and from it we derive Gaussian approximations of the dynamics, valid in the limit of large, but finite, population sizes. As an application of our theory we study predator-prey models with delay dynamics due to gestation or lag periods to reach the reproductive age. In particular, we focus on the effects of delay on noise-induced cycles.

Oxygen reduction on a Pt(111) catalyst in HT-PEM fuel cells by density functional theory

NASA Astrophysics Data System (ADS)

Sun, Hong; Li, Jie; Almheiri, Saif; Xiao, Jianyu

2017-08-01

The oxygen reduction reaction plays an important role in the performance of high-temperature proton exchange membrane (HT-PEM) fuel cells. In this study, a molecular dynamics model, which is based on the density functional theory and couples the system's energy, the exchange-correlation energy functional, the charge density distribution function, and the simplified Kohn-Sham equation, was developed to simulate the oxygen reduction reaction on a Pt(111) surface. Additionally, an electrochemical reaction system on the basis of a four-electron reaction mechanism was also developed for this simulation. The reaction path of the oxygen reduction reaction, the product structure of each reaction step and the system's energy were simulated. It is found that the first step reaction of the first hydrogen ion with the oxygen molecule is the controlling step of the overall reaction. Increasing the operating temperature speeds up the first step reaction rate and slightly decreases its reaction energy barrier. Our results provide insight into the working principles of HT-PEM fuel cells.

Dynamics of a Two-Link Vehicle in an L-Shaped Corridor Revisited

NASA Astrophysics Data System (ADS)

Antonyuk, E. Ya.; Zabuga, A. T.

2014-03-01

The kinematics of a two-link mobile robot with three steerable wheels moving in an L-shaped corridor is analyzed. A smooth (with continuous first derivative) path is designed maintaining the optimal maneuverability of the vehicle. The motion of the vehicle along this path is planned. Analytical expressions for the reactions at the contact of the wheels with the ground are given in the general case of motion. The radius of curvature of the programmed path is shown to have a strong influence on the reactions.

Committor of elementary reactions on multistate systems

NASA Astrophysics Data System (ADS)

Király, Péter; Kiss, Dóra Judit; Tóth, Gergely

2018-04-01

In our study, we extend the committor concept on multi-minima systems, where more than one reaction may proceed, but the feasible data evaluation needs the projection onto partial reactions. The elementary reaction committor and the corresponding probability density of the reactive trajectories are defined and calculated on a three-hole two-dimensional model system explored by single-particle Langevin dynamics. We propose a method to visualize more elementary reaction committor functions or probability densities of reactive trajectories on a single plot that helps to identify the most important reaction channels and the nonreactive domains simultaneously. We suggest a weighting for the energy-committor plots that correctly shows the limits of both the minimal energy path and the average energy concepts. The methods also performed well on the analysis of molecular dynamics trajectories of 2-chlorobutane, where an elementary reaction committor, the probability densities, the potential energy/committor, and the free-energy/committor curves are presented.

Microsolvated Model for the Kinetics and Thermodynamics of Glycosidic Bond Dissociative Cleavage of Nucleoside D4G.

PubMed

Jiang, Yang; Xue, Ying; Zeng, Yi

2018-02-15

Using the microsolvated model that involves explicit water molecules and implicit solvent in the optimization, two proposed dissociative hydrolysis mechanisms of 2',3'-didehydro-2',3'-dideoxyguanosine (d4G) have been first investigated by means of M06-2X(CPCM, water)/6-31++G(d,p) method. The glycosidic bond dissociation for the generation of the oxacarbenium ion intermediate is the rate-determining step (RDS). The subsequent nucleophilic water attack from different side of the oxacarbenium ion intermediate gives either the α-product [(2S,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-ol] or β-product [(2R,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-ol] and is thus referred to as α-path (inversion) and β-path (retention). Two to five explicit water molecules (n = 2-5) are considered in the microsolvated model, and n = 3 or 4 is the smallest model capable of minimizing the activation energy for α-path and β-path, respectively. Our theoretical results suggest that α-path (n = 3) is more kinetically favorable with lower free energy barrier (RDS) of 27.7 kcal mol -1 , in contrast to that of 30.7 kcal mol -1 for the β-path (n = 4). The kinetic preference of the α-path is rationalized by NBO analysis. Whereas thte β-path is more thermodynamically favorable over the α-path, where the formation of β-product and α-product are exergonic and endergonic, respectively, providing theoretical support for the experimental observation that the β-cleavage product was the major one after sufficient reaction time. Comparisons of d4G with analogous cyclo-d4G and dG from kinetic free energy barriers and thermodynamic heterolytic dissociation energies were also carried out. Our kinetic and thermodynamic results manifest that the order of glycosidic bond stability should be d4G < cyclo-d4G < dG, which agrees well with the reported experimental stability order of d4G compounds and analogues and gives further understanding on the influence of 6-cyclopropylamino and unsaturated ribose to the glycosidic bond instability of d4G.

Simplification of Markov chains with infinite state space and the mathematical theory of random gene expression bursts.

PubMed

Jia, Chen

2017-09-01

Here we develop an effective approach to simplify two-time-scale Markov chains with infinite state spaces by removal of states with fast leaving rates, which improves the simplification method of finite Markov chains. We introduce the concept of fast transition paths and show that the effective transitions of the reduced chain can be represented as the superposition of the direct transitions and the indirect transitions via all the fast transition paths. Furthermore, we apply our simplification approach to the standard Markov model of single-cell stochastic gene expression and provide a mathematical theory of random gene expression bursts. We give the precise mathematical conditions for the bursting kinetics of both mRNAs and proteins. It turns out that random bursts exactly correspond to the fast transition paths of the Markov model. This helps us gain a better understanding of the physics behind the bursting kinetics as an emergent behavior from the fundamental multiscale biochemical reaction kinetics of stochastic gene expression.

Simplification of Markov chains with infinite state space and the mathematical theory of random gene expression bursts

NASA Astrophysics Data System (ADS)

Jia, Chen

2017-09-01

Here we develop an effective approach to simplify two-time-scale Markov chains with infinite state spaces by removal of states with fast leaving rates, which improves the simplification method of finite Markov chains. We introduce the concept of fast transition paths and show that the effective transitions of the reduced chain can be represented as the superposition of the direct transitions and the indirect transitions via all the fast transition paths. Furthermore, we apply our simplification approach to the standard Markov model of single-cell stochastic gene expression and provide a mathematical theory of random gene expression bursts. We give the precise mathematical conditions for the bursting kinetics of both mRNAs and proteins. It turns out that random bursts exactly correspond to the fast transition paths of the Markov model. This helps us gain a better understanding of the physics behind the bursting kinetics as an emergent behavior from the fundamental multiscale biochemical reaction kinetics of stochastic gene expression.

DEF: an automated dead-end filling approach based on quasi-endosymbiosis.

PubMed

Liu, Lili; Zhang, Zijun; Sheng, Taotao; Chen, Ming

2017-02-01

Gap filling for the reconstruction of metabolic networks is to restore the connectivity of metabolites via finding high-confidence reactions that could be missed in target organism. Current methods for gap filling either fall into the network topology or have limited capability in finding missing reactions that are indirectly related to dead-end metabolites but of biological importance to the target model. We present an automated dead-end filling (DEF) approach, which is derived from the wisdom of endosymbiosis theory, to fill gaps by finding the most efficient dead-end utilization paths in a constructed quasi-endosymbiosis model. The recalls of reactions and dead ends of DEF reach around 73% and 86%, respectively. This method is capable of finding indirectly dead-end-related reactions with biological importance for the target organism and is applicable to any given metabolic model. In the E. coli iJR904 model, for instance, about 42% of the dead-end metabolites were fixed by our proposed method. DEF is publicly available at http://bis.zju.edu.cn/DEF/. mchen@zju.edu.cn Supplementary data are available at Bioinformatics online.

Efficient approach to obtain free energy gradient using QM/MM MD simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asada, Toshio; Koseki, Shiro; The Research Institute for Molecular Electronic Devices

2015-12-31

The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means ofmore » FEG and the nudged elastic band (NEB) method.« less

Using the Prototype/Willingness model to predict smoking behaviour among Norwegian adolescents.

PubMed

Hukkelberg, Silje Sommer; Dykstra, Jennifer L

2009-03-01

This paper examines cognitive antecedents of non-smoking among adolescents who reported smoking less than 1-2 times a week, and reported non-smoking intentions and willingness, in the framework of the Prototype/Willingness model. Two waves of data were obtained from a nation-wide sample of 760 Norwegian adolescents who responded to a school-based survey on smoking. Structural equation modelling was used to evaluate the predictive power of the social reaction pathway (prototype and willingness) of the P/W model, and in addition, the constructs from the Theory of Reasoned Action (subjective norm, attitude and intention). Results demonstrated the unique importance of the social reaction path when examining smoking behaviour among non-smoking adolescents. Implications of the findings and possible applications are discussed.

Influence of oxygen-, nitrogen-, and sulfur-containing compounds on the hydrodeoxygenation of phenols over sulfided CoMo/[gamma]-Al[sub 2]O[sub 3] and NiMo/[gamma]-Al[sub 2]O[sub 3] catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laurent, E.; Delmon, B.

1993-11-01

The hydrodeoxygenation (HDO) of phenols is a key reaction of the hydroprocessing of bio-oils, because phenolic molecules represent an important part of these oils and they are among the most difficult to deoxygenate. This reaction is also a very good reaction test for the characterization of the hydrogenation and hydrogenolysis functions of hydrotreating catalysts. In this work, the influence of competitors on the activity and selectivity of 4-methylphenol HDO over conventional CoMo and NiMo hydrotreating catalysts was evaluated in batch reaction tests. The inhibiting strength followed the order H[sub 2]O << 2-ethylphenol < H[sub 2]S < NH[sub 3]. In allmore » cases, the hydrogenolysis path was more inhibited than the hydrogenation path, indicating a higher adsorption strength and electrophilicity of associated sites. The inhibition was quantified according to a Langmuir adsorption concept. The deviations from this model were attributed to a distribution of the adsorption strength. As opposed to other competitors, hydrogen sulfide slightly promotes the hydrogenation activity of CoMo but not of NiMo. These observations were interpreted as the result of an interconversion of the hydrogenolysis and hydrogenation active sites.« less

Computational study of the reactions of methanol with the hydroperoxyl and methyl radicals. 2. Accurate thermal rate constants.

PubMed

Alecu, I M; Truhlar, Donald G

2011-12-29

Multistructural canonical variational-transition-state theory with multidimensional tunneling (MS-CVT/MT) is employed to calculate thermal rate constants for the abstraction of hydrogen atoms from both positions of methanol by the hydroperoxyl and methyl radicals over the temperature range 100-3000 K. The M08-HX hybrid meta-generalized gradient approximation density functional and M08-HX with specific reaction parameters, both with the maug-cc-pVTZ basis set, were validated in part 1 of this study (Alecu, I. M.; Truhlar, D. G. J. Phys. Chem. A2011, 115, 2811) against highly accurate CCSDT(2)(Q)/CBS calculations for the energetics of these reactions, and they are used here to compute the properties of all stationary points and the energies, gradients, and Hessians of nonstationary points along each considered reaction path. The internal rotations in some of the transition states are found to be highly anharmonic and strongly coupled to each other, and they generate multiple structures (conformations) whose contributions are included in the partition function. It is shown that the previous estimates for these rate constants used to build kinetic models for the combustion of methanol, some of which were based on transition state theory calculations with one-dimensional tunneling corrections and harmonic-oscillator approximations or separable one-dimensional hindered rotor treatments of torsions, are appreciably different than the ones presently calculated using MS-CVT/MT. The rate constants obtained from the best MS-CVT/MT calculations carried out in this study, in which the important effects of corner cutting due to small and large reaction path curvature are captured via a microcanonical optimized multidimensional tunneling (μOMT) treatment, are recommended for future refinement of the kinetic model for methanol combustion. © 2011 American Chemical Society

Self-consistent collective coordinate for reaction path and inertial mass

NASA Astrophysics Data System (ADS)

Wen, Kai; Nakatsukasa, Takashi

2016-11-01

We propose a numerical method to determine the optimal collective reaction path for a nucleus-nucleus collision, based on the adiabatic self-consistent collective coordinate (ASCC) method. We use an iterative method, combining the imaginary-time evolution and the finite amplitude method, for the solution of the ASCC coupled equations. It is applied to the simplest case, α -α scattering. We determine the collective path, the potential, and the inertial mass. The results are compared with other methods, such as the constrained Hartree-Fock method, Inglis's cranking formula, and the adiabatic time-dependent Hartree-Fock (ATDHF) method.

Semiquantitative FMO Analysis of Substituent Effect on the Reaction of Permanganate Ion with Unsymmetrical Alkenes.

PubMed

Ogino, Toshio; Watanabe, Toru; Matsuura, Masato; Watanabe, Chikara; Ozaki, Hidetoshi

1998-04-17

The substituent effects on the reactions of permanganate ion with unsymmetrical alkenes are analyzed on the assumption of a concerted (3 + 2) cycloaddition model by using an equation obtained by approximation based on the FMO theory in which development and localization of the frontier molecular orbitals at the reaction sites with progress of the reaction are considered. The Hammett plots are successfully reproduced with the newly obtained rate data for the reactions of trans-chalcone and its derivatives and the data for methyl cinnamates, cinnamate ions, and alkyl vinyl ethers taken from the literature using FMO energies and orbital coefficients calculated by the PM3 method. It was indicated that a factor introduced to the basic equation in order to estimate the extent of localization of the molecular orbitals at the transition state is closely related to the position of the transition state along the reaction path.

Ab initio computational study of reaction mechanism of peptide bond formation on HF/6-31G(d,p) level

NASA Astrophysics Data System (ADS)

Siahaan, P.; Lalita, M. N. T.; Cahyono, B.; Laksitorini, M. D.; Hildayani, S. Z.

2017-02-01

Peptide plays an important role in modulation of various cell functions. Therefore, formation reaction of the peptide is important for chemical reactions. One way to probe the reaction of peptide synthesis is a computational method. The purpose of this research is to determine the reaction mechanism for peptide bond formation on Ac-PV-NH2 and Ac-VP-NH2 synthesis from amino acid proline and valine by ab initio computational approach. The calculations were carried out by theory and basis set HF/6-31G(d,p) for four mechanisms (path 1 to 4) that proposed in this research. The results show that the highest of the rate determining step between reactant and transition state (TS) for path 1, 2, 3, and 4 are 163.06 kJ.mol-1, 1868 kJ.mol-1, 5685 kJ.mol-1, and 1837 kJ.mol-1. The calculation shows that the most preferred reaction of Ac-PV-NH2 and Ac-VP-NH2 synthesis from amino acid proline and valine are on the path 1 (initiated with the termination of H+ in proline amino acid) that produce Ac-PV-NH2.

Coupled alkali feldspar dissolution and secondary mineral precipitation in batch systems: 4. Numerical modeling of kinetic reaction paths

NASA Astrophysics Data System (ADS)

Zhu, Chen; Lu, Peng; Zheng, Zuoping; Ganor, Jiwchar

2010-07-01

This paper explores how dissolution and precipitation reactions are coupled in batch reactor experimental systems at elevated temperatures. This is the fourth paper in our series of "Coupled Alkali Feldspar Dissolution and Secondary Mineral Precipitation in Batch Systems". In our third paper, we demonstrated via speciation-solubility modeling that partial equilibrium between secondary minerals and aqueous solutions was not attained in feldspar hydrolysis batch reactors at 90-300 °C and that a strong coupling between dissolution and precipitation reactions follows as a consequence of the slower precipitation of secondary minerals ( Zhu and Lu, 2009). Here, we develop this concept further by using numerical reaction path models to elucidate how the dissolution and precipitation reactions are coupled. Modeling results show that a quasi-steady state was reached. At the quasi-steady state, dissolution reactions proceeded at rates that are orders of magnitude slower than the rates measured at far from equilibrium. The quasi-steady state is determined by the relative rate constants, and strongly influenced by the function of Gibbs free energy of reaction ( ΔG) in the rate laws. To explore the potential effects of fluid flow rates on the coupling of reactions, we extrapolate a batch system ( Ganor et al., 2007) to open systems and simulated one-dimensional reactive mass transport for oligoclase dissolution and kaolinite precipitation in homogeneous porous media. Different steady states were achieved at different locations along the one-dimensional domain. The time-space distribution and saturation indices (SI) at the steady states were a function of flow rates for a given kinetic model. Regardless of the differences in SI, the ratio between oligoclase dissolution rates and kaolinite precipitation rates remained 1.626, as in the batch system case ( Ganor et al., 2007). Therefore, our simulation results demonstrated coupling among dissolution, precipitation, and flow rates. Results reported in this communication lend support to our hypothesis that slow secondary mineral precipitation explains part of the well-known apparent discrepancy between lab measured and field estimated feldspar dissolution rates ( Zhu et al., 2004). Here we show how the slow secondary mineral precipitation provides a regulator to explain why the systems are held close to equilibrium and show how the most often-quoted "near equilibrium" explanation for an apparent field-lab discrepancy can work quantitatively. The substantiated hypothesis now offers the promise of reconciling part of the apparent field-lab discrepancy.

Geometric phase effects in ultracold chemistry

NASA Astrophysics Data System (ADS)

Hazra, Jisha; Naduvalath, Balakrishnan; Kendrick, Brian K.

2016-05-01

In molecules, the geometric phase, also known as Berry's phase, originates from the adiabatic transport of the electronic wavefunction when the nuclei follow a closed path encircling a conical intersection between two electronic potential energy surfaces. It is demonstrated that the inclusion of the geometric phase has an important effect on ultracold chemical reaction rates. The effect appears in rotationally and vibrationally resolved integral cross sections as well as cross sections summed over all product quantum states. It arises from interference between scattering amplitudes of two reaction pathways: a direct path and a looping path that encircle the conical intersection between the two lowest adiabatic electronic potential energy surfaces. Illustrative results are presented for the O+ OH --> H+ O2 reaction and for hydrogen exchange in H+ H2 and D+HD reactions. It is also qualitatively demonstrated that the geometric phase effect can be modulated by applying an external electric field allowing the possibility of quantum control of chemical reactions in the ultracold regime. This work was supported in part by NSF Grant PHY-1505557 (N.B.) and ARO MURI Grant No. W911NF-12-1-0476 (N.B.).

Solvent effects on the excited-state double proton transfer mechanism in the 7-azaindole dimer: a TDDFT study with the polarizable continuum model.

PubMed

Yu, Xue-Fang; Yamazaki, Shohei; Taketsugu, Tetsuya

2017-08-30

Solvent effects on the excited-state double proton transfer (ESDPT) mechanism in the 7-azaindole (7AI) dimer were investigated using the time-dependent density functional theory (TDDFT) method. Excited-state potential energy profiles along the reaction paths in a locally excited (LE) state and a charge transfer (CT) state were calculated using the polarizable continuum model (PCM) to include the solvent effect. A series of non-polar and polar solvents with different dielectric constants were used to examine the polarity effect on the ESDPT mechanism. The present results suggest that in a non-polar solvent and a polar solvent with a small dielectric constant, ESDPT follows a concerted mechanism, similar to the case in the gas phase. In a polar solvent with a relatively large dielectric constant, however, ESDPT is likely to follow a stepwise mechanism via a stable zwitterionic intermediate in the LE state on the adiabatic potential energy surface, although inclusion of zero-point vibrational energy (ZPE) corrections again suggests the concerted mechanism. In the meantime, the stepwise reaction path involving the CT state with neutral intermediates is also examined, and is found to be less competitive than the concerted or stepwise path in the LE state in both non-polar and polar solvents. The present study provides a new insight into the experimental controversy of the ESDPT mechanism of the 7AI dimer in a solution.

Effect of Molecule–Surface Reaction Mechanism on the Electronic Characteristics and Photovoltaic Performance of Molecularly Modified Si

PubMed Central

2013-01-01

We report on the passivation properties of molecularly modified, oxide-free Si(111) surfaces. The reaction of 1-alcohol with the H-passivated Si(111) surface can follow two possible paths, nucleophilic substitution (SN) and radical chain reaction (RCR), depending on adsorption conditions. Moderate heating leads to the SN reaction, whereas with UV irradiation RCR dominates, with SN as a secondary path. We show that the site-sensitive SN reaction leads to better electrical passivation, as indicated by smaller surface band bending and a longer lifetime of minority carriers. However, the surface-insensitive RCR reaction leads to more dense monolayers and, therefore, to much better chemical stability, with lasting protection of the Si surface against oxidation. Thus, our study reveals an inherent dissonance between electrical and chemical passivation. Alkoxy monolayers, formed under UV irradiation, benefit, though, from both chemical and electronic passivation because under these conditions both SN and RCR occur. This is reflected in longer minority carrier lifetimes, lower reverse currents in the dark, and improved photovoltaic performance, over what is obtained if only one of the mechanisms operates. These results show how chemical kinetics and reaction paths impact electronic properties at the device level. It further suggests an approach for effective passivation of other semiconductors. PMID:24205409

Mass transfer and fluid evolution in late-metamorphic veins, Rhenish Massif (Germany): insight from alteration geochemistry and fluid-mineral equilibria modeling

NASA Astrophysics Data System (ADS)

Marsala, Achille; Wagner, Thomas

2016-08-01

Element mobility and fluid-rock interaction related to the formation of late-metamorphic quartz veins have been studied by combination of mineral chemistry, whole-rock geochemistry, mass balance analysis and fluid-mineral equilibria modeling. The quartz veins are hosted by very low-grade metasedimentary rocks of the fold-and-thrust belt of the Rhenish Massif (Germany). The veins record two stages of evolution, a massive vein filling assemblage with elongate-blocky quartz, chlorite, apatite and albite, and a later open space filling assemblage with euhedral crystals of quartz, ankerite-dolomite and minor calcite and sulfides. Detailed mass balance analysis of an alteration profile adjacent to a representative quartz vein demonstrates that element mobility is restricted to the proximal zone. The most important element changes are gain of Ca, Fe, Mg, Mn, P and CO2, and loss of Si, K and Na. The data demonstrate that wall-rock carbonation is one of the main alteration features, whereas mobility of Si, K and Na are related to dissolution of quartz and destruction of detrital feldspar and muscovite. The whole-rock geochemical data, in conjunction with fluid composition data and pressure-temperature estimates, were used as input for fluid-mineral equilibria modeling in the system Si-Al-Fe-Mg-Ca-Na-K-C-S-O-H-B-F-Cl. Modeling involved calculation of rock-buffered fluid compositions over the temperature interval 100-500 °C, and reaction-path simulations where a rock-buffered high-temperature fluid reacts with fresh host-rocks at temperatures of 400, 300 and 200 °C. Calculated rock-buffered fluid compositions demonstrate that retrograde silica solubility is a strong driving force for quartz leaching in the temperature-pressure window of 380-450 °C and 0.5 kbar. These conditions overlap with the estimated temperatures for the initial stage of vein formation. Reaction-path models show that high-temperature alteration can produce the observed silica leaching, suggesting that fast advection of external hot fluids from deeper crustal levels was essential for the early stage of vein formation. Fluid advection must have occurred as multiple pulses, which allowed for periods of influx of fluids that leached quartz, alternating with periods of cooling and quartz precipitation in the veins. Reaction-path models at high temperatures (300-400 °C) do not produce carbonate alteration, whereas fluid-rock reaction at 200 °C produces carbonate alteration, consistent with the temperature estimates for the late-stage vein carbonate assemblage. Comparison between modeling results and geochemical data suggests that the observed alteration features are the product of fluid-rock reaction under conditions where the external fluid gradually cooled down and evolved with time. The results of this study highlight the importance of late-orogenic fluid migration for the formation of quartz vein arrays in fold-and-thrust belts.

Quantum Mechanics and Molecular Mechanics Study of the Catalytic Mechanism of Human AMSH-LP Domain Deubiquitinating Enzymes.

PubMed

Zhu, Wenyou; Liu, Yongjun; Ling, Baoping

2015-08-25

Deubiquitinating enzymes (DUBs) catalyze the cleavage of the isopeptide bond in polyubiquitin chains to control and regulate the deubiquitination process in all known eukaryotic cells. The human AMSH-LP DUB domain specifically cleaves the isopeptide bonds in the Lys63-linked polyubiquitin chains. In this article, the catalytic mechanism of AMSH-LP has been studied using a combined quantum mechanics and molecular mechanics method. Two possible hydrolysis processes (Path 1 and Path 2) have been considered. Our calculation results reveal that the activation of Zn(2+)-coordinated water molecule is the essential step for the hydrolysis of isopeptide bond. In Path 1, the generated hydroxyl first attacks the carbonyl group of Gly76, and then the amino group of Lys63 is protonated, which is calculated to be the rate limiting step with an energy barrier of 13.1 kcal/mol. The energy barrier of the rate limiting step and the structures of intermediate and product are in agreement with the experimental results. In Path 2, the protonation of amino group of Lys63 is prior to the nucleophilic attack of activated hydroxyl. The two proton transfer processes in Path 2 correspond to comparable overall barriers (33.4 and 36.1 kcal/mol), which are very high for an enzymatic reaction. Thus, Path 2 can be ruled out. During the reaction, Glu292 acts as a proton transfer mediator, and Ser357 mainly plays a role in stabilizing the negative charge of Gly76. Besides acting as a Lewis acid, Zn(2+) also influences the reaction by coordinating to the reaction substrates (W1 and Gly76).

Partner Pressure, Victimization History, and Alcohol: Women’s Condom-Decision Abdication Mediated by Mood and Anticipated Negative Partner Reaction

PubMed Central

George, William H.; Davis, Kelly Cue; Masters, N. Tatiana; Kajumulo, Kelly F.; Stappenbeck, Cynthia A.; Norris, Jeanette; Heiman, Julia R.; Staples, Jennifer M.

2015-01-01

Highly intoxicated versus sober women were evaluated using multi-group path analyses to test the hypothesis that sexual victimization history would interact with partner pressure to forgo condom use, resulting in greater condom-decision abdication – letting the man decide whether or not to use a condom. After beverage administration, community women (n=408) projected themselves into a scenario depicting a male partner exerting high or low pressure for unprotected sex. Mood, anticipated negative reactions from the partner, and condom-decision abdication were assessed. In both control and alcohol models, high pressure increased anticipated negative partner reaction, and positive mood was associated with increased abdication. In the alcohol model, victimization predicted abdication via anticipated negative partner reaction, and pressure decreased positive mood and abdication. In the control model, under high pressure, victimization history severity was positively associated with abdication. Findings implicate condom-decision abdication as an important construct in understanding how women’s sexual victimization histories may exert sustained impact on sexual interactions. PMID:26340952

Modeling the hydrothermal circulation and the hydrogen production at the Rainbow site with Cast3M

NASA Astrophysics Data System (ADS)

Perez, F.; Mügler, C.; Charlou, J.; Jean-baptiste, P.

2012-12-01

On the Mid-Atlantic Ridge, the Rainbow venting site is described as an ultramafic-hosted active hydrothermal site and releases high fluxes of methane and hydrogen [1, 2]. This behavior has first been interpreted as the result of serpentinization processes. But geochemical reactions involving olivine and plagioclase assemblages, and leading to chlorite, tremolite, talc and magnetite assemblages, could contribute to the observed characteristics of the exiting fluid [2]. The predominance of one of these geochemical reactions or their coexistence strongly depend on the hydrothermal fluid circulation. We developed and validated a 2D/3D numerical model using a Finite Volume method to simulate heat driven fluid flows in the framework of the Cast3M code [3, 4]. We also developed a numerical model for hydrogen production and transport that is based on experimental studies of the serpentinization processes [5-6]. This geochemical model takes into account the exothermic and water-consuming behavior of the serpentinization reaction and it can be coupled to our thermo-hydrogeological model. Our simulations provide temperatures, mass fluxes and venting surface areas very close to those estimated in-situ [7]. We showed that a single-path model [8] was necessary to simulate high values such as the in-situ measured temperatures and estimated water mass fluxes of the Rainbow site [7]. This single-path model will be used to model the production and transport of hydrogen at the Rainbow hydrothermal site. References [1]Charlou et al. (2010) AGU Monograph series. [2]Seyfried et al. (2011) Geochim. Cosmochim. Acta 75, 1574-1593. [3]http://www-cast3m.cea.fr. [4]Martin & Fyfe (1970) Chem. Geol. 6, 185-202. [5] Marcaillou et al. (2011) Earth and Planet. Sci. Lett. 303, 281-290. [6]Malvoisin et al. (2012) JGR, 117, B01104. [7]Perez et al. (2012) submited to Computational Geosciences. [8]Lowell & Germanovich (2004) AGU, Washington DC, USA.

Predictive Modeling in Actinide Chemistry and Catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Ping

2016-05-16

These are slides from a presentation on predictive modeling in actinide chemistry and catalysis. The following topics are covered in these slides: Structures, bonding, and reactivity (bonding can be quantified by optical probes and theory, and electronic structures and reaction mechanisms of actinide complexes); Magnetic resonance properties (transition metal catalysts with multi-nuclear centers, and NMR/EPR parameters); Moving to more complex systems (surface chemistry of nanomaterials, and interactions of ligands with nanoparticles); Path forward and conclusions.

CO oxidation reaction on Pt(111) studied by the dynamic Monte Carlo method including lateral interactions of adsorbates.

PubMed

Nagasaka, Masanari; Kondoh, Hiroshi; Nakai, Ikuyo; Ohta, Toshiaki

2007-01-28

The dynamics of adsorbate structures during CO oxidation on Pt(111) surfaces and its effects on the reaction were studied by the dynamic Monte Carlo method including lateral interactions of adsorbates. The lateral interaction energies between adsorbed species were calculated by the density functional theory method. Dynamic Monte Carlo simulations were performed for the oxidation reaction over a mesoscopic scale, where the experimentally determined activation energies of elementary paths were altered by the calculated lateral interaction energies. The simulated results reproduced the characteristics of the microscopic and mesoscopic scale adsorbate structures formed during the reaction, and revealed that the complicated reaction kinetics is comprehensively explained by a single reaction path affected by the surrounding adsorbates. We also propose from the simulations that weakly adsorbed CO molecules at domain boundaries promote the island-periphery specific reaction.

Dynamics of 17F + 58Ni reaction via complete and incomplete fusion processes at above barrier energies

NASA Astrophysics Data System (ADS)

Grover, Neha; Sandhu, Kirandeep; Sharma, Manoj K.

2018-06-01

The dynamics of 17F + 58Ni reaction induced via a loosely bound projectile (17F) is examined using the collective clusterization approach of the dynamical cluster decay model (DCM) with respect to the recent experimental data available at beam energies Ebeam = 54.1 and 58.5 MeV. The calculations are done for quadrupole deformations of fragments using the optimum orientation approach. In view of the loosely bound nature of 17F, the main focus of the present work is on the comparison of complete and incomplete fusion. It is studied using various components such as fragmentation potential, mass distribution, and barrier modification. Different decay modes (ER, IMF, HMF, and fission) are also compared to determine the complete fusion and incomplete fusion paths. Additionally, the decay paths of the nucleus formed from loosely bound (17F) and tightly bound (16O) projectiles are compared. Furthermore, the role of temperature-dependent pairing strength is analyzed in terms of the binary fragmentation of the compound system formed.

Pathways involving traumatic losses, worry about family, adult separation anxiety and posttraumatic stress symptoms amongst refugees from West Papua.

PubMed

Tay, Alvin Kuowei; Rees, Susan; Chen, Jack; Kareth, Moses; Silove, Derrick

2015-10-01

There is some evidence that adult separation anxiety disorder (ASAD) symptoms are closely associated with posttraumatic stress disorder (PTSD) amongst refugees exposed to traumatic events (TEs), but the pathways involved remain to be elucidated. A recent study suggests that separation anxiety disorder precedes and predicts onset of PTSD. We examined a path model testing whether ASAD symptoms and worry about family mediated the path from traumatic losses to PTSD symptoms amongst 230 refugees from West Papua. Culturally adapted measures were applied to assess TE exposure and symptoms of ASAD and PTSD. A structural equation model indicated that ASAD symptoms played an important role in mediating the effects of traumatic losses and worry about family in the pathway to PTSD symptoms. Although based on cross-sectional data, our findings suggest that ASAD symptoms may play a role in the path from traumatic losses to PTSD amongst refugees. We propose an evolutionary model in which the ASAD and PTSD reactions represent complementary survival responses designed to protect the individual and close attachments from external threats. Copyright © 2015 Elsevier Ltd. All rights reserved.

An interactive code (NETPATH) for modeling NET geochemical reactions along a flow PATH, version 2.0

USGS Publications Warehouse

Plummer, Niel; Prestemon, Eric C.; Parkhurst, David L.

1994-01-01

NETPATH is an interactive Fortran 77 computer program used to interpret net geochemical mass-balance reactions between an initial and final water along a hydrologic flow path. Alternatively, NETPATH computes the mixing proportions of two to five initial waters and net geochemical reactions that can account for the observed composition of a final water. The program utilizes previously defined chemical and isotopic data for waters from a hydrochemical system. For a set of mineral and (or) gas phases hypothesized to be the reactive phases in the system, NETPATH calculates the mass transfers in every possible combination of the selected phases that accounts for the observed changes in the selected chemical and (or) isotopic compositions observed along the flow path. The calculations are of use in interpreting geochemical reactions, mixing proportions, evaporation and (or) dilution of waters, and mineral mass transfer in the chemical and isotopic evolution of natural and environmental waters. Rayleigh distillation calculations are applied to each mass-balance model that satisfies the constraints to predict carbon, sulfur, nitrogen, and strontium isotopic compositions at the end point, including radiocarbon dating. DB is an interactive Fortran 77 computer program used to enter analytical data into NETPATH, and calculate the distribution of species in aqueous solution. This report describes the types of problems that can be solved, the methods used to solve problems, and the features available in the program to facilitate these solutions. Examples are presented to demonstrate most of the applications and features of NETPATH. The codes DB and NETPATH can be executed in the UNIX or DOS1 environment. This report replaces U.S. Geological Survey Water-Resources Investigations Report 91-4078, by Plummer and others, which described the original release of NETPATH, version 1.0 (dated December, 1991), and documents revisions and enhancements that are included in version 2.0. 1 The use of trade, brand or product names in this report is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.

Elucidation of the mechanism of N-demethylation catalyzed by cytochrome P450 monooxygenase is facilitated by exploiting nitrogen-15 heavy isotope effects.

PubMed

Kwiecień, Renata A; Molinié, Roland; Paneth, Piotr; Silvestre, Virginie; Lebreton, Jacques; Robins, Richard J

2011-06-01

(15)N heavy isotope effects are especially useful when detail is sought pertaining to the reaction mechanism for the cleavage of a C-N bond. Their potential in assisting to describe the mechanism of N-demethylation of tertiary amines by the action of cytochrome P450 monooxygenase has been investigated. As a working model for the first step, oxidation of the N-methyl group to N-methoxyl, tropine and a cytochrome P450 monooxygenase reaction centre composed of a truncated heme with sulfhydryl as the axial ligand were used. It is apparent that this first step of the reaction proceeds via a hydrogen atom transfer mechanism. Transition states for this step are described for both the high spin ((4)TS(H)) and low spin ((2)TS(H)) pathways in both gas and solvation states. Hence, overall normal secondary (15)N KIE could be calculated for the reaction path modeled in the low spin state, and inverse for the reaction modeled in the high spin state. This partial reaction has been identified as the probable rate limiting step. The model for the second step, fission of the C-N bond, consisted of N-methoxylnortropine and two molecules of water. A transition state described for this step, TS(CN), gives a strongly inverse overall theoretical (15)N KIE. Copyright © 2011 Elsevier Inc. All rights reserved.

Metabolic PathFinding: inferring relevant pathways in biochemical networks.

PubMed

Croes, Didier; Couche, Fabian; Wodak, Shoshana J; van Helden, Jacques

2005-07-01

Our knowledge of metabolism can be represented as a network comprising several thousands of nodes (compounds and reactions). Several groups applied graph theory to analyse the topological properties of this network and to infer metabolic pathways by path finding. This is, however, not straightforward, with a major problem caused by traversing irrelevant shortcuts through highly connected nodes, which correspond to pool metabolites and co-factors (e.g. H2O, NADP and H+). In this study, we present a web server implementing two simple approaches, which circumvent this problem, thereby improving the relevance of the inferred pathways. In the simplest approach, the shortest path is computed, while filtering out the selection of highly connected compounds. In the second approach, the shortest path is computed on the weighted metabolic graph where each compound is assigned a weight equal to its connectivity in the network. This approach significantly increases the accuracy of the inferred pathways, enabling the correct inference of relatively long pathways (e.g. with as many as eight intermediate reactions). Available options include the calculation of the k-shortest paths between two specified seed nodes (either compounds or reactions). Multiple requests can be submitted in a queue. Results are returned by email, in textual as well as graphical formats (available in http://www.scmbb.ulb.ac.be/pathfinding/).

Scaling Hydrologic Exchange Flows and Biogeochemical Reactions from Bedforms to Basins

NASA Astrophysics Data System (ADS)

Harvey, J. W.; Gomez-Velez, J. D.

2015-12-01

River water moves in and out of the main channel along pathways that are perpendicular to the channel's main axis that flow across or beneath the ground surface. These hydrologic exchange flows (HEFs) are difficult to measure, yet no less important than a river's downstream flow, or exchanges with the atmosphere and deeper groundwater (Harvey and Gooseff, 2015, WRR). There are very few comprehensive investigations of exchange fluxes to understand patterns with river size and relative importance of specific types of exchanges. We used the physically based model NEXSS to simulate multiple scales of hyporheic flow and their cumulative effects on solute reaction in large basins (on the order of Chesapeake Bay basin or larger). Our goal was to explain where and when particular types of hyporheic flow are important in enhancing key biogeochemical reactions, such as organic carbon respiration and denitrification. Results demonstrate that hyporheic flux (expressed per unit area of streambed) varies surprisingly little across the continuum of first-order streams to eighth-order rivers, and vertical exchange beneath small bedforms dominates in comparison with lateral flow beneath gravel bars and meanders. Also, the river's entire volume is exchanged many times with hyporheic flow within a basin, and the turnover length (after one entire river volume is exchanged) is strongly influenced by hydrogeomorphic differences between physiographic regions as well as by river size. The cumulative effects on biogeochemical reactions were assessed using a the reaction significance factor, RSF, which computes the cumulative potential for hyporheic reactions using a dimensionless index that balances reaction progress in a single hyporheic flow path against overall processing efficiency of river turnover through hyporheic flow paths of that type. Reaction significance appears to be strongly dominated by hydrologic factors rather than biogeochemical factors, and seems to be dominated by vertical exchange beneath small bedforms throughout river networks. Future implementations of NEXSS will expand the model to consider flow variation and to consider HEFs beyond hyporheic flow to include exchange with marginal surface waters such as riparian wetlands, floodplains, and ponded water.

Experimental Insights into Multiphase (H2O-CO2) Fluid-Rock Interactions in Geothermal Systems

NASA Astrophysics Data System (ADS)

Kaszuba, J. P.; Lo Re, C.; Martin, J.; McPherson, B. J.; Moore, J. N.

2012-12-01

Integrated hydrothermal experiments and geochemical modeling elucidate fluid-rock interactions and reaction pathways in both natural and anthropogenic systems, including enhanced geothermal systems (EGS) in which CO2 is introduced as a working fluid. Experiments are conducted in rocker bombs and flexible Au-Ti reaction cells. Individual experiments require one to three months to complete; intensive in-situ fluid/gas sampling gauges reaction progress. Investigation of granitic reservoirs and associated vein minerals are broadly based on the Roosevelt Hot Springs thermal area, Utah, USA. The granite consists of subequal amounts of quartz, perthitic K-feldspar (~25% wt% albite and 75% wt% K-feldspar), and oligoclase (An23), and 4 wt% Fe-rich biotite. Vein minerals include epidote and chlorite (clinochlore). Experiments are conducted at 250°C and 25 to 45 MPa. Each experiment uses mineral powders (75 wt% of rock mass, ground to <45 um) to increase reactivity and also mineral pieces (0.1-0.7 cm in size) to promote petrologic evaluation of mineral reactions. The water (I ≈ 0.1 molal) initially contains millimolal quantities of SiO2, Al, Ca, Mg, K, SO4, and HCO3 and is designed to be saturated with all of the minerals present at the start of each experiment. Excess CO2 is injected to saturate the water and maintain an immiscible supercritical fluid phase. The entire evolutionary path of the natural system is not replicated at laboratory scales. Instead, experiments define a segment of the reaction path and, in combination with geochemical modeling, provide clear trajectories towards equilibrium. Reaction of granite+water yields illite+zeolite; smectite subsequently precipitates in response to CO2 injection. Reaction of granite+epidote+water yields illite+zeolite+smectite; zeolite does not precipitate after CO2 is injected. Water in all experiments become saturated with chalcedony. Carbonate minerals do not precipitate but are predicted as final equilbrium products. Enhanced Geothermal Systems are expected to follow similar reaction pathways and produce metastable minerals during initial development.

Longitudinal distribution of ozone and chlorine in the human respiratory tract: simulation of nasal and oral breathing with the single-path diffusion model.

PubMed

Bush, M L; Zhang, W; Ben-Jebria, A; Ultman, J S

2001-06-15

In the single-path model of the respiratory system, gas transport occurs within a conduit of progressively increasing cross-sectional and surface areas by a combination of flow, longitudinal dispersion, and lateral absorption. The purpose of this study was to use bolus inhalation data previously obtained for chlorine (Cl(2)) and for ozone (O(3)) to test the predictive capability of the single-path model and to adjust input parameters for applying the model to other exposure conditions. The data, consisting of uptake fraction as a function of bolus penetration volume, were recorded on 10 healthy nonsmokers breathing orally as well as nasally at alternative air flows of 150, 250, and 1000 ml/s. By employing published data for airway anatomy, gas-phase dispersion coefficients, and gas-phase mass transfer coefficients while neglecting diffusion limitations in the mucus phase, the single-path model was capable of predicting the uptake distribution for O(3) but not the steeper distribution that was observed for Cl(2). To simultaneously explain the data for these two gases, it was necessary to increase gas-phase mass transfer coefficients and to include a finite diffusion resistance of O(3) within the mucous layer. The O(3) reaction rate constants that accounted for this diffusion resistance, 2 x 10(6) s(-1) in the mouth and 8 x 10(6) s(-1) in the nose and lower airways, were much greater than previously reported reactivities of individual substrates found in mucus. Copyright 2001 Academic Press.

An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Padgett, Jill M. A.; Ilie, Silvana, E-mail: silvana@ryerson.ca

2016-03-15

Stochastic modelling is critical for studying many biochemical processes in a cell, in particular when some reacting species have low population numbers. For many such cellular processes the spatial distribution of the molecular species plays a key role. The evolution of spatially heterogeneous biochemical systems with some species in low amounts is accurately described by the mesoscopic model of the Reaction-Diffusion Master Equation. The Inhomogeneous Stochastic Simulation Algorithm provides an exact strategy to numerically solve this model, but it is computationally very expensive on realistic applications. We propose a novel adaptive time-stepping scheme for the tau-leaping method for approximating themore » solution of the Reaction-Diffusion Master Equation. This technique combines effective strategies for variable time-stepping with path preservation to reduce the computational cost, while maintaining the desired accuracy. The numerical tests on various examples arising in applications show the improved efficiency achieved by the new adaptive method.« less

Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Bret, E-mail: jackson@chem.umass.edu; Nattino, Francesco; Kroes, Geert-Jan

The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrationalmore » basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.« less

Linking structure to function: The search for active sites in non-platinum group metal oxygen reduction reaction catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holby, Edward F.; Zelenay, Piotr

Atomic-scale structures of oxygen reduction reaction (ORR) active sites in non-platinum group metal (non-PGM) catalysts, made from pyrolysis of carbon, nitrogen, and transition-metal (TM) precursors have been the subject of continuing discussion in the fuel cell electrocatalysis research community. We found that quantum chemical modeling is a path forward for understanding of these materials and how they catalyze the ORR. Here, we demonstrate through literature examples of how such modeling can be used to better understand non-PGM ORR active site relative stability and activity and how such efforts can also aid in the interpretation of experimental signatures produced by thesemore » materials.« less

Linking structure to function: The search for active sites in non-platinum group metal oxygen reduction reaction catalysts

DOE PAGES

Holby, Edward F.; Zelenay, Piotr

2016-05-17

Atomic-scale structures of oxygen reduction reaction (ORR) active sites in non-platinum group metal (non-PGM) catalysts, made from pyrolysis of carbon, nitrogen, and transition-metal (TM) precursors have been the subject of continuing discussion in the fuel cell electrocatalysis research community. We found that quantum chemical modeling is a path forward for understanding of these materials and how they catalyze the ORR. Here, we demonstrate through literature examples of how such modeling can be used to better understand non-PGM ORR active site relative stability and activity and how such efforts can also aid in the interpretation of experimental signatures produced by thesemore » materials.« less

Glycerol electro-oxidation on a carbon-supported platinum catalyst at intermediate temperatures

NASA Astrophysics Data System (ADS)

Ishiyama, Keisuke; Kosaka, Fumihiko; Shimada, Iori; Oshima, Yoshito; Otomo, Junichiro

2013-03-01

The electro-oxidation of glycerol on a carbon-supported platinum catalyst (Pt/C) in combination with a reaction products analysis was investigated at intermediate temperatures (235-260 °C) using a single cell with a CsH2PO4 proton conducting solid electrolyte. A high current density was achieved. The main products were H2, CO2 and CO but the formation of C2 compounds, such as glycolic acid and ethane, was also observed. In addition, several C3 compounds were detected as minor products. A reaction products analysis revealed that the C-C bond dissociation ratio of glycerol was 70-80% at both low and high potentials (>200 mV vs. reversible hydrogen electrode) at 250 °C, suggesting that rapid dissociation occurs on Pt/C. The reaction products analysis also suggested that hydrogen production via thermal decomposition and/or steam reforming of glycerol (indirect path) and direct electro-oxidation of glycerol (direct path) proceed in parallel. More detailed reaction paths involving C1, C2 and C3 reaction products are discussed as well as the possible rate-determining step in glycerol electro-oxidation at intermediate temperatures.

Improving Density Functional Tight Binding Predictions of Free Energy Surfaces for Slow Chemical Reactions in Solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

2017-06-01

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for reactions that are fast relative to DFT simulation times (<10 ps), but the effects on slow reactions and the free energy surface are not well-known. We present a force matching approach to improve the chemical accuracy of DFTB. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Dehydroxyl effect of Sn-doped silicon oxide resistance random access memory with supercritical CO2 fluid treatment

NASA Astrophysics Data System (ADS)

Tsai, Tsung-Ming; Chang, Kuan-Chang; Chang, Ting-Chang; Syu, Yong-En; Liao, Kuo-Hsiao; Tseng, Bae-Heng; Sze, Simon M.

2012-09-01

The tin-doped can supply conduction path to induce resistance switching behavior. However, the defect of tin-doped silicon oxide (Sn:SiOx) increased the extra leakage path lead to power consumption and joule heating degradation. In the study, supercritical CO2 fluids treatment was used to improve resistive switching property. The current conduction of high resistant state in post-treated Sn:SiOx film was transferred to Schottky emission from Frenkel-Poole due to the passivation effect. The molecular reaction model is proposed that the defect was passivated through dehydroxyl effect of supercritical fluid technology, verified by material analyses of x-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy.

Effect of friction on electron transfer: The two reaction coordinate case

NASA Astrophysics Data System (ADS)

Onuchic, José Nelson

1987-04-01

Electron transfer is a very important reaction in many biological processes such as photosynthesis and oxidative phosphorylation. In many of these reactions, most of the interesting dynamics can be included by using two reaction coordinates: one fast (local high frequency vibration modes) and one slow (outersphere modes such as solvent polarization). We report a model to describe this problem, which uses path integral techniques to calculate electron transfer rates, and also to obtain the Fokker-Planck equations associated with this model. Different limiting cases lead to qualitatively different results such as exponential or nonexponential time decay for the donor survival probability. Conditions for the validity of the adiabatic or the nonadiabatic limits will be discussed. Application of this model to real systems is proposed, in particular for a porphyrin rigidly linked to a quinone, which is a very interesting model compound for primary events of photosynthesis. This model can also be used for other multicoordinate biological reactions such as ligand binding to heme proteins. Also, in the concluding part of Sec. III, we discuss the important limit where the fast vibronic mode is much faster than all the other nuclear modes coupled to the problem. In this limit the fast mode ``renormalizes'' the electronic matrix element, and this considerably simplifies the treatment of the problem, reducing it to coupling only to the slow modes.

Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields

NASA Astrophysics Data System (ADS)

Steffen, Julien; Hartke, Bernd

2017-10-01

Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

Reaction chemistry in rechargeable Li-O2 batteries.

PubMed

Lim, Hee-Dae; Lee, Byungju; Bae, Youngjoon; Park, Hyeokjun; Ko, Youngmin; Kim, Haegyeom; Kim, Jinsoo; Kang, Kisuk

2017-05-22

The seemingly simple reaction of Li-O 2 batteries involving lithium and oxygen makes this chemistry attractive for high-energy-density storage systems; however, achieving this reaction in practical rechargeable Li-O 2 batteries has proven difficult. The reaction paths leading to the final Li 2 O 2 discharge products can be greatly affected by the operating conditions or environment, which often results in major side reactions. Recent research findings have begun to reveal how the reaction paths may be affected by the surrounding conditions and to uncover the factors contributing to the difficulty in achieving the reactions of lithium and oxygen. This progress report describes the current state of understanding of the electrode reaction mechanisms in Li-O 2 batteries; the factors that affect reaction pathways; and the effect of cell components such as solvents, salts, additives, and catalysts on the discharge product and its decomposition during charging. This comprehensive review of the recent progress in understanding the reaction chemistry of the Li-O 2 system will serve as guidelines for future research and aid in the development of reliable high-energy-density rechargeable Li-O 2 batteries.

Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

PubMed

Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

2016-02-01

Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Using Multiscale Modeling to Study Coupled Flow, Transport, Reaction and Biofilm Growth Processes in Porous Media

NASA Astrophysics Data System (ADS)

Valocchi, A. J.; Laleian, A.; Werth, C. J.

2017-12-01

Perturbation of natural subsurface systems by fluid inputs may induce geochemical or microbiological reactions that change porosity and permeability, leading to complex coupled feedbacks between reaction and transport processes. Some examples are precipitation/dissolution processes associated with carbon capture and storage and biofilm growth associated with contaminant transport and remediation. We study biofilm growth due to mixing controlled reaction of multiple substrates. As biofilms grow, pore clogging occurs which alters pore-scale flow paths thus changing the mixing and reaction. These interactions are challenging to quantify using conventional continuum-scale porosity-permeability relations. Pore-scale models can accurately resolve coupled reaction, biofilm growth and transport processes, but modeling at this scale is not feasible for practical applications. There are two approaches to address this challenge. Results from pore-scale models in generic pore structures can be used to develop empirical relations between porosity and continuum-scale parameters, such as permeability and dispersion coefficients. The other approach is to develop a multiscale model of biofilm growth in which non-overlapping regions at pore and continuum spatial scales are coupled by a suitable method that ensures continuity of flux across the interface. Thus, regions of high reactivity where flow alteration occurs are resolved at the pore scale for accuracy while regions of low reactivity are resolved at the continuum scale for efficiency. This approach thus avoids the need for empirical upscaling relations in regions with strong feedbacks between reaction and porosity change. We explore and compare these approaches for several two-dimensional cases.

Characterization of the Minimum Energy Paths and Energetics for the Reaction of Vinylidene with Acetylene

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Taylor, Peter R.

1995-01-01

The reaction of vinylidene (CH2C) with acetylene may be an initiating reaction in soot formation. We report minimum energy paths and accurate energetics for a pathway leading to vinyl-acetylene and for a number of isomers of C4H4. The calculations use complete active space self-consistent field (CASSCF) derivative methods to characterize the stationary points and internally contacted configuration interaction (ICCI) and/or coupled cluster singles and doubles with a perturbational estimate of triple excitations (CCSD(T)) to determine the energetics. We find an entrance channel barrier of about 5 kcal/mol for the addition of vinylidene to acetylene, but no barriers above reactants for the reaction pathway leading to vinyl-acetylene.

Characterization of the Minimum Energy Paths and Energetics for the reaction of Vinylidene with Acetylene

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Taylor, Peter R.

1995-01-01

The reaction of vinylidene (CH2C) with acetylene may be an initiating reaction in soot formation. We report minimum energy paths and accurate energetics for a pathway leading to vinylacetylene and for a number of isomers Of C4H4. The calculations use complete active space self-consistent field (CASSCF) derivative methods to characterize the stationary points and internally contacted configuration interaction (ICCI) and/or coupled cluster singles and doubles with a perturbational estimate of triple excitations (CCSD(T)) to determine the energetics. We find an entrance channel barrier of about 5 kcal/mol for the addition of vinylidene to acetylene, but no barriers above reactants for the reaction pathway leading to vinylacetylene.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schachtl, Eva; Yoo, Jong Suk; Gutiérrez, Oliver Y.

The reaction network and elementary steps of the hydrogenation of phenanthrene are explored on parent and Ni-promoted MoS2/c-Al2O3. Two pathways were identified, i.e., Path 1: Phenanthrene _ 9,10-dihydrophenanthrene (DiHPhe)?1,2,3,4,4a,9,10,10a-octahydro-phenanthrene (asymOHPhe), and Path 2: Phenanthrene ?1,2,3,4-tetrahydrophenanthrene (TetHPhe)?1,2,3,4,5,6,7,8-octahydrophenan threne. The steps TetHPhe?asymOHPhe (hydrogenation), and DiHPhe?TetHPhe (hydrogenationisomerization) become notable at phenanthrene conversions above 20%. The reaction preferentially proceeds via Path 1 (90% selectivity) on MoS2/Al2O3. Ni promotion (Ni/(Ni + Mo) molar ratio of 0.3 at the edges on MoS2) increases the hydrogenation activity per active edge twofold and leads to 50% selectivity to both pathways. The reaction orders in H2 vary from _0.8more » on MoS2/Al2O3 to _1.2 on Ni-MoS2/Al2O3, whereas the reaction orders in phenanthrene (_0.6) hardly depend on Ni promotion. The reaction orders in H2S are zero on MoS2/Al2O3 and slightly negative on Ni-MoS2/Al2O3. DFT calculations indicate that phenanthrene is preferentially adsorbed parallel to the basal planes, while H is located at the edges perpendicular to the basal planes. Theory also suggests that Ni atoms, incorporated preferentially on the S-edges, increase the stability of hydrogenated intermediates. Hydrogenation of phenanthrene proceeds through quasi-equilibrated adsorption of the reactants followed by consecutive addition of hydrogen pairs to the adsorbed hydrocarbon. The rate determining steps for the formation of DiHPhe and TetHPhe are the addition of the first and second hydrogen pair, respectively. The concentration of SH groups (activated H at the edges) increases with Ni promotion linearly correlating the rates of Path 1 and Path 2, albeit with different functions. The enhancing effect of Ni on Path 2 is attributed to accelerated hydrogen addition to adsorbed hydrocarbons without important changes in their coverages.« less

Applying the Rule Space Model to Develop a Learning Progression for Thermochemistry

NASA Astrophysics Data System (ADS)

Chen, Fu; Zhang, Shanshan; Guo, Yanfang; Xin, Tao

2017-12-01

We used the Rule Space Model, a cognitive diagnostic model, to measure the learning progression for thermochemistry for senior high school students. We extracted five attributes and proposed their hierarchical relationships to model the construct of thermochemistry at four levels using a hypothesized learning progression. For this study, we developed 24 test items addressing the attributes of exothermic and endothermic reactions, chemical bonds and heat quantity change, reaction heat and enthalpy, thermochemical equations, and Hess's law. The test was administered to a sample base of 694 senior high school students taught in 3 schools across 2 cities. Results based on the Rule Space Model analysis indicated that (1) the test items developed by the Rule Space Model were of high psychometric quality for good analysis of difficulties, discriminations, reliabilities, and validities; (2) the Rule Space Model analysis classified the students into seven different attribute mastery patterns; and (3) the initial hypothesized learning progression was modified by the attribute mastery patterns and the learning paths to be more precise and detailed.

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

PubMed Central

Cao, Youfang; Liang, Jie

2013-01-01

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape. PMID:23862966

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

NASA Astrophysics Data System (ADS)

Cao, Youfang; Liang, Jie

2013-07-01

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method.

PubMed

Cao, Youfang; Liang, Jie

2013-07-14

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.

Integrated structural and optical modeling of the orbiting stellar interferometer

NASA Astrophysics Data System (ADS)

Shaklan, Stuart B.; Yu, Jeffrey W.; Briggs, Hugh C.

1993-11-01

The Integrated Modeling of Optical Systems (IMOS) Integration Workbench at JPL has been used to model the effects of structural perturbations on the optics in the proposed Orbiting Stellar Interferometer (OSI). OSI consists of 3 pairs of interferometers and delay lines attached to a 7.5 meter truss. They are interferometrically monitored from a separate boom by a laser metrology system. The spatially distributed nature of the science instrument calls for a high level of integration between the optics and support structure. Because OSI is designed to achieve micro-arcsecond astrometry, many of its alignment, stability, and knowledge tolerances are in the submicron regime. The spacecraft will be subject to vibrations caused by reaction wheels and on-board equipment, as well as thermal strain due to solar and terrestrial heating. These perturbations affect optical parameters such as optical path differences and beam co-parallelism which are critical to instrument performance. IMOS provides an environment that allows one to design and perturb the structure, attach optics to structural or non-structural nodes, trace rays, and analyze the impact of mechanical perturbations on optical performance. This tool makes it simple to change the structure and immediately see performance enhancement/degradation. We have employed IMOS to analyze the effect of reaction wheel disturbances on the optical path difference in both the science and metrology interferometers.

Neuromorphic transistor achieved by redox reaction of WO3 thin film

NASA Astrophysics Data System (ADS)

Tsuchiya, Takashi; Jayabalan, Manikandan; Kawamura, Kinya; Takayanagi, Makoto; Higuchi, Tohru; Jayavel, Ramasamy; Terabe, Kazuya

2018-04-01

An all-solid-state neuromorphic transistor composed of a WO3 thin film and a proton-conducting electrolyte was fabricated for application to next-generation information and communication technology including artificial neural networks. The drain current exhibited a 4-order-of-magnitude increment by redox reaction of the WO3 thin film owing to proton migration. Learning and forgetting characteristics were well tuned by the gate control of WO3 redox reactions owing to the separation of the current reading path and pulse application path in the transistor structure. This technique should lead to the development of versatile and low-power-consumption neuromorphic devices.

Clinical and pathological tools for identifying microsatellite instability in colorectal cancer

PubMed Central

Krivokapić, Zoran; Marković, Srdjan; Antić, Jadranka; Dimitrijević, Ivan; Bojić, Daniela; Svorcan, Petar; Jojić, Njegica; Damjanović, Svetozar

2012-01-01

Aim To assess practical accuracy of revised Bethesda criteria (BGrev), pathological predictive model (MsPath), and histopathological parameters for detection of high-frequency of microsatellite instability (MSI-H) phenotype in patients with colorectal carcinoma (CRC). Method Tumors from 150 patients with CRC were analyzed for MSI using a fluorescence-based pentaplex polymerase chain reaction technique. For all patients, we evaluated age, sex, family history of cancer, localization, tumor differentiation, mucin production, lymphocytic infiltration (TIL), and Union for International Cancer Control stage. Patients were classified according to the BGrev, and the groups were compared. The utility of the BGrev, MsPath, and clinical and histopathological parameters for predicting microsatellite tumor status were assessed by univariate logistic regression analysis and by calculating the sensitivity, specificity, and positive (PPV) and negative (NPV) predictive values. Results Fifteen out of 45 patients who met and 4 of 105 patients who did not meet the BGrev criteria had MSI-H CRC. Sensitivity, specificity, PPV, and NPV for BGrev were 78.9%, 77%, 30%, and 70%, respectively. MSI histology (the third BGrev criterion without age limit) was as sensitive as BGrev, but more specific. MsPath model was more sensitive than BGrev (86%), with similar specificity. Any BGrev criterion fulfillment, mucinous differentiation, and right-sided CRC were singled out as independent factors to identify MSI-H colorectal cancer. Conclusion The BGrev, MsPath model, and MSI histology are useful tools for selecting patients for MSI testing. PMID:22911525

HCN and chromophore formation on Jupiter

NASA Technical Reports Server (NTRS)

Ferris, James P.; Ishikawa, Yoji

1987-01-01

Reaction paths for the formation of HCN and chromophores on Jupiter are suggested. The reactions involve photolysis of ammonia/acetylene mixtures. Experimental data supporting these pathways are reported.

Dynamical correlation effects on photoisomerization: Ab initio multiple spawning dynamics with MS-CASPT2 for a model trans-protonated Schiff base

DOE PAGES

Liu, Lihong; Liu, Jian; Martinez, Todd J.

2015-12-17

Here, we investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multi-state second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerizationmore » are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.« less

A compilation of rate parameters of water-mineral interaction kinetics for application to geochemical modeling

USGS Publications Warehouse

Palandri, James L.; Kharaka, Yousif K.

2004-01-01

Geochemical reaction path modeling is useful for rapidly assessing the extent of water-aqueous-gas interactions both in natural systems and in industrial processes. Modeling of some systems, such as those at low temperature with relatively high hydrologic flow rates, or those perturbed by the subsurface injection of industrial waste such as CO2 or H2S, must account for the relatively slow kinetics of mineral-gas-water interactions. We have therefore compiled parameters conforming to a general Arrhenius-type rate equation, for over 70 minerals, including phases from all the major classes of silicates, most carbonates, and many other non-silicates. The compiled dissolution rate constants range from -0.21 log moles m-2 s-1 for halite, to -17.44 log moles m-2 s-1 for kyanite, for conditions far from equilibrium, at 25 ?C, and pH near neutral. These data have been added to a computer code that simulates an infinitely well-stirred batch reactor, allowing computation of mass transfer as a function of time. Actual equilibration rates are expected to be much slower than those predicted by the selected computer code, primarily because actual geochemical processes commonly involve flow through porous or fractured media, wherein the development of concentration gradients in the aqueous phase near mineral surfaces, which results in decreased absolute chemical affinity and slower reaction rates. Further differences between observed and computed reaction rates may occur because of variables beyond the scope of most geochemical simulators, such as variation in grain size, aquifer heterogeneity, preferred fluid flow paths, primary and secondary mineral coatings, and secondary minerals that may lead to decreased porosity and clogged pore throats.

Understanding the physics and chemistry of reaction mechanisms from atomic contributions: a reaction force perspective.

PubMed

Vöhringer-Martinez, Esteban; Toro-Labbé, Alejandro

2012-07-12

Studying chemical reactions involves the knowledge of the reaction mechanism. Despite activation barriers describing the kinetics or reaction energies reflecting thermodynamic aspects, identifying the underlying physics and chemistry along the reaction path contributes essentially to the overall understanding of reaction mechanisms, especially for catalysis. In the past years the reaction force has evolved as a valuable tool to discern between structural changes and electrons' rearrangement in chemical reactions. It provides a framework to analyze chemical reactions and additionally a rational partition of activation and reaction energies. Here, we propose to separate these energies further in atomic contributions, which will shed new insights in the underlying reaction mechanism. As first case studies we analyze two intramolecular proton transfer reactions. Despite the atom based separation of activation barriers and reaction energies, we also assign the participation of each atom in structural changes or electrons' rearrangement along the intrinsic reaction coordinate. These participations allow us to identify the role of each atom in the two reactions and therfore the underlying chemistry. The knowledge of the reaction chemistry immediately leads us to suggest replacements with other atom types that would facilitate certain processes in the reaction. The characterization of the contribution of each atom to the reaction energetics, additionally, identifies the reactive center of a molecular system that unites the main atoms contributing to the potential energy change along the reaction path.

Potential energy function for CH3+CH3 ⇆ C2H6: Attributes of the minimum energy path

NASA Astrophysics Data System (ADS)

Robertson, S. H.; Wardlaw, D. M.; Hirst, D. M.

1993-11-01

The region of the potential energy surface for the title reaction in the vicinity of its minimum energy path has been predicted from the analysis of ab initio electronic energy calculations. The ab initio procedure employs a 6-31G** basis set and a configuration interaction calculation which uses the orbitals obtained in a generalized valence bond calculation. Calculated equilibrium properties of ethane and of isolated methyl radical are compared to existing theoretical and experimental results. The reaction coordinate is represented by the carbon-carbon interatomic distance. The following attributes are reported as a function of this distance and fit to functional forms which smoothly interpolate between reactant and product values of each attribute: the minimum energy path potential, the minimum energy path geometry, normal mode frequencies for vibrational motion orthogonal to the reaction coordinate, a torsional potential, and a fundamental anharmonic frequency for local mode, out-of-plane CH3 bending (umbrella motion). The best representation is provided by a three-parameter modified Morse function for the minimum energy path potential and a two-parameter hyperbolic tangent switching function for all other attributes. A poorer but simpler representation, which may be satisfactory for selected applications, is provided by a standard Morse function and a one-parameter exponential switching function. Previous applications of the exponential switching function to estimate the reaction coordinate dependence of the frequencies and geometry of this system have assumed the same value of the range parameter α for each property and have taken α to be less than or equal to the ``standard'' value of 1.0 Å-1. Based on the present analysis this is incorrect: The α values depend on the property and range from ˜1.2 to ˜1.8 Å-1.

PHREEQCI; a graphical user interface for the geochemical computer program PHREEQC

USGS Publications Warehouse

Charlton, Scott R.; Macklin, Clifford L.; Parkhurst, David L.

1997-01-01

PhreeqcI is a Windows-based graphical user interface for the geochemical computer program PHREEQC. PhreeqcI provides the capability to generate and edit input data files, run simulations, and view text files containing simulation results, all within the framework of a single interface. PHREEQC is a multipurpose geochemical program that can perform speciation, inverse, reaction-path, and 1D advective reaction-transport modeling. Interactive access to all of the capabilities of PHREEQC is available with PhreeqcI. The interface is written in Visual Basic and will run on personal computers under the Windows(3.1), Windows95, and WindowsNT operating systems.

Construction of an Exploratory List of Chemicals to Initiate the Search for Halon Alternatives

DTIC Science & Technology

1991-06-01

of owne-depletion effectiveness is based on atmospheric modeling. The only experimental work is the determination of possible reaction paths and...results, and additional relevant comments. These compounds should be tested in a selective series of experiments based on the insights used in the...will generate initial information with regard to the relative ordering of the compounds in terms of screen properties. Careful experimentation will

Theoretical Study of Tautomerization Reactions for the Ground and First Excited Electronic States of Adenine

NASA Technical Reports Server (NTRS)

Salter, Latasha M.; Chaban, Galina M.; Kwak, Dochan (Technical Monitor)

2002-01-01

Geometrical structures and energetic properties for different tautomers of adenine are calculated in this study, using multi-configurational wave functions. Both the ground and the lowest singlet excited state potential energy surfaces are studied. Four tautomeric forms are considered, and their energetic order is found to be different on the ground and the excited state potential energy surfaces. Minimum energy reaction paths are obtained for hydrogen atom transfer (tautomerization) reactions in the ground and the lowest excited electronic states. It is found that the barrier heights and the shapes of the reaction paths are different for the ground and the excited electronic states, suggesting that the probability of such tautomerization reaction is higher on the excited state potential energy surface. This tautomerization process should become possible in the presence of water or other polar solvent molecules and should play an important role in the photochemistry of adenine.

Fluid-loop reaction system

NASA Technical Reports Server (NTRS)

Lurie, Boris J. (Inventor); Schier, J. Alan (Inventor); Iskenderian, Theodore C. (Inventor)

1991-01-01

An improved fluid actuating system for imparting motion to a body such as a spacecraft is disclosed. The fluid actuating system consists of a fluid mass that may be controllably accelerated through at least one fluid path whereby an opposite acceleration is experienced by the spacecraft. For full control of the spacecraft's orientation, the system would include a plurality of fluid paths. The fluid paths may be circular or irregular, and the fluid paths may be located on the interior or exterior of the spacecraft.

NetPath: a public resource of curated signal transduction pathways

PubMed Central

2010-01-01

We have developed NetPath as a resource of curated human signaling pathways. As an initial step, NetPath provides detailed maps of a number of immune signaling pathways, which include approximately 1,600 reactions annotated from the literature and more than 2,800 instances of transcriptionally regulated genes - all linked to over 5,500 published articles. We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches. PMID:20067622

Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohisa, M.; Yamataka, H.; Dupuis, Michel

2007-12-05

Two-dimensional free-energy surfaces are calculated for alkyl chloride/chloride exchange/inversion reactions: Cl- + RCl (R = Me and t-Bu) surrounded by one hundred H2O molecules as a model of solvent. The methodology of free-energy calculation by perturbation theory based on a mixed-Hamiltonian model (QM/MM) combined with Monte Carlo sampling of the solvent configurations was used to obtain the changes in solvation free energy. We devised a special procedure to analyze the two-dimensional free-energy surfaces to gain unique insight into the differences in the reaction mechanisms between the two systems. The inversion reaction path for R = t-Bu on the free-energy surfacemore » is found to proceed in an asynchronous way within a concerted framework via the ion-pair region. This is in contrast to the R = Me system that proceeds as a typical SN2 reaction. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program. The Pacific Northwest National Laboratory is operated by Battelle for DOE.« less

A QM/MM study of the reaction mechanism of (R)-hydroxynitrile lyases from Arabidopsis thaliana (AtHNL).

PubMed

Zhu, Wenyou; Liu, Yongjun; Zhang, Rui

2015-01-01

Hydroxynitrile lyases (HNLs) catalyze the conversion of chiral cyanohydrins to hydrocyanic acid (HCN) and aldehyde or ketone. Hydroxynitrile lyase from Arabidopsis thaliana (AtHNL) is the first R-selective HNL enzyme containing an α/β-hydrolases fold. In this article, the catalytic mechanism of AtHNL was theoretically studied by using QM/MM approach based on the recently obtained crystal structure in 2012. Two computational models were constructed, and two possible reaction pathways were considered. In Path A, the calculation results indicate that the proton transfer from the hydroxyl group of cyanohydrin occurs firstly, and then the cleavage of C1-C2 bond and the rotation of the generated cyanide ion (CN(-)) follow, afterwards, CN(-) abstracts a proton from His236 via Ser81. The C1-C2 bond cleavage and the protonation of CN(-) correspond to comparable free energy barriers (12.1 vs. 12.2 kcal mol(-1)), suggesting that both of the two processes contribute a lot to rate-limiting. In Path B, the deprotonation of the hydroxyl group of cyanohydrin and the cleavage of C1-C2 bond take place in a concerted manner, which corresponds to the highest free energy barrier of 13.2 kcal mol(-1). The free energy barriers of Path A and B are very similar and basically agree well with the experimental value of HbHNL, a similar enzyme of AtHNL. Therefore, both of the two pathways are possible. In the reaction, the catalytic triad (His236, Ser81, and Asp208) acts as the general acid/base, and the generated CN(-) is stabilized by the hydroxyl group of Ser81 and the main-chain NH-groups of Ala13 and Phe82. © 2014 Wiley Periodicals, Inc.

Donor anxiety, needle pain, and syncopal reactions combine to determine retention: a path analysis of two-year donor return data.

PubMed

France, Christopher R; France, Janis L; Wissel, Mary Ellen; Ditto, Blaine; Dickert, Tara; Himawan, Lina K

2013-09-01

Efforts to expand the donor pool by recruiting younger donors have resulted in higher numbers of initial donations, but retention of young donors continues to be challenging. Path analysis was used to examine the simultaneous relationships among syncopal reactions, donation anxiety, needle pain, donor satisfaction, and donation intention in predicting repeat donation. Participants included 421 first- and second-time donors recruited for a study comparing the effects of predonation water loading with and without the use of applied muscle tension during donation (52% female, 60.8% first-time donor, mean age 20.3 years). For this longitudinal follow-up study, donor database records were accessed 2 years after the index donation to assess repeat donation. Results of a series of path analyses demonstrated the influential role of donor anxiety in shaping donor retention (final model χ(2) = 35.75, root mean square error of approximation 0.03, comparative fit index 0.98, weighted root mean square residual 0.74). First, anxiety exerted a direct negative influence on donation intention, the proximal and sole direct predictor of repeat donation. Second, anxiety increased the likelihood of donor-reported needle pain, adversely affecting donation satisfaction and, subsequently, donation intention. Finally, anxiety was associated with donor ratings of syncopal reactions through its impact on needle pain, which also contributed to decreased donation intention. These results provide novel evidence that donation anxiety plays a central role in shaping future donation behavior. Individual differences in anxiety must be considered when developing and testing strategies to enhance blood donor retention. © 2013 American Association of Blood Banks.

Parameters governing ruthenium sawhorse-based decarboxylation of oleic acid

USDA-ARS?s Scientific Manuscript database

Ruthenium-catalyzed decarboxylation of 9-cisoctadecenoic is a path to produce biobased olefins. Here, a mechanistic study of this reaction was undertaken utilizing a closed reaction system and a pressure reactor. The proposed mechanism of an isomerization followed by a decarboxylation reaction was c...

Reliable Transition State Searches Integrated with the Growing String Method.

PubMed

Zimmerman, Paul

2013-07-09

The growing string method (GSM) is highly useful for locating reaction paths connecting two molecular intermediates. GSM has often been used in a two-step procedure to locate exact transition states (TS), where GSM creates a quality initial structure for a local TS search. This procedure and others like it, however, do not always converge to the desired transition state because the local search is sensitive to the quality of the initial guess. This article describes an integrated technique for simultaneous reaction path and exact transition state search. This is achieved by implementing an eigenvector following optimization algorithm in internal coordinates with Hessian update techniques. After partial convergence of the string, an exact saddle point search begins under the constraint that the maximized eigenmode of the TS node Hessian has significant overlap with the string tangent near the TS. Subsequent optimization maintains connectivity of the string to the TS as well as locks in the TS direction, all but eliminating the possibility that the local search leads to the wrong TS. To verify the robustness of this approach, reaction paths and TSs are found for a benchmark set of more than 100 elementary reactions.

Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks.

PubMed

Meng, X Flora; Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M

2017-05-01

Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. © 2017 The Author(s).

Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks

PubMed Central

Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M.

2017-01-01

Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. PMID:28566513

Dissolved Organic Carbon 14C in Southern Nevada Groundwater and Implications for Groundwater Travel Times

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hershey, Ronald L.; Fereday, Wyall; Thomas, James M

Dissolved inorganic carbon (DIC) carbon-14 ( 14C) ages must be corrected for complex chemical and physical reactions and processes that change the amount of 14C in groundwater as it flows from recharge to downgradient areas. Because of these reactions, DIC 14C can produce unrealistically old ages and long groundwater travel times that may, or may not, agree with travel times estimated by other methods. Dissolved organic carbon (DOC) 14C ages are often younger than DIC 14C ages because there are few chemical reactions or physical processes that change the amount of DOC 14C in groundwater. However, there are several issuesmore » that create uncertainty in DOC 14C groundwater ages including limited knowledge of the initial (A 0) DOC 14C in groundwater recharge and potential changes in DOC composition as water moves through an aquifer. This study examines these issues by quantifying A 0 DOC 14C in recharge areas of southern Nevada groundwater flow systems and by evaluating changes in DOC composition as water flows from recharge areas to downgradient areas. The effect of these processes on DOC 14C groundwater ages is evaluated and DOC and DIC 14C ages are then compared along several southern Nevada groundwater flow paths. Twenty-seven groundwater samples were collected from springs and wells in southern Nevada in upgradient, midgradient, and downgradient locations. DOC 14C for upgradient samples ranged from 96 to 120 percent modern carbon (pmc) with an average of 106 pmc, verifying modern DOC 14C ages in recharge areas, which decreases uncertainty in DOC 14C A 0 values, groundwater ages, and travel times. The HPLC spectra of groundwater along a flow path in the Spring Mountains show the same general pattern indicating that the DOC compound composition does not change along this flow path. Although DOC concentration decreases from recharge-area to downgradient groundwater, the organic compounds are similar, indicating that DOC 14C is unaffected by other processes such as microbial degradation. A small amount of organic carbon was leached from crushed volcanic and carbonate aquifer outcrop rock in rock-leaching experiments. The leached DOC was high in 14C (75 pmc carbonate rocks, 91 pmc volcanic) suggesting that the leached DOC likely came from microbes in the rock samples. The small amount of DOC and high 14C indicates that the amount of old organic carbon in these rocks is low so there should be minimal impact on groundwater DOC 14C ages. Based on the results from this study, DOC 14C ages do not require additional corrections. Several correction models were applied to DIC 14C ages to correct for water-rock reactions along two carbonate and two volcanic flow paths and the corresponding travel times were compare to DOC 14C travel times. The DOC 14C travel times were hundreds to thousands of years shorter than uncorrected and corrected DIC 14C travel times except for the upper section of one carbonate flow path. DOC 14C travel times ranged from 400 to 5,400 years as compared to DIC 14C that ranged from modern to 20,900 years. The DIC 14C ages are greatly influenced by carbonate mineral and gas reactions and other processes such as matrix diffusion, isotope exchange, or adsorption, which are not always adequately accounted for in DIC 14C groundwater age correction models.« less

Determination of reaction rates and activation energy in aerobic composting processes for yard waste.

PubMed

Uma, R N; Manjula, G; Meenambal, T

2007-04-01

The reaction rates and activation energy in aerobic composting processes for yard waste were determined using specifically designed reactors. Different mixture ratios were fixed before the commencement of the process. The C/N ratio was found to be optimum for a mixture ratio of 1:6 containing one part of coir pith to six parts of other waste which included yard waste, yeast sludge, poultry yard waste and decomposing culture (Pleurotosis). The path of stabilization of the wastes was continuously monitored by observing various parameters such as temperature, pH, Electrical Conductivity, C.O.D, VS at regular time intervals. Kinetic analysis was done to determine the reaction rates and activation energy for the optimum mixture ratio under forced aeration condition. The results of the analysis clearly indicated that the temperature dependence of the reaction rates followed the Arrhenius equation. The temperature coefficients were also determined. The degradation of the organic fraction of the yard waste could be predicted using first order reaction model.

Quantum Monte Carlo tunneling from quantum chemistry to quantum annealing

NASA Astrophysics Data System (ADS)

Mazzola, Guglielmo; Smelyanskiy, Vadim N.; Troyer, Matthias

2017-10-01

Quantum tunneling is ubiquitous across different fields, from quantum chemical reactions and magnetic materials to quantum simulators and quantum computers. While simulating the real-time quantum dynamics of tunneling is infeasible for high-dimensional systems, quantum tunneling also shows up in quantum Monte Carlo (QMC) simulations, which aim to simulate quantum statistics with resources growing only polynomially with the system size. Here we extend the recent results obtained for quantum spin models [Phys. Rev. Lett. 117, 180402 (2016), 10.1103/PhysRevLett.117.180402], and we study continuous-variable models for proton transfer reactions. We demonstrate that QMC simulations efficiently recover the scaling of ground-state tunneling rates due to the existence of an instanton path, which always connects the reactant state with the product. We discuss the implications of our results in the context of quantum chemical reactions and quantum annealing, where quantum tunneling is expected to be a valuable resource for solving combinatorial optimization problems.

Force and moment rotordynamic coefficients for pump-impeller shroud surfaces

NASA Technical Reports Server (NTRS)

Childs, Dara W.

1987-01-01

Governing equations of motion are derived for a bulk-flow model of the leakage path between an impeller shroud and a pump housing. The governing equations consist of a path-momentum, a circumferential - momentum, and a continuity equation. The fluid annulus between the impeller shroud and pump housing is assumed to be circumferentially symmetric when the impeller is centered; i.e., the clearance can vary along the pump axis but does not vary in the circumferential direction. A perturbation expansion of the governing equations in the eccentricity ratio yields a set of zeroth and first-order governing equations. The zeroth-order equations define the leaking rate and the circumferential and path velocity distributions and pressure distributions for a centered impeller position. The first-order equations define the perturbations in the velocity and pressure distributions due to either a radial-displacement perturbation or a tilt perturbation of the impeller. Integration of the perturbed pressure and shear-stress distribution acting on the rotor yields the reaction forces and moments acting on the impeller face.

Perspective: Maximum caliber is a general variational principle for dynamical systems

NASA Astrophysics Data System (ADS)

Dixit, Purushottam D.; Wagoner, Jason; Weistuch, Corey; Pressé, Steve; Ghosh, Kingshuk; Dill, Ken A.

2018-01-01

We review here Maximum Caliber (Max Cal), a general variational principle for inferring distributions of paths in dynamical processes and networks. Max Cal is to dynamical trajectories what the principle of maximum entropy is to equilibrium states or stationary populations. In Max Cal, you maximize a path entropy over all possible pathways, subject to dynamical constraints, in order to predict relative path weights. Many well-known relationships of non-equilibrium statistical physics—such as the Green-Kubo fluctuation-dissipation relations, Onsager's reciprocal relations, and Prigogine's minimum entropy production—are limited to near-equilibrium processes. Max Cal is more general. While it can readily derive these results under those limits, Max Cal is also applicable far from equilibrium. We give examples of Max Cal as a method of inference about trajectory distributions from limited data, finding reaction coordinates in bio-molecular simulations, and modeling the complex dynamics of non-thermal systems such as gene regulatory networks or the collective firing of neurons. We also survey its basis in principle and some limitations.

Perspective: Maximum caliber is a general variational principle for dynamical systems.

PubMed

Dixit, Purushottam D; Wagoner, Jason; Weistuch, Corey; Pressé, Steve; Ghosh, Kingshuk; Dill, Ken A

2018-01-07

We review here Maximum Caliber (Max Cal), a general variational principle for inferring distributions of paths in dynamical processes and networks. Max Cal is to dynamical trajectories what the principle of maximum entropy is to equilibrium states or stationary populations. In Max Cal, you maximize a path entropy over all possible pathways, subject to dynamical constraints, in order to predict relative path weights. Many well-known relationships of non-equilibrium statistical physics-such as the Green-Kubo fluctuation-dissipation relations, Onsager's reciprocal relations, and Prigogine's minimum entropy production-are limited to near-equilibrium processes. Max Cal is more general. While it can readily derive these results under those limits, Max Cal is also applicable far from equilibrium. We give examples of Max Cal as a method of inference about trajectory distributions from limited data, finding reaction coordinates in bio-molecular simulations, and modeling the complex dynamics of non-thermal systems such as gene regulatory networks or the collective firing of neurons. We also survey its basis in principle and some limitations.

Roles of Impulsivity, Motivation, and Emotion Regulation in Procrastination - Path Analysis and Comparison Between Students and Non-students.

PubMed

Wypych, Marek; Matuszewski, Jacek; Dragan, Wojciech Ł

2018-01-01

Procrastination - an irrational delay of intended actions despite expecting to be worse off - is a complex and non-homogenous phenomenon. Previous studies have found a number of correlates of procrastination, some of which seem to be particularly important. Impulsivity is closely connected to procrastination on behavioral, genetic, and neuronal levels. Difficulties in emotion regulation have also been shown to be strongly related to procrastination. Procrastination can also be considered as a motivation-based problem. To try to disentangle the connections of impulsivity, emotion regulation, and motivation to procrastination we collected data from over 600 subjects using multiple questionnaires (PPS - Pure Procrastination Scale; UPPSP - Impulsive Behavior Scale, ERQ - Emotion Regulation Questionnaire and MDT - Motivational Diagnostic Test). Structural equation modeling was performed to test several possible relationships between the measured variables. The effects of student status and age have also been investigated. The final path model was a directional model based on six explanatory variables and accounted for 70% of the variance in procrastination. Path analysis revealed that the strongest contributions to procrastination came from lack of value, delay discounting, and lack of perseverance, suggesting the involvement of motivation and impulsivity. The model also revealed the moderating role of expressive suppression between several aspects of impulsivity and procrastination. Close inspection of the paths' weights suggests that there may be two partly competing strategies for dealing with impulsivity and negative emotions: either to suppress emotions and impulsive reactions or to react impulsively, discarding previous plans, and to procrastinate. Path invariance analysis showed the significant moderating roles of student status and age. Both in non-students and high-age groups, the path leading from suppression to procrastination was insignificant. This suggests that caution should be used in generalizing the results of studies carried out on students. These results support previous findings that procrastination may serve as a short-term mood regulation strategy. However, as the spectrum of the emotion regulation strategies included in the study was very limited, we conclude that future studies should seek more insight into the relationship between emotion regulation, self-control, and procrastination.

Cognitive and psychological reactions of the general population three months after the 2011 Tohoku earthquake and tsunami.

PubMed

Kyutoku, Yasushi; Tada, Ryoko; Umeyama, Takahiko; Harada, Kenji; Kikuchi, Senichiro; Watanabe, Eiju; Liegey-Dougall, Angela; Dan, Ippeita

2012-01-01

The largest earthquake on record in Japan (magnitude 9.0) occurred on March 11, 2011, and the subsequent tsunami devastated the Pacific coast of Northern Japan. These further triggered the Fukushima I nuclear power plant accidents. Such a hugely complex disaster inevitably has negative psychological effects on general populations as well as on the direct victims. While previous disaster studies enrolled descriptive approaches focusing on direct victims, the structure of the psychological adjustment process of people from the general population has remained uncertain. The current study attempted to establish a path model that sufficiently reflects the early psychological adaptation process of the general population to large-scale natural disasters. Participants from the primary disaster area (n = 1083) and other areas (n = 2372) voluntarily participated in an online questionnaire study. By constructing path models using a structural equation model procedure (SEM), we examined the structural relationship among psychological constructs known related to disasters. As post-traumatic stress symptoms (PTS) were significantly more present in people in the primarily affected area than in those in secondary- or non-affected areas, the path models were constructed for the primary victims. The parsimoniously depicted model with the best fit was achieved for the psychological-adjustment centered model with quality of life (QoL) as a final outcome. The paths to QoL via negative routes (from negative cognitive appraisal, PTS, and general stress) were dominant, suggesting the importance of clinical intervention for reducing negative cognitive appraisal, and for caring for general stress and PTS to maintain QoL at an early stage of psychological adaptation to a disaster. The model also depicted the presence of a positive route where positive cognitive appraisal facilitates post-traumatic growth (PTG) to achieve a higher QoL, suggesting the potential importance of positive psychological preventive care for unexpected natural disasters.

Cognitive and Psychological Reactions of the General Population Three Months After the 2011 Tohoku Earthquake and Tsunami

PubMed Central

Kyutoku, Yasushi; Tada, Ryoko; Umeyama, Takahiko; Harada, Kenji; Kikuchi, Senichiro; Watanabe, Eiju; Liegey-Dougall, Angela; Dan, Ippeita

2012-01-01

Background The largest earthquake on record in Japan (magnitude 9.0) occurred on March 11, 2011, and the subsequent tsunami devastated the Pacific coast of Northern Japan. These further triggered the Fukushima I nuclear power plant accidents. Such a hugely complex disaster inevitably has negative psychological effects on general populations as well as on the direct victims. While previous disaster studies enrolled descriptive approaches focusing on direct victims, the structure of the psychological adjustment process of people from the general population has remained uncertain. The current study attempted to establish a path model that sufficiently reflects the early psychological adaptation process of the general population to large-scale natural disasters. Methods and Findings Participants from the primary disaster area (n = 1083) and other areas (n = 2372) voluntarily participated in an online questionnaire study. By constructing path models using a structural equation model procedure (SEM), we examined the structural relationship among psychological constructs known related to disasters. As post-traumatic stress symptoms (PTS) were significantly more present in people in the primarily affected area than in those in secondary- or non-affected areas, the path models were constructed for the primary victims. The parsimoniously depicted model with the best fit was achieved for the psychological-adjustment centered model with quality of life (QoL) as a final outcome. Conclusion The paths to QoL via negative routes (from negative cognitive appraisal, PTS, and general stress) were dominant, suggesting the importance of clinical intervention for reducing negative cognitive appraisal, and for caring for general stress and PTS to maintain QoL at an early stage of psychological adaptation to a disaster. The model also depicted the presence of a positive route where positive cognitive appraisal facilitates post-traumatic growth (PTG) to achieve a higher QoL, suggesting the potential importance of positive psychological preventive care for unexpected natural disasters. PMID:22347421

From Bunsen Burners to Fuel Cells: Invoking Energy Transducers to Exemplify "Paths" and Unify the Energy-Related Concepts of Thermochemistry and Thermodynamics

ERIC Educational Resources Information Center

Hladky, Paul W.

2009-01-01

The conversion of chemical energy entirely into thermal energy by Bunsen burners and into thermal energy and electrical energy by fuel cells of varying efficiencies illustrates different paths by which a chemical reaction can occur. Using the efficiency of producing electrical energy as a path label allows all of the energy-related quantities to…

Variational transition state theory: theoretical framework and recent developments.

PubMed

Bao, Junwei Lucas; Truhlar, Donald G

2017-12-11

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications. The theoretical methods reviewed here include multidimensional quantum mechanical tunneling, multistructural VTST (MS-VTST), multi-path VTST (MP-VTST), both reaction-path VTST (RP-VTST) and variable reaction coordinate VTST (VRC-VTST), system-specific quantum Rice-Ramsperger-Kassel theory (SS-QRRK) for predicting pressure-dependent rate constants, and VTST in the solid phase, liquid phase, and enzymes. We also provide some perspectives regarding the general applicability of VTST.

The Path of Carbon in Photosynthesis IX. Photosynthesis, Photoreduction, and the Hydrogen-Oxygen-Carbon Dioxide Dark Reaction

DOE R&D Accomplishments Database

Badin, E. J.; Calvin, M.

1950-02-01

A comparison of the rates of fixation of Carbon 14 dioxide in algae for the processes of photosynthesis, photoreduction and the hydrogen-oxygen-carbon dioxide dark reaction has been made. For the same series of experiments, rates of incorporation of tracer carbon into the separate soluble components using the radiogram method have been determined. The mechanism of carbon dioxide uptake has been shown to occur via two distinct paths. In all cases studied, essentially the same compounds appear radioactive. The distribution with time, however, differs markedly.

Formation of furan fatty alkyl esters from their bis-epoxide fatty esters

USDA-ARS?s Scientific Manuscript database

Epoxidation of vegetable oils and consecutive epoxide ring-opening reaction is a widely investigated path for producing biobased lubricants and polymers. The reaction mechanism and products are considered well-studied and known. In the current study, the reactions of epoxidized alkyl soyate with fou...

Liquid waveguide spectrophotometric measurement of nanomolar ammonium in seawater based on the indophenol reaction with o-phenylphenol (OPP).

PubMed

Hashihama, Fuminori; Kanda, Jota; Tauchi, Ami; Kodama, Taketoshi; Saito, Hiroaki; Furuya, Ken

2015-10-01

We describe a highly sensitive colorimetric method for the determination of nanomolar concentrations of ammonium in seawater based on the indophenol reaction with o-phenylphenol [(1,1'-biphenyl)-2-ol, abbreviated as OPP]. OPP is available as non-toxic, stable flaky crystals with no caustic odor and has some advantages over phenol in practical use. The method was established by using a gas-segmented continuous flow analyzer equipped with two types of long path liquid waveguide capillary cell, LWCCs (100 cm and 200 cm) and an UltraPath (200 cm), which have inner diameters of 0.55 mm and 2 mm, respectively. The reagent concentrations, flow rates of the pumping tubes, and reaction path and temperature were determined on the basis of a manual indophenol blue method with OPP (Kanda, Water Res. 29 (1995) 2746-2750). The sample mixed with reagents that form indophenol blue dye was measured at 670 nm. Aged subtropical surface water was used as a blank, a matrix of standards, and the carrier. The detection limits of the analytical systems with a 100 cm LWCC, a 200 cm LWCC, and a 200 cm UltraPath were 6, 4, and 4 nM, respectively. These systems had high precision (<4% at 100 nM) and a linear dynamic range up to 200 nM. Non-linear baseline drift did not occur when using the UltraPath system. This is due to the elimination of cell clogging because of the larger inner diameter of the UltraPath compared to the LWCCs. The UltraPath system is thus more suitable for long-term measurements compared with the LWCC systems. The results of the proposed sensitive colorimetry and a conventional colorimetry for the determination of seawater samples showed no significant difference. The proposed analytical systems were applied to underway surface monitoring and vertical observation in the oligotrophic South Pacific. Copyright © 2015 Elsevier B.V. All rights reserved.

Compressibility effects on rotor forces in the leakage path between a shrouded pump impeller and its housing

NASA Technical Reports Server (NTRS)

Cao, Nhai The

1993-01-01

A modified approach to Childs' previous work on fluid-structure interaction forces in the leakage path between an impeller shroud and its housing is presented in this paper. Three governing equations consisting of continuity, path-momentum, and circumferential-momentum equations were developed to describe the leakage path inside a pump impeller. Radial displacement perturbations were used to solve for radial and circumferential force coefficients. In addition, impeller-discharge pressure disturbances were used to obtain pressure oscillation responses due to precessing impeller pressure wave pattern. Childs' model was modified from an incompressible model to a compressible barotropic-fluid model (the density of the working fluid is a function of the pressure and a constant temperature only). Results obtained from this model yielded interaction forces for radial and circumferential force coefficients. Radial and circumferential forces define reaction forces within the impeller leakage path. An acoustic model for the same leakage path was also developed. The convective, Coriolis, and centrifugal acceleration terms are removed from the compressible model to obtain the acoustics model. A solution due to impeller discharge pressure disturbances model was also developed for the compressible and acoustics models. The results from these modifications are used to determine what effects additional perturbation terms in the compressible model have on the acoustic model. The results show that the additional fluid mechanics terms in the compressible model cause resonances (peaks) in the force coefficient response curves. However, these peaks only occurred at high values of inlet circumferential velocity ratios greater than 0.7. The peak pressure oscillation was shown to occur at the wearing ring seal. Introduction of impeller discharge disturbances with n = 11 diametral nodes showed that maximum peak pressure oscillations occurred at nondimensional precession frequencies of f = 6.4 and f = 7.8 for this particular pump. Bolleter's results suggest that for peak pressure oscillations to occur at the wearing ring seal, the nondimensional excitation frequency should be on the order of f = 2.182 for n = 11. The resonances found in this research do not match the excitation frequencies predicted by Bolleter. At the predicted peak excitation frequencies given by Bolleter, the compressible model shows an attenuation of the pressure oscillations at the seal exit. The compressibility of the fluid does not have a significant influence on the model at low values of nondimensional excitation frequency. At high values of nondimensional frequency, the effects of compressibility become more significant. For the acoustic analysis, the convective, Coriolis, and centrifugal acceleration terms do affect the results to a limited extent for precession excitation and to a large extent for a pressure excitation when the fluid operates at relatively high Mach numbers.

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

NASA Astrophysics Data System (ADS)

Moradi, Mahmoud; Sagui, Celeste; Roland, Christopher

2014-01-01

We have developed a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. In this paper, we set the theoretical framework for employing nonequilibrium work relations to estimate the relative reaction rates associated with different classes of transition pathways. Particularly, we derive an extension of Crook's transient fluctuation theorem, which relates the relative transition rates of driven systems in the forward and reverse directions, and allows for the calculation of these relative rates using work measurements (e.g., in Steered Molecular Dynamics). The formalism presented here can be combined with Transition Path Theory to relate the equilibrium and driven transition rates. The usefulness of this framework is illustrated by means of a Gaussian model and a driven proline dimer.

Kudi: A free open-source python library for the analysis of properties along reaction paths.

PubMed

Vogt-Geisse, Stefan

2016-05-01

With increasing computational capabilities, an ever growing amount of data is generated in computational chemistry that contains a vast amount of chemically relevant information. It is therefore imperative to create new computational tools in order to process and extract this data in a sensible way. Kudi is an open source library that aids in the extraction of chemical properties from reaction paths. The straightforward structure of Kudi makes it easy to use for users and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. A use case for Kudi is shown for the tautomerization reaction of formic acid. Kudi is available free of charge at www.github.com/stvogt/kudi.

Carbon sequestration via reaction with basaltic rocks: geochemical modeling and experimental results

USGS Publications Warehouse

Rosenbauer, Robert J.; Thomas, Burt; Bischoff, James L.; Palandri, James

2012-01-01

Basaltic rocks are potential repositories for sequestering carbon dioxide (CO2) because of their capacity for trapping CO2 in carbonate minerals. We carried out a series of thermodynamic equilibrium models and high pressure experiments, reacting basalt with CO2-charged fluids over a range of conditions from 50 to 200 °C at 300 bar. Results indicate basalt has a high reactivity to CO2 acidified brine. Carbon dioxide is taken up from solution at all temperatures from 50 to 200 °C, 300 bar, but the maximum extent and rate of reaction occurs at 100 °C, 300 bar. Reaction path simulations utilizing the geochemical modeling program CHILLER predicted an equilibrium carbonate alteration assemblage of calcite, magnesite, and siderite, but the only secondary carbonate identified in the experiments was a ferroan magnesite. The amount of uptake at 100 °C, 300 bar ranged from 8% by weight for a typical tholeite to 26% for a picrite. The actual amount of CO2 uptake and extent of rock alteration coincides directly with the magnesium content of the rock suggesting that overall reaction extent is controlled by bulk basalt Mg content. In terms of sequestering CO2, an average basaltic MgO content of 8% is equivalent to 2.6 × 108 metric ton CO2/km3 basalt.

On the ion-pair dissociation mechanisms in the small NaCl·(H2 O)6 cluster: A perspective from reaction path search calculations.

PubMed

Takayanagi, Toshiyuki; Nakatomi, Taiki; Yonetani, Yoshiteru

2018-04-20

We performed reaction path search calculations for the NaCl·(H 2 O) 6 cluster using the global reaction route mapping (GRRM) code to understand the atomic-level mechanisms of the NaCl → Na +  + Cl - ionic dissociation induced by water solvents. Low-lying minima, transition states connecting two local minima and corresponding intrinsic reaction coordinates on the potential energy surface are explored. We found that the NaCl distances at the transitions states for the dissociation pathways were distributed in a relatively wide range of 2.7-3.7 Å and that the NaCl distance at the transition state did not correlate with the commonly used solvation coordinates. This suggests that the definition of the transition states with specific structures as well as good reaction coordinate is very difficult for the ionic dissociation process even in a small water cluster. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Branching and competition of ultrafast photochemical reactions of cyclooctatriene and bicyclooctadiene

NASA Astrophysics Data System (ADS)

Kosma, Kyriaki; Trushin, Sergei A.; Schmid, Wolfram E.; Fuß, Werner

2015-12-01

The main primary photoproducts of cycloocta-1,3,5-triene (COT) are a strained mono-E isomer, Z,Z-octatetraene (OT, from electrocyclic ring opening) and benzene + ethylene. We investigated the excited-state dynamics of COT by time-resolved mass spectroscopy, probing by near-IR photoionization. Unexpectedly, we found only one reaction channel. We assign it to the pericyclic reactions. Evidence for an early branching between this and the Z-E channel is taken from previous resonance Raman data. This channel confirms previously formulated rules on the excited states involved, the reaction path and driving forces and contributes to their rationalization. Bicyclo[4.2.0]octa-2,4-diene undergoes only two pericyclic reactions: ring opening to OT and cleavage to benzene + ethylene. We investigated it briefly in its equilibrium mixture with COT. The data are consistent with a common path on the excited surfaces. Suggestions are made for structures of conical intersections, and driving forces are considered. All processes were found to be barrierless.

Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates: BIOFILM DISTRIBUTION AND RATE SCALING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Zhifeng; Liu, Chongxuan; Liu, Yuanyuan

Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models, and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X-ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical propertiesmore » was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.« less

Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates

NASA Astrophysics Data System (ADS)

Yan, Zhifeng; Liu, Chongxuan; Liu, Yuanyuan; Bailey, Vanessa L.

2017-11-01

Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X-ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical properties was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.

Environmental geochemistry of a Kuroko-type massive sulfide deposit at the abandoned Valzinco mine, Virginia, USA

USGS Publications Warehouse

Seal, R.R.; Hammarstrom, J.M.; Johnson, A.N.; Piatak, N.M.; Wandless, G.A.

2008-01-01

The abandoned Valzinco mine, which worked a steeply dipping Kuroko-type massive sulfide deposit in the Virginia Au-pyrite belt, contributed significant metal-laden acid-mine drainage to the Knight's Branch watershed. The host rocks were dominated by metamorphosed felsic volcanic rocks, which offered limited acid-neutralizing potential. The ores were dominated by pyrite, sphalerite, galena, and chalcopyrite, which represented significant acid-generating potential. Acid-base accounting and leaching studies of flotation tailings - the dominant mine waste at the site - indicated that they were acid generating and therefore, should have liberated significant quantities of metals to solution. Field studies of mine drainage from the site confirmed that mine drainage and the impacted stream waters had pH values from 1.1 to 6.4 and exceeded aquatic ecosystem toxicity limits for Fe, Al, Cd, Cu, Pb and Zn. Stable isotope studies of water, dissolved SO42 -, and primary and secondary sulfate and sulfide minerals indicated that two distinct sulfide oxidation pathways were operative at the site: one dominated by Fe(III) as the oxidant, and another by molecular O2 as the oxidant. Reaction-path modeling suggested that geochemical interactions between tailings and waters approached a steady state within about a year. Both leaching studies and geochemical reaction-path modeling provided reasonable predictions of the mine-drainage chemistry.

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

PubMed

Branduardi, Davide; Faraldo-Gómez, José D

2013-09-10

The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a pre-defined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a non-trivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use of Cartesian reaction coordinates in freely tumbling molecular systems. In addition, this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism of the simulated process. This detailed analysis also provides a physically-meaningful criterion to coarse-grain the representation of the path. To demonstrate the accuracy of the method we analyze the isomerization of the alanine dipeptide in vacuum and the chair-to-inverted-chair transition of β -D mannose in explicit water. Notwithstanding the simplicity of these systems, the SOMA approach reveals novel insights into the atomic mechanism of these isomerizations. In both cases, we find that the dynamics and the energetics of these processes are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show that a coarse-grained SOMA calculation defined in terms of these subsets of atoms yields nearidentical minimum free-energy paths and committor distributions to those obtained via a highly-dimensional string.

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems

PubMed Central

Branduardi, Davide; Faraldo-Gómez, José D.

2014-01-01

The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a pre-defined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a non-trivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use of Cartesian reaction coordinates in freely tumbling molecular systems. In addition, this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism of the simulated process. This detailed analysis also provides a physically-meaningful criterion to coarse-grain the representation of the path. To demonstrate the accuracy of the method we analyze the isomerization of the alanine dipeptide in vacuum and the chair-to-inverted-chair transition of β-D mannose in explicit water. Notwithstanding the simplicity of these systems, the SOMA approach reveals novel insights into the atomic mechanism of these isomerizations. In both cases, we find that the dynamics and the energetics of these processes are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show that a coarse-grained SOMA calculation defined in terms of these subsets of atoms yields nearidentical minimum free-energy paths and committor distributions to those obtained via a highly-dimensional string. PMID:24729762

Mechanistic Study of Nitric Oxide Reduction by Hydrogen on Pt(100) (I): A DFT Analysis of the Reaction Network

DOE PAGES

Bai, Yunhai; Mavrikakis, Manos

2017-05-08

Periodic, self-consistent density functional theory (DFT-GGA, PW91) calculations are used to study the reaction mechanism for nitric oxide (NO) reduction by hydrogen (H 2) on Pt(100). Energetics of various N–O activation paths, including both direct and hydrogen-assisted N–O bond-breaking paths, and the formation of three different N-containing products (N 2, N 2O, and NH3), are systematically studied. On the basis of our analysis, NO* dissociation has a lower barrier than NO* hydrogenation to HNO* or NOH*, and therefore, the direct NO dissociation path is predicted to dominate N–O activation on clean Pt(100). The reaction of atomic N* with N* andmore » NO* is proposed as the mechanism for N 2 and N 2O formation, respectively. NH 3 formation from N* via three successive hydrogenation steps is also studied and is found to be kinetically more difficult than N 2 and N 2O formation from N*. Finally, NO adsorption phase diagrams on Pt(100) are constructed, and these phase diagrams suggest that, at low temperatures (e.g., 400 K), the Pt(100) surface may be covered by half a monolayer of NO. We propose that high NO coverage might affect the NO + H 2 reaction mechanism, and therefore, one should explicitly take the NO coverage into consideration in first-principles studies to determine the reaction mechanism on catalyst surfaces under reaction conditions. In conclusion, a detailed analysis of high NO coverage effects on the reaction mechanism will be presented in a separate contribution.« less

Mechanistic Study of Nitric Oxide Reduction by Hydrogen on Pt(100) (I): A DFT Analysis of the Reaction Network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, Yunhai; Mavrikakis, Manos

Periodic, self-consistent density functional theory (DFT-GGA, PW91) calculations are used to study the reaction mechanism for nitric oxide (NO) reduction by hydrogen (H 2) on Pt(100). Energetics of various N–O activation paths, including both direct and hydrogen-assisted N–O bond-breaking paths, and the formation of three different N-containing products (N 2, N 2O, and NH3), are systematically studied. On the basis of our analysis, NO* dissociation has a lower barrier than NO* hydrogenation to HNO* or NOH*, and therefore, the direct NO dissociation path is predicted to dominate N–O activation on clean Pt(100). The reaction of atomic N* with N* andmore » NO* is proposed as the mechanism for N 2 and N 2O formation, respectively. NH 3 formation from N* via three successive hydrogenation steps is also studied and is found to be kinetically more difficult than N 2 and N 2O formation from N*. Finally, NO adsorption phase diagrams on Pt(100) are constructed, and these phase diagrams suggest that, at low temperatures (e.g., 400 K), the Pt(100) surface may be covered by half a monolayer of NO. We propose that high NO coverage might affect the NO + H 2 reaction mechanism, and therefore, one should explicitly take the NO coverage into consideration in first-principles studies to determine the reaction mechanism on catalyst surfaces under reaction conditions. In conclusion, a detailed analysis of high NO coverage effects on the reaction mechanism will be presented in a separate contribution.« less

Life Prediction of Large Lithium-Ion Battery Packs with Active and Passive Balancing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Ying; Smith, Kandler A; Zane, Regan

Lithium-ion battery packs take a major part of large-scale stationary energy storage systems. One challenge in reducing battery pack cost is to reduce pack size without compromising pack service performance and lifespan. Prognostic life model can be a powerful tool to handle the state of health (SOH) estimate and enable active life balancing strategy to reduce cell imbalance and extend pack life. This work proposed a life model using both empirical and physical-based approaches. The life model described the compounding effect of different degradations on the entire cell with an empirical model. Then its lower-level submodels considered the complex physicalmore » links between testing statistics (state of charge level, C-rate level, duty cycles, etc.) and the degradation reaction rates with respect to specific aging mechanisms. The hybrid approach made the life model generic, robust and stable regardless of battery chemistry and application usage. The model was validated with a custom pack with both passive and active balancing systems implemented, which created four different aging paths in the pack. The life model successfully captured the aging trajectories of all four paths. The life model prediction errors on capacity fade and resistance growth were within +/-3% and +/-5% of the experiment measurements.« less

Formation of Anionic C, N-bearing Chains in the Interstellar Medium via Reactions of H- with HC x N for Odd-valued x from 1 to 7

NASA Astrophysics Data System (ADS)

Gianturco, F. A.; Satta, M.; Yurtsever, E.; Wester, R.

2017-11-01

We investigate the relative efficiencies of low-temperature chemical reactions in the interstellar medium with H- anion reacting in the gas phase with cyanopolyyne neutral molecules, leading to the formation of anionic {{{C}}}x{{{N}}}- linear chains of different lengths and of H2. All the reactions turn out to be without barriers, highly exothermic reactions that provide a chemical route to the formation of anionic chains of the same length. Some of the anions have been observed in the dark molecular clouds and in the diffuse interstellar envelopes. Quantum calculations are carried out for the corresponding reactive potential energy surfaces for all the odd-numbered members of the series (x = 1, 3, 5, 7). We employ the minimum energy paths to obtain the relevant transition state configurations and use the latter within the variational transition state model to obtain the chemical rates. The present results indicate that at typical temperatures around 100 K, a set of significantly larger rate values exists for x = 3 and x = 5, while the rate values are smaller for CN- and {{{C}}}7{{{N}}}-. At those temperatures, however, all the rates turn out to be larger than the estimates in the current literature for the radiative electron attachment (REA) rates, thus indicating the greater importance of the present chemical path with respect to REA processes at those temperatures. The physical reasons for our findings are discussed in detail and linked with the existing observational findings.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khinkis, Mark J.; Kozlov, Aleksandr P.

A radiant, non-catalytic recuperative reformer has a flue gas flow path for conducting hot exhaust gas from a thermal process and a reforming mixture flow path for conducting a reforming mixture. At least a portion of the reforming mixture flow path is positioned adjacent to the flue gas flow path to permit heat transfer from the hot exhaust gas to the reforming mixture. The reforming mixture flow path contains substantially no material commonly used as a catalyst for reforming hydrocarbon fuel (e.g., nickel oxide, platinum group elements or rhenium), but instead the reforming mixture is reformed into a higher calorificmore » fuel via reactions due to the heat transfer and residence time. In a preferred embodiment, a portion of the reforming mixture flow path is positioned outside of flue gas flow path for a relatively large residence time.« less

Modeling the migration of fluids in subduction zones

NASA Astrophysics Data System (ADS)

Spiegelman, M.; Wilson, C. R.; van Keken, P. E.; Hacker, B. R.

2010-12-01

Fluids play a major role in the formation of arc volcanism and the generation of continental crust. Progressive dehydration reactions in the downgoing slab release fluids to the hot overlying mantle wedge, causing flux melting and the migration of melts to the volcanic front. While the qualitative concept is well established the quantitative details of fluid release and especially that of fluid migration and generation of hydrous melting in the wedge is still poorly understood. Here we present new models of the fluid migration through the mantle wedge for subduction zones that span the spectrum of arcs worldwide. We focus on the flow of water and use an existing set of high resolution thermal and metamorphic models (van Keken et al., JGR, in review) to predict the regions of water release from the sediments, upper and lower crust, and upper most mantle. We use this water flux as input for the fluid migration calculation based on new finite element models built on advanced computational libraries (FEniCS/PETSc) for efficient and flexible solution of coupled multi-physics problems. The first generation of these models solves for the evolution of porosity and fluid-pressure/flux throughout the slab and wedge given solid flow, viscosity and thermal fields from the existing thermal models. Fluid flow in the new models depends on both permeability and the rheology of the slab-wedge system as interaction with rheological variability can induce additional pressure gradients that affect the fluid flow pathways. We will explore the sensitivity of fluid flow paths for a range of subduction zones and fluid flow parameters with emphasis on variability of the location of the volcanic arc with respect to flow paths and expected degrees of hydrous melting which can be estimated given a variety of wet-melting parameterizations (e.g. Katz et al, 2003, Kelley et al, 2010). The current models just include dehydration reactions but work continues on the next generation of models which will include both dehydration and hydration reactions as well as parameterized flux melting in a consistent reactive-flow framework. We have also begun work on re-implementing the solid-flow thermal calculations in FEniCS/PETSc which are open-source libraries in preparation for developing a fully coupled fluid-solid dynamics models for exploring subduction zone processes

Ultrafast electron crystallography of the cooperative reaction path in vanadium dioxide

PubMed Central

Yang, Ding-Shyue; Baum, Peter; Zewail, Ahmed H.

2016-01-01

Time-resolved electron diffraction with atomic-scale spatial and temporal resolution was used to unravel the transformation pathway in the photoinduced structural phase transition of vanadium dioxide. Results from bulk crystals and single-crystalline thin-films reveal a common, stepwise mechanism: First, there is a femtosecond V−V bond dilation within 300 fs, second, an intracell adjustment in picoseconds and, third, a nanoscale shear motion within tens of picoseconds. Experiments at different ambient temperatures and pump laser fluences reveal a temperature-dependent excitation threshold required to trigger the transitional reaction path of the atomic motions. PMID:27376103

Laser cutting with chemical reaction assist

DOEpatents

Gettemy, Donald J.

1992-01-01

A method for cutting with a laser beam where an oxygen-hydrocarbon reaction is used to provide auxiliary energy to a metal workpiece to supplement the energy supplied by the laser. Oxygen is supplied to the laser focus point on the workpiece by a nozzle through which the laser beam also passes. A liquid hydrocarbon is supplied by coating the workpiece along the cutting path with the hydrocarbon prior to laser irradiation or by spraying a stream of hydrocarbon through a nozzle aimed at a point on the cutting path which is just ahead of the focus point during irradiation.

Laser cutting with chemical reaction assist

DOEpatents

Gettemy, D.J.

1992-11-17

A method is described for cutting with a laser beam where an oxygen-hydrocarbon reaction is used to provide auxiliary energy to a metal workpiece to supplement the energy supplied by the laser. Oxygen is supplied to the laser focus point on the workpiece by a nozzle through which the laser beam also passes. A liquid hydrocarbon is supplied by coating the workpiece along the cutting path with the hydrocarbon prior to laser irradiation or by spraying a stream of hydrocarbon through a nozzle aimed at a point on the cutting path which is just ahead of the focus point during irradiation. 1 figure.

Effect of Electronic Excitation on Hydrogen Atom Transfer (Tautomerization) Reactions for the DNA Base Adenine

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Salter, Latasha M.; Kwak, Dochan (Technical Monitor)

2002-01-01

Geometrical structures and energetic properties for four different tautomers of adenine are calculated in this study, using multi-configurational wave functions. Both the ground and the lowest single excited state potential energy surface are studied. The energetic order of the tautomers on the ground state potential surface is 9H less than 7H less than 3H less than 1H, while on the excited state surface this order is found to be different: 3H less than 1H less than 9H less than 7H. Minimum energy reaction paths are obtained for hydrogen atom transfer (9 yields 3 tautomerization) reactions in the ground and the lowest excited electronic state. It is found that the barrier heights and the shapes of the reaction paths are different for the ground and the excited electronic state, suggesting that the probability of such tautomerization reaction is higher on the excited state potential energy surface. The barrier for this reaction in the excited state may become very low in the presence of water or other polar solvent molecules, and therefore such tautomerization reaction may play an important role in the solution phase photochemistry of adenine.

Chemical evolution of groundwater in the Wilcox aquifer of the northern Gulf Coastal Plain, USA

NASA Astrophysics Data System (ADS)

Haile, Estifanos; Fryar, Alan E.

2017-12-01

The Wilcox aquifer is a major groundwater resource in the northern Gulf Coastal Plain (lower Mississippi Valley) of the USA, yet the processes controlling water chemistry in this clastic aquifer have received relatively little attention. The current study combines analyses of solutes and stable isotopes in groundwater, petrography of core samples, and geochemical modeling to identify plausible reactions along a regional flow path ˜300 km long. The hydrochemical facies evolves from Ca-HCO3 upgradient to Na-HCO3 downgradient, with a sequential zonation of terminal electron-accepting processes from Fe(III) reduction through SO4 2- reduction to methanogenesis. In particular, decreasing SO4 2- and increasing δ34S of SO4 2- along the flow path, as well as observations of authigenic pyrite in core samples, provide evidence of SO4 2- reduction. Values of δ13C in groundwater suggest that dissolved inorganic carbon is contributed both by oxidation of sedimentary organic matter and calcite dissolution. Inverse modeling identified multiple plausible sets of reactions between sampled wells, which typically involved cation exchange, pyrite precipitation, CH2O oxidation, and dissolution of amorphous Fe(OH)3, calcite, or siderite. These reactions are consistent with processes identified in previous studies of Atlantic Coastal Plain aquifers. Contrasts in groundwater chemistry between the Wilcox and the underlying McNairy and overlying Claiborne aquifers indicate that confining units are relatively effective in limiting cross-formational flow, but localized cross-formational mixing could occur via fault zones. Consequently, increased pumping in the vicinity of fault zones could facilitate upward movement of saline water into the Wilcox.

Geochemical evolution of groundwater in the Culebra dolomite near the Waste Isolation Pilot Plant, southeastern New Mexico, USA

USGS Publications Warehouse

Siegel, M.D.; Anderholm, S.

1994-01-01

The Culebra Dolomite Member of the Rustler Formation, a thin (10 m) fractured dolomite aquifer, lies approximately 450 m above the repository horizon of the Waste Isolation Pilot Plant (WIPP) in southeastern New Mexico, USA. Salinities of water in the Culebra range roughly from 10,000 to 200,000 mg/L within the WIPP site. A proposed model for the post-Pleistocene hydrochemical evolution of the Culebra tentatively identifies the major sources and sinks for many of the groundwater solutes. Reaction-path simulations with the PHRQPITZ code suggest that the Culebra dolomite is a partial chemical equilibrium system whose composition is controlled by an irreversible process (dissolution of evaporites) and equilibrium with gypsum and calcite. Net geochemical reactions along postulated modern flow paths, calculated with the NETPATH code, include dissolution of halite, carbonate and evaporite salts, and ion exchange. R-mode principal component analysis revealed correlations among the concentrations of Si, Mg, pH, Li, and B that are consistent with several clay-water reactions. The results of the geochemical calculations and mineralogical data are consistent with the following hydrochemical model: 1. (1) solutes are added to the Culebra by dissolution of evaporite minerals 2. (2) the solubilities of gypsum and calcite increase as the salinity increases; these minerals dissolve as chemical equilibrium is maintained between them and the groundwater 3. (3) equilibrium is not maintained between the waters and dolomite; sufficient Mg is added to the waters by dissolution of accessory carnallite or polyhalite such that the degree of dolomite supersaturation increases with ionic strength 4. (4) clays within the fractures and rock matrix exert some control on the distribution of Li, B, Mg, and Si via sorption, ion exchange, and dissolution. ?? 1994.

Chemical modeling constraints on Martian surface mineralogies formed in an early, warm, wet climate, and speculations on the occurrence of phosphate minerals in the Martian regolith

NASA Technical Reports Server (NTRS)

Plumlee, Geoffrey S.; Ridley, W. Ian; Debraal, Jeffrey D.

1992-01-01

This is one in a series of reports summarizing our chemical modeling studies of water-rock-gas interactions at the martian surface through time. The purpose of these studies is to place constraints on possible mineralogies formed at the martian surface and to model the geochemical implications of martian surficial processes proposed by previous researchers. Plumlee and Ridley summarize geochemical processes that may have occurred as a result of inferred volcano- and impact-driven hydrothermal activity on Mars. DeBraal et al. model the geochemical aspects of water-rock interactions and water evaporation near 0 C, as a prelude to future calculations that will model sub-0 C brine-rock-clathrate interactions under the current martian climate. In this report, we discuss reaction path calculations that model chemical processes that may have occurred at the martian surface in a postulated early, warm, wet climate. We assume a temperature of 25 C in all our calculations. Processes we model here include (1) the reaction of rainwater under various ambient CO2 and O2 pressures with basaltic rocks at the martian surface, (2) the formation of acid rain by volcanic gases such as HCl and SO2, (3) the reactions of acid rain with basaltic surficial materials, and (4) evaporation of waters resulting from rainwater-basalt interactions.

Astrophysical quests for neutron capture data of unstable nuclei

NASA Astrophysics Data System (ADS)

Käppeler, F.

2016-11-01

The abundances of the chemical elements heavier than iron can be attributed in about equal parts to the r and to the s process, which are taking place in supernova explosions and during the He and C burning phases of stellar evolution, respectively. So far, quantitative studies on the extremely short-lived neutron-rich nuclei constituting the ( n, γ) network of the r process are out of reach. On the contrary, the situation for the s -process is far advanced, as the reaction path of the s process from 12C to the Pb/Bi region is located within the valley of stability. Accordingly, a comprehensive database of experimental ( n, γ) cross sections has been established. While for many stable isotopes the necessary accuracy is still to be reached, reliable cross sections for the involved unstable isotopes are almost completely missing. Because of the intrinsic γ background of radioactive samples, successful time-of-flight measurements are depending on intense pulsed neutron sources. Such data are fundamental for our understanding of branchings in the s -process reaction path, which carry important model-independent information on neutron flux and temperature in the deep stellar interior.

Associations between heat exposure, vigilance, and balance performance in summer tree fruit harvesters.

PubMed

Spector, June T; Krenz, Jennifer; Calkins, Miriam; Ryan, Dawn; Carmona, Jose; Pan, Mengjie; Zemke, Anna; Sampson, Paul D

2018-02-01

We sought to evaluate potential mediators of the relationship between heat exposure and traumatic injuries in outdoor agricultural workers. Linear mixed models were used to estimate associations between maximum work-shift Wet Bulb Globe Temperature (WBGT max ) and post-shift vigilance (reaction time) and postural sway (total path length) in a cross-sectional sample of 46 Washington State tree fruit harvesters in August-September 2015. The mean (SD) WBGT max was 27.4 (3.2)°C in August and 21.2 (2.0)°C in September. The mean pre-work-shift participant urine specific gravity indicated minimal dehydration. Twenty-four percent of participants exhibited possible excessive sleepiness. There was no association between WBGT max and post-shift reaction time or total path length. Heat exposure was not associated with impaired vigilance or balance in this study, in which the overall mean (SD) WBGT max was 25.9 (4.2)°C. However, the study identified opportunities to ensure adequate pre-work-shift hydration and to optimize sleep and work-shift timing in order to reduce occupational injury and heat-related illness risk. Copyright © 2017 Elsevier Ltd. All rights reserved.

New experimental developments for s- and p-process research

NASA Astrophysics Data System (ADS)

Reifarth, R.; Ershova, O.; Glorius, J.; Göbel, K.; Langer, C.; Meusel, O.; Plag, R.; Schmidt, S.; Sonnabend, K.; Heil, M.

2012-12-01

Almost all of the heavy elements are produced via neutron-induced processes in a multitude of stellar production sites. The remaining minor part is produced via photon- and proton-induced reactions. The predictive power of the underlying stellar models is currently limited because they contain poorly constrained physics components such as convection, rotation or magnetic fields. An important tool to determine such components is the comparison of observed with modeled abundance distributions based on improved nuclear physics input. The FRANZ facility at the Goethe University Frankfurt, which is currently under construction will provide unprecedented neutron fluxes and proton currents available for nuclear astrophysics. It will be possible to investigate important branchpoint nuclei of the s-process nucleosynthesis path and proton-induced reactions important for p-process modeling. At the GSI close to Darmstadt radioactive isotopes can be investigated in inverse kinematics. This allows experiments such as proton-induced cross section measurements using a heavy-ion storage ring or measurements of gamma-induced reactions using the Coulomb dissociation method. The future FAIR facility will allow similar experiments on very exotic nuclei, since orders of magnitude higher radioactive ions beams will be possible.

Effects of Stochastic Traffic Flow Model on Expected System Performance

DTIC Science & Technology

2012-12-01

NSWC-PCD has made considerable improvements to their pedestrian flow modeling . In addition to the linear paths, the 2011 version now includes...using stochastic paths. 2.2 Linear Paths vs. Stochastic Paths 2.2.1 Linear Paths and Direct Maximum Pd Calculation Modeling pedestrian traffic flow...as a stochastic process begins with the linear path model . Let the detec- tion area be R x C voxels. This creates C 2 total linear paths, path(Cs

Planning Paths Through Singularities in the Center of Mass Space

NASA Technical Reports Server (NTRS)

Doggett, William R.; Messner, William C.; Juang, Jer-Nan

1998-01-01

The center of mass space is a convenient space for planning motions that minimize reaction forces at the robot's base or optimize the stability of a mechanism. A unique problem associated with path planning in the center of mass space is the potential existence of multiple center of mass images for a single Cartesian obstacle, since a single center of mass location can correspond to multiple robot joint configurations. The existence of multiple images results in a need to either maintain multiple center of mass obstacle maps or to update obstacle locations when the robot passes through a singularity, such as when it moves from an elbow-up to an elbow-down configuration. To illustrate the concepts presented in this paper, a path is planned for an example task requiring motion through multiple center of mass space maps. The object of the path planning algorithm is to locate the bang- bang acceleration profile that minimizes the robot's base reactions in the presence of a single Cartesian obstacle. To simplify the presentation, only non-redundant robots are considered and joint non-linearities are neglected.

Interaction of SO{sub x} and NO{sub x} with soot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chughtai, A.R.; Atteya, M.M.O.; Konowalchuk, B.K.

1996-12-31

As part of a continuing study of the heterogeneous reactions of black carbon with gas phase oxidant species, the adsorption of low concentrations (30 - 2000 ppm) of so, and NO{sub 2} individually, together, and in the presence of other adsorbates have been studied by spectroscopic and microgravimetric techniques. Previous work in this study has revealed a dual path mechanism for the reaction of NO{sub 2}/N{sub 2}O{sub 4} with n-hexane soot over concentration range 9 ppm - 200 torr. (This soot has been used throughout these investigations as a model for fossil fuel-produced black carbon). Interaction of SO{sub 2} andmore » carbon represent the most intensively studied of the heterogeneous systems containing carbon. An attempt to understand the molecular dynamics involved in the reactions of carbon in the presence of multiple reactants, such as SO{sub 2} and NO{sub 2}, underlies the present work.« less

Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

PubMed Central

Hummer, Gerhard

2015-01-01

We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green's function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions. PMID:26005592

Geochemistry of spring water, southeastern Uinta Basin, Utah and Colorado

USGS Publications Warehouse

Kimball, Briant A.

1981-01-01

The chemical quality of water in the southeastern Uinta Basin, Utah and Colorado, is important to the future development of the abundant oil-shale resources of the area. This report examines the observed changes in chemistry as water circulates in both shallow and deep ground-water systems. Mass-balance and mass- transfer calculations are used to define reactions that simulate the observed water chemistry in the mixed sandstone, siltstone, and carbonate lithology of the Green River Formation of Tertiary age.The mass-transfer calculations determine a reaction path particular to this system. The early dominance of calcite dissolution produces a calcium carbonate water. After calcite saturation, deeper circulation and further rock-water interaction cause the reprecipitation of calcite, the dissolution of dolomite and plagioclase, and the oxidation of pyrite; all combining to produce a calcium magnesium sodium bicarbonate sulfate water. The calculations suggest that silica concentrations are controlled by a kaolinite-Ca-montmorillonite phase boundary. Close agreement of mineral-saturation indices calculated by both an aqueous-equilibrium model and the mass-transfer model support the selection of reactions from the mass-transfer calculations.

Explorations into Chemical Reactions and Biochemical Pathways.

PubMed

Gasteiger, Johann

2016-12-01

A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Master Equation Analysis of Thermal and Nonthermal Microwave Effects.

PubMed

Ma, Jianyi

2016-10-11

Master equation is a successful model to describe the conventional heating reaction, it is expanded to capture the "microwave effect" in this work. The work equation of "microwave effect" included master equation presents the direct heating, indirect heating, and nonthermal effect about the microwave field. The modified master equation provides a clear physics picture to the nonthermal microwave effect: (1) The absorption and the emission of the microwave, which is dominated by the transition dipole moment between two corresponding states and the intensity of the microwave field, provides a new path to change the reaction rate constants. (2) In the strong microwave field, the distribution of internal states of the molecules will deviate from the equilibrium distribution, and the system temperature defined in the conventional heating reaction is no longer available. According to the general form of "microwave effect" included master equation, a two states model for unimolecular dissociation is proposed and is used to discuss the microwave nonthermal effect particularly. The average rate constants can be increased up to 2400 times for some given cases without the temperature changed in the two states model. Additionally, the simulation of a model system was executed using our State Specified Master Equation package. Three important conclusions can be obtained in present work: (1) A reasonable definition of the nonthermal microwave effect is given in the work equation of "microwave effect" included master equation. (2) Nonthermal microwave effect possibly exists theoretically. (3) The reaction rate constants perhaps can be changed obviously by the microwave field for the non-RRKM and the mode-specified reactions.

Path-oriented early reaction to approaching disruptions in ASDEX Upgrade and TCV in view of the future needs for ITER and DEMO

NASA Astrophysics Data System (ADS)

Maraschek, M.; Gude, A.; Igochine, V.; Zohm, H.; Alessi, E.; Bernert, M.; Cianfarani, C.; Coda, S.; Duval, B.; Esposito, B.; Fietz, S.; Fontana, M.; Galperti, C.; Giannone, L.; Goodman, T.; Granucci, G.; Marelli, L.; Novak, S.; Paccagnella, R.; Pautasso, G.; Piovesan, P.; Porte, L.; Potzel, S.; Rapson, C.; Reich, M.; Sauter, O.; Sheikh, U.; Sozzi, C.; Spizzo, G.; Stober, J.; Treutterer, W.; ZancaP; ASDEX Upgrade Team; TCV Team; the EUROfusion MST1 Team

2018-01-01

Routine reaction to approaching disruptions in tokamaks is currently largely limited to machine protection by mitigating an ongoing disruption, which remains a basic requirement for ITER and DEMO [1]. Nevertheless, a mitigated disruption still generates stress to the device. Additionally, in future fusion devices, high-performance discharge time itself will be very valuable. Instead of reacting only on generic features, occurring shortly before the disruption, the ultimate goal is to actively avoid approaching disruptions at an early stage, sustain the discharges whenever possible and restrict mitigated disruptions to major failures. Knowledge of the most relevant root causes and the corresponding chain of events leading to disruption, the disruption path, is a prerequisite. For each disruption path, physics-based sensors and adequate actuators must be defined and their limitations considered. Early reaction facilitates the efficiency of the actuators and enhances the probability of a full recovery. Thus, sensors that detect potential disruptions in time are to be identified. Once the entrance into a disruption path is detected, we propose a hierarchy of actions consisting of (I) recovery of the discharge to full performance or at least continuation with a less disruption-prone backup scenario, (II) complete avoidance of disruption to sustain the discharge or at least delay it for a controlled termination and, (III), only as last resort, a disruption mitigation. Based on the understanding of disruption paths, a hierarchical and path-specific handling strategy must be developed. Such schemes, testable in present devices, could serve as guidelines for ITER and DEMO operation. For some disruption paths, experiments have been performed at ASDEX Upgrade and TCV. Disruptions were provoked in TCV by impurity injection into ELMy H-mode discharges and in ASDEX Upgrade by forcing a density limit in H-mode discharges. The new approach proposed in this paper is discussed for these cases. For the H-mode density limit sensors used so far react too late. Thus a plasma-state boundary is proposed, that can serve as an adequate early sensor for avoiding density limit disruptions in H-modes and for recovery to full performance.

Organic functional group transformations in water at elevated temperature and pressure: Reversibility, reactivity, and mechanisms

NASA Astrophysics Data System (ADS)

Shipp, Jessie; Gould, Ian R.; Herckes, Pierre; Shock, Everett L.; Williams, Lynda B.; Hartnett, Hilairy E.

2013-03-01

Many transformation reactions involving hydrocarbons occur in the presence of H2O in hydrothermal systems and deep sedimentary systems. We investigate these reactions using laboratory-based organic chemistry experiments at high temperature and pressure (300 °C and 100 MPa). Organic functional group transformation reactions using model organic compounds based on cyclohexane with one or two methyl groups provided regio- and stereochemical markers that yield information about reversibility and reaction mechanisms. We found rapidly reversible interconversion between alkanes, alkenes, dienes, alcohols, ketones, and enones. The alkane-to-ketone reactions were not only completely reversible, but also exhibited such extensive reversibility that any of the functional groups along the reaction path (alcohol, ketone, and even the diene) could be used as the reactant and form all the other groups as products. There was also a propensity for these ring-based structures to dehydrogenate; presumably from the alkene, through a diene, to an aromatic ring. The product suites provide strong evidence that water behaved as a reactant and the various functional groups showed differing degrees of reactivity. Mechanistically-revealing products indicated reaction mechanisms that involve carbon-centered cation intermediates. This work therefore demonstrates that a wide range of organic compound types can be generated by abiotic reactions at hydrothermal conditions.

Electrophilic assistance to the cleavage of an RNA model phopshodiester via specific and general base-catalyzed mechanisms.

PubMed

Corona-Martínez, David Octavio; Gomez-Tagle, Paola; Yatsimirsky, Anatoly K

2012-10-19

Kinetics of transesterification of the RNA model substrate 2-hydroxypropyl 4-nitrophenyl phosphate promoted by Mg(2+) and Ca(2+), the most common biological metals acting as cofactors for nuclease enzymes and ribozymes, as well as by Co(NH(3))(6)(3+), Co(en)(3)(3+), Li(+), and Na(+) cations, often employed as mechanistic probes, was studied in 80% v/v (50 mol %) aqueous DMSO, a medium that allows one to discriminate easily specific base (OH(-)-catalyzed) and general base (buffer-catalyzed) reaction paths. All cations assist the specific base reaction, but only Mg(2+) and Na(+) assist the general base reaction. For Mg(2+)-assisted reactions, the solvent deuterium isotope effects are 1.23 and 0.25 for general base and specific base mechanisms, respectively. Rate constants for Mg(2+)-assisted general base reactions measured with different bases fit the Brønsted correlation with a slope of 0.38, significantly lower than the slope for the unassisted general base reaction (0.77). Transition state binding constants for catalysts in the specific base reaction (K(‡)(OH)) both in aqueous DMSO and pure water correlate with their binding constants to 4-nitrophenyl phosphate dianion (K(NPP)) used as a minimalist transition state model. It was found that K(‡)(OH) ≈ K(NPP) for "protic" catalysts (Co(NH(3))(6)(3+), Co(en)(3)(3+), guanidinium), but K(‡)(OH) ≫ K(NPP) for Mg(2+) and Ca(2+) acting as Lewis acids. It appears from results of this study that Mg(2+) is unique in its ability to assist efficiently the general base-catalyzed transesterification often occurring in active sites of nuclease enzymes and ribozymes.

Roles of Impulsivity, Motivation, and Emotion Regulation in Procrastination – Path Analysis and Comparison Between Students and Non-students

PubMed Central

Wypych, Marek; Matuszewski, Jacek; Dragan, Wojciech Ł.

2018-01-01

Procrastination – an irrational delay of intended actions despite expecting to be worse off – is a complex and non-homogenous phenomenon. Previous studies have found a number of correlates of procrastination, some of which seem to be particularly important. Impulsivity is closely connected to procrastination on behavioral, genetic, and neuronal levels. Difficulties in emotion regulation have also been shown to be strongly related to procrastination. Procrastination can also be considered as a motivation-based problem. To try to disentangle the connections of impulsivity, emotion regulation, and motivation to procrastination we collected data from over 600 subjects using multiple questionnaires (PPS – Pure Procrastination Scale; UPPSP – Impulsive Behavior Scale, ERQ – Emotion Regulation Questionnaire and MDT – Motivational Diagnostic Test). Structural equation modeling was performed to test several possible relationships between the measured variables. The effects of student status and age have also been investigated. The final path model was a directional model based on six explanatory variables and accounted for 70% of the variance in procrastination. Path analysis revealed that the strongest contributions to procrastination came from lack of value, delay discounting, and lack of perseverance, suggesting the involvement of motivation and impulsivity. The model also revealed the moderating role of expressive suppression between several aspects of impulsivity and procrastination. Close inspection of the paths’ weights suggests that there may be two partly competing strategies for dealing with impulsivity and negative emotions: either to suppress emotions and impulsive reactions or to react impulsively, discarding previous plans, and to procrastinate. Path invariance analysis showed the significant moderating roles of student status and age. Both in non-students and high-age groups, the path leading from suppression to procrastination was insignificant. This suggests that caution should be used in generalizing the results of studies carried out on students. These results support previous findings that procrastination may serve as a short-term mood regulation strategy. However, as the spectrum of the emotion regulation strategies included in the study was very limited, we conclude that future studies should seek more insight into the relationship between emotion regulation, self-control, and procrastination. PMID:29922205

Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations

NASA Astrophysics Data System (ADS)

Wong, Kin-Yiu

We have simulated two enzymatic reactions with molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) techniques. One reaction is the hydrolysis of the insecticide paraoxon catalyzed by phosphotriesterase (PTE). PTE is a bioremediation candidate for environments contaminated by toxic nerve gases (e.g., sarin) or pesticides. Based on the potential of mean force (PMF) and the structural changes of the active site during the catalysis, we propose a revised reaction mechanism for PTE. Another reaction is the hydrolysis of the second-messenger cyclic adenosine 3'-5'-monophosphate (cAMP) catalyzed by phosphodiesterase (PDE). Cyclicnucleotide PDE is a vital protein in signal-transduction pathways and thus a popular target for inhibition by drugs (e.g., ViagraRTM). A two-dimensional (2-D) free-energy profile has been generated showing that the catalysis by PDE proceeds in a two-step SN2-type mechanism. Furthermore, to characterize a chemical reaction mechanism in experiment, a direct probe is measuring kinetic isotope effects (KIEs). KIEs primarily arise from internuclear quantum-statistical effects, e.g., quantum tunneling and quantization of vibration. To systematically incorporate the quantum-statistical effects during MD simulations, we have developed an automated integration-free path-integral (AIF-PI) method based on Kleinert's variational perturbation theory for the centroid density of Feynman's path integral. Using this analytic method, we have performed ab initio pathintegral calculations to study the origin of KIEs on several series of proton-transfer reactions from carboxylic acids to aryl substituted alpha-methoxystyrenes in water. In addition, we also demonstrate that the AIF-PI method can be used to systematically compute the exact value of zero-point energy (beyond the harmonic approximation) by simply minimizing the centroid effective potential.

A DAG Scheduling Scheme on Heterogeneous Computing Systems Using Tuple-Based Chemical Reaction Optimization

PubMed Central

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems. PMID:25143977

A DAG scheduling scheme on heterogeneous computing systems using tuple-based chemical reaction optimization.

PubMed

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems.

Surfactants-aided syntheses of different sizes and triangular shape of gold nanoparticles using trisodium citrate in environmentally friendly and photoinduced methods.

PubMed

Su, Yen Hsun; Lai, Wei Hao; Chang, Shih-Hui; Hon, Min Hsiung

2007-09-01

We prepared gold nanoparticles (Au NPs) by only using trisodium citrate as the stabilizer. The detailed reaction mechanisms of S(N)1 and E1 reactions are examined and evidenced in this study by FTIR data. Citric acid is a kind of tertiary substrate. In aqueous solution, the substitution nucleophile path 1 (S(N)1) reaction and Elimination path 1 (E1) reaction usually occur simultaneously. Chloride ions, the substitution nucleophile, play a very important role to launch the mechanisms of S(N)1 and E1 reactions. Controlling the concentration of the chloride ions with the addition of HCl(aq) according to Le Chatelier theory, the average particle size of Au NPs (5.5 nm) was achieved to overcome the minimum limited size (approximately 10 nm). Two stages of the photoinduced method, aggregation into triangular conglomerates and growth into triangular particles, were determined form TEM observations. This preparation of Au NPs has potential in tuning the size, shape, and mechanism of Au NP formation by using only environmentally friendly trisodium citrate and the photoinduced method.

Non-catalytic recuperative reformer

DOEpatents

Khinkis, Mark J.; Kozlov, Aleksandr P.; Kurek, Harry

2015-12-22

A non-catalytic recuperative reformer has a flue gas flow path for conducting hot flue gas from a thermal process and a reforming mixture flow path for conducting a reforming mixture. At least a portion of the reforming mixture flow path is embedded in the flue gas flow path to permit heat transfer from the hot flue gas to the reforming mixture. The reforming mixture flow path contains substantially no material commonly used as a catalyst for reforming hydrocarbon fuel (e.g., nickel oxide, platinum group elements or rhenium), but instead the reforming mixture is reformed into a higher calorific fuel via reactions due to the heat transfer and residence time. In a preferred embodiment, extended surfaces of metal material such as stainless steel or metal alloy that are high in nickel content are included within at least a portion of the reforming mixture flow path.

Species differences in unlocking B-side electron transfer in bacterial reaction centers

DOE PAGES

Dylla, Nicholas P.; Faries, Kaitlyn M.; Wyllie, Ryan M.; ...

2016-06-21

The structure of the bacterial photosynthetic reaction center (RC) reveals symmetry-related electron transfer (ET) pathways, but only one path is used in native RCs. Analogous mutations have been made in two Rhodobacter (R.) species. A glutamic acid at position 133 in the M subunit increases transmembrane charge separation via the naturally inactive (B-side) path through impacts on primary ET in mutant R. sphaeroidesRCs. Prior work showed that the analogous substitution in the R. capsulatusRC also increases B-side activity, but mainly affects secondary ET. Finally, the overall yields of transmembrane ET are similar, but enabled in fundamentally different ways.

Species differences in unlocking B-side electron transfer in bacterial reaction centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dylla, Nicholas P.; Faries, Kaitlyn M.; Wyllie, Ryan M.

The structure of the bacterial photosynthetic reaction center (RC) reveals symmetry-related electron transfer (ET) pathways, but only one path is used in native RCs. Analogous mutations have been made in two Rhodobacter (R.) species. A glutamic acid at position 133 in the M subunit increases transmembrane charge separation via the naturally inactive (B-side) path through impacts on primary ET in mutant R. sphaeroidesRCs. Prior work showed that the analogous substitution in the R. capsulatusRC also increases B-side activity, but mainly affects secondary ET. Finally, the overall yields of transmembrane ET are similar, but enabled in fundamentally different ways.

Predictors of quality of life: A quantitative investigation of the stress-coping model in children with asthma

PubMed Central

Peeters, Yvette; Boersma, Sandra N; Koopman, Hendrik M

2008-01-01

Background Aim of this study is to further explore predictors of health related quality of life in children with asthma using factors derived from to the extended stress-coping model. While the stress-coping model has often been used as a frame of reference in studying health related quality of life in chronic illness, few have actually tested the model in children with asthma. Method In this survey study data were obtained by means of self-report questionnaires from seventy-eight children with asthma and their parents. Based on data derived from these questionnaires the constructs of the extended stress-coping model were assessed, using regression analysis and path analysis. Results The results of both regression analysis and path analysis reveal tentative support for the proposed relationships between predictors and health related quality of life in the stress-coping model. Moreover, as indicated in the stress-coping model, HRQoL is only directly predicted by coping. Both coping strategies 'emotional reaction' (significantly) and 'avoidance' are directly related to HRQoL. Conclusion In children with asthma, the extended stress-coping model appears to be a useful theoretical framework for understanding the impact of the illness on their quality of life. Consequently, the factors suggested by this model should be taken into account when designing optimal psychosocial-care interventions. PMID:18366753

Reactive trajectories of the Ru2+/3+ self-exchange reaction and the connection to Marcus' theory.

PubMed

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.

A model for lignin alteration - Part II: Numerical model of natural gas generation and application to the Piceance Basin, Western Colorado

USGS Publications Warehouse

Payne, D.F.; Ortoleva, P.J.

2001-01-01

The model presented here simulates a network of parallel and sequential reactions that describe the structural and chemical transformation of lignin-derived sedimentary organic matter (SOM) and the resulting generation of mobile species from shallow burial to approximately low-volatile bituminous rank. The model is calibrated to the Upper Cretaceous Williams Fork Formation coal of the Piceance Basin at the Multi-Well Experiment (MWX) Site, assuming this coal is largely derived from lignin. The model calculates the content of functional groups on the residual molecular species, C, H, and O elemental weight percents of the residual species, and moles of residual molecular species and mobile species (including components of natural gas) through time. The model is generally more sensitive to initial molecular structure of the lignin-derived molecule and the H2O content of the system than to initial temperature, as the former affect the fundamental reaction paths. The model is used to estimate that a total of 314 trillion cubic feet (tcf) of methane is generated by the Williams Fork coal over the basin history. ?? 2001 Elsevier Science Ltd. All rights reserved.

Children's Understanding of Psychogenic Bodily Reactions.

ERIC Educational Resources Information Center

Notaro, Paul C.; Gelman, Susan A.; Zimmerman, Marc A.

2001-01-01

Two studies compared how preschoolers through fifth graders and adults reasoned about psychogenic bodily reactions such as stress-induced headaches. Results supported a developmental path: younger children view psychogenic bodily responses as wholly physical, but with age, view them as both physical and psychological. (Author/KB)

Multiple-path model of spectral reflectance of a dyed fabric.

PubMed

Rogers, Geoffrey; Dalloz, Nicolas; Fournel, Thierry; Hebert, Mathieu

2017-05-01

Experimental results are presented of the spectral reflectance of a dyed fabric as analyzed by a multiple-path model of reflection. The multiple-path model provides simple analytic expressions for reflection and transmission of turbid media by applying the Beer-Lambert law to each path through the medium and summing over all paths, each path weighted by its probability. The path-length probability is determined by a random-walk analysis. The experimental results presented here show excellent agreement with predictions made by the model.

Explanation of the unusual temperature dependence of the atmospherically important OH + H(2)S --> H(2)O + HS reaction and prediction of the rate constant at combustion temperatures.

PubMed

Ellingson, Benjamin A; Truhlar, Donald G

2007-10-24

Rate constants for the OH + H2S --> H2O + HS reaction, which is important for both atmospheric chemistry and combustion, are calculated by direct dynamics with the M06-2X density functional using the MG3S basis set. Energetics are compared to high-level MCG3/3//MC-QCISD/3 wave function theory and to results obtained by other density functionals. We employ canonical variational transition-state theory with multidimensional tunneling contributions and scaled generalized normal-mode frequencies evaluated in redundant curvilinear coordinates with anharmonicity included in the torsion. The transition state has a quantum mechanically distinguishable, nonsuperimposable mirror image that corresponds to a separate classical reaction path; the effect of the multiple paths is examined through use of a symmetry number and by torsional methods. Calculations with the reference-potential Pitzer-Gwinn treatment of the torsional mode agree with experiment, within experimental scatter, and predict a striking temperature dependence of the activation energy, increasing from -0.1 kcal/mol at 200 K to 0.2, 1.0, 3.4, and 9.8 kcal/mol at 300, 500, 1000, and 2400 K. The unusual temperature dependence arises from a dynamical bottleneck at an energy below reactants, following an addition complex on the reaction path with a classical binding energy of 4.4 kcal/mol. As a way to check the mechanism, kinetic isotope effects of the OH + D2S and OD + D2S reactions have been predicted.

Understanding chemical binding using the Berlin function and the reaction force

NASA Astrophysics Data System (ADS)

Chakraborty, Debajit; Cárdenas, Carlos; Echegaray, Eleonora; Toro-Labbe, Alejandro; Ayers, Paul W.

2012-06-01

We use the derivative of the electron density with respect to the reaction coordinate, interpreted through the Berlin binding function, to identify portions of the reaction path where chemical bonds are breaking and forming. The results agree with the conventional description for SN2 reactions, but they are much more general and can be used to elucidate other types of reactions also. Our analysis offers support for, and detailed information about, the use of the reaction force profile to separate the reaction coordinates into intervals, each with characteristic extents of geometry change and electronic rearrangement.

Mixing and reactions in multiphase flow through porous media

NASA Astrophysics Data System (ADS)

Jimenez-Martinez, J.; Le Borgne, T.; Meheust, Y.; Porter, M. L.; De Anna, P.; Hyman, J.; Tabuteau, H.; Turuban, R.; Carey, J. W.; Viswanathan, H. S.

2016-12-01

The understanding and quantification of flow and transport processes in multiphase systems remains a grand scientific and engineering challenge in natural and industrial systems (e.g., soils and vadose zone, CO2 sequestration, unconventional oil and gas extraction, enhanced oil recovery). Beyond the kinetic of the chemical reactions, mixing processes in porous media play a key role in controlling both fluid-fluid and fluid-solid reactions. However, conventional continuum-scale models and theories oversimplify and/or ignore many important pore-scale processes. Multiphase flows, with the creation of highly heterogeneous fluid velocity fields (i.e., low velocities regions or stagnation zones, and high velocity regions or preferential paths), makes conservative and reactive transport more complex. We present recent multi-scale experimental developments and theoretical approaches to quantify transport, mixing, and reaction and their coupling with multiphase flows. We discuss our main findings: i) the sustained concentration gradients and enhanced reactivity in a two-phase system for a continuous injection, and the comparison with a pulse line injection; ii) the enhanced mixing by a third mobile-immiscible phase; and iii) the role that capillary forces play in the localization of the fluid-solid reactions. These experimental results are for highly-idealized geometries, however, the proposed models are related to basic porous media and unsaturated flow properties, and could be tested on more complex systems.

Cis-to- Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics.

PubMed

Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark

2018-04-10

Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of reaction rates and an improved understanding of activated states.

Revised users manual, Pulverized Coal Gasification or Combustion: 2-dimensional (87-PCGC-2): Final report, Volume 2. [87-PCGC-2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, P.J.; Smoot, L.D.; Brewster, B.S.

1987-12-01

A two-dimensional, steady-state model for describing a variety of reactive and non-reactive flows, including pulverized coal combustion and gasification, is presented. Recent code revisions and additions are described. The model, referred to as 87-PCGC-2, is applicable to cylindrical axi-symmetric systems. Turbulence is accounted for in both the fluid mechanics equations and the combustion scheme. Radiation from gases, walls, and particles is taken into account using either a flux method or discrete ordinates method. The particle phase is modeled in a Lagrangian framework, such that mean paths of particle groups are followed. Several multi-step coal devolatilization schemes are included along withmore » a heterogeneous reaction scheme that allows for both diffusion and chemical reaction. Major gas-phase reactions are modeled assuming local instantaneous equilibrium, and thus the reaction rates are limited by the turbulent rate mixing. A NO/sub x/ finite rate chemistry submodel is included which integrates chemical kinetics and the statistics of the turbulence. The gas phase is described by elliptic partial differential equations that are solved by an iterative line-by-line technique. Under-relaxation is used to achieve numerical stability. The generalized nature of the model allows for calculation of isothermal fluid mechanicsgaseous combustion, droplet combustion, particulate combustion and various mixtures of the above, including combustion of coal-water and coal-oil slurries. Both combustion and gasification environments are permissible. User information and theory are presented, along with sample problems. 106 refs.« less

A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction.

PubMed

Elsässer, Brigitta; Valiev, Marat; Weare, John H

2009-03-25

The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an A(N)+D(N) reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH(-) species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2' position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States

NASA Astrophysics Data System (ADS)

de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M.

2018-03-01

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

Total Solar Eclipse: “Through The Eyes of NASA,” Part 4

NASA Image and Video Library

2017-08-21

During the eclipse, 14 states across the U.S. were in the path of totality and experienced more than two minutes of darkness in the middle of the day – with a partial eclipse viewable all across North America. The broadcast – Eclipse Across America: Through the Eyes of NASA – covered locations along the path of totality, from Oregon to South Carolina including public reactions from all ages. The eclipse’s long path over land provided a unique opportunity to study the Sun, Earth, Moon and their interaction.

Total Solar Eclipse: “Through The Eyes of NASA,” Part 3

NASA Image and Video Library

2017-08-21

During the eclipse, 14 states across the U.S. were in the path of totality and experienced more than two minutes of darkness in the middle of the day – with a partial eclipse viewable all across North America. The broadcast – Eclipse Across America: Through the Eyes of NASA – covered locations along the path of totality, from Oregon to South Carolina including public reactions from all ages. The eclipse’s long path over land provided a unique opportunity to study the Sun, Earth, Moon and their interaction.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.

PubMed

de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M

2018-03-23

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers

PubMed Central

Weyland, Mathias S.; Fellermann, Harold; Hadorn, Maik; Sorek, Daniel; Lancet, Doron; Rasmussen, Steen; Füchslin, Rudolf M.

2013-01-01

We propose an automaton, a theoretical framework that demonstrates how to improve the yield of the synthesis of branched chemical polymer reactions. This is achieved by separating substeps of the path of synthesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of fixed successive compartments. We describe the automaton in mathematical terms and show how it can be configured automatically in order to synthesize a given branched polymer target. The algorithm we present finds an optimal path of synthesis in linear time. We discuss how the automaton models compartmentalized structures found in cells, such as the endoplasmic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers such as oligosaccharides. Lastly, we show examples of artificial branched polymers and discuss how the automaton can be configured to synthesize them with maximal yield. PMID:24489601

Comparison of Path Length and Ranges of Movement of the Center of Pressure and Reaction Time and Between Paired-Play and Solo-Play of a Virtual Reality Game.

PubMed

Portnoy, Sigal; Hersch, Ayelet; Sofer, Tal; Tresser, Sarit

2017-06-01

To test whether paired-play will induce longer path length and ranges of movement of the center of pressure (COP), which reflects on balance performance and stability, compared to solo-play and to test the difference in the path length and ranges of movement of the COP while playing the virtual reality (VR) game with the dominant hand compared to playing it with the nondominant hand. In this cross-sectional study 20 children (age 6.1 ± 0.7 years old) played an arm movement controlled VR game alone and with a peer while each of them stood on a pressure measuring pad to track the path length and ranges of movement of the COP. The total COP path was significantly higher during the paired-play (median 295.8 cm) compared to the COP path during the solo-play (median 189.2 cm). No significant differences were found in the reaction time and the mediolateral and anterior-posterior COP ranges between solo-play and paired-play. No significant differences were found between the parameters extracted during paired-play with the dominant or nondominant hand. Our findings imply that the paired-play is advantageous compared to solo-play since it induces a greater movement for the child, during which, higher COP velocities are reached that may contribute to improving the balance control of the child. Apart from the positive social benefits of paired-play, this positive effect on the COP path length is a noteworthy added value in the clinical setting when treating children with balance disorder.

Excitation of nucleobases from a computational perspective I: reaction paths.

PubMed

Giussani, Angelo; Segarra-Martí, Javier; Roca-Sanjuán, Daniel; Merchán, Manuela

2015-01-01

The main intrinsic photochemical events in nucleobases can be described on theoretical grounds within the realm of non-adiabatic computational photochemistry. From a static standpoint, the photochemical reaction path approach (PRPA), through the computation of the respective minimum energy path (MEP), can be regarded as the most suitable strategy in order to explore the electronically excited isolated nucleobases. Unfortunately, the PRPA does not appear widely in the studies reported in the last decade. The main ultrafast decay observed experimentally for the gas-phase excited nucleobases is related to the computed barrierless MEPs from the bright excited state connecting the initial Franck-Condon region and a conical intersection involving the ground state. At the highest level of theory currently available (CASPT2//CASPT2), the lowest excited (1)(ππ*) hypersurface for cytosine has a shallow minimum along the MEP deactivation pathway. In any case, the internal conversion processes in all the natural nucleobases are attained by means of interstate crossings, a self-protection mechanism that prevents the occurrence of photoinduced damage of nucleobases by ultraviolet radiation. Many alternative and secondary paths have been proposed in the literature, which ultimately provide a rich and constructive interplay between experimentally and theoretically oriented research.

Mechanisms and dynamics of protonation and lithiation of ferrocene.

PubMed

Sharma, Nishant; Ajay, Jayanth K; Venkatasubbaiah, Krishnan; Lourderaj, Upakarasamy

2015-09-14

By elucidating the mechanism of the simplest electrophilic substitution reaction of ferrocene, it was found that the verification of the protonation reaction has been a difficulty. In the work reported here, ab initio chemical dynamics simulations were performed at B3LYP/DZVP level of theory to understand the atomic level mechanisms of protonation and lithiation of ferrocene. Protonation of ferrocene resulted in the agostic and metal-protonated forms. Trajectory calculations revealed that protonation of ferrocene occurs by exo and endo mechanisms, with exo being the major path. H(+) was found to be mobile and hopped from the Cp ring to the metal center and vice versa after the initial attack on ferrocene, with the metal-complex having a shorter lifetime. These results remove the ambiguity surrounding the mechanism, as proposed in earlier experimental and computational studies. Lithiation of ferrocene resulted in the formation of cation-π and metal-lithiated complexes. Similar to protonation, trajectory results revealed that both exo and endo paths were followed, with the exo path being the major one. In addition, lithiated-ferrocene exhibited planetary motion. The major path (exo) followed in the protonation and lithiation of ferrocene is consistent with the observations in earlier experimental studies for other hard electrophiles.

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

PubMed Central

Trnka, Tomáš; Kozmon, Stanislav; Tvaroška, Igor; Koča, Jaroslav

2015-01-01

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals. PMID:25849117

Stepwise catalytic mechanism via short-lived intermediate inferred from combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2.

PubMed

Trnka, Tomáš; Kozmon, Stanislav; Tvaroška, Igor; Koča, Jaroslav

2015-04-01

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals.

Electrode assembly for use in a solid polymer electrolyte fuel cell

DOEpatents

Raistrick, Ian D.

1989-01-01

A gas reaction fuel cell may be provided with a solid polymer electrolyte membrane. Porous gas diffusion electrodes are formed of carbon particles supporting a catalyst which is effective to enhance the gas reactions. The carbon particles define interstitial spaces exposing the catalyst on a large surface area of the carbon particles. A proton conducting material, such as a perfluorocarbon copolymer or ruthenium dioxide contacts the surface areas of the carbon particles adjacent the interstitial spaces. The proton conducting material enables protons produced by the gas reactions adjacent the supported catalyst to have a conductive path with the electrolyte membrane. The carbon particles provide a conductive path for electrons. A suitable electrode may be formed by dispersing a solution containing a proton conducting material over the surface of the electrode in a manner effective to coat carbon surfaces adjacent the interstitial spaces without impeding gas flow into the interstitial spaces.

(99)Tc(VII) Retardation, Reduction, and Redox Rate Scaling in Naturally Reduced Sediments.

PubMed

Liu, Yuanyuan; Liu, Chongxuan; Kukkadapu, Ravi K; McKinley, James P; Zachara, John; Plymale, Andrew E; Miller, Micah D; Varga, Tamas; Resch, Charles T

2015-11-17

An experimental and modeling study was conducted to investigate pertechnetate (Tc(VII)O4(-)) retardation, reduction, and rate scaling in three sediments from Ringold formation at U.S. Department of Energy's Hanford site, where (99)Tc is a major contaminant in groundwater. Tc(VII) was reduced in all the sediments in both batch reactors and diffusion columns, with a faster rate in a sediment containing a higher concentration of HCl-extractable Fe(II). Tc(VII) migration in the diffusion columns was reductively retarded with retardation degrees correlated with Tc(VII) reduction rates. The reduction rates were faster in the diffusion columns than those in the batch reactors, apparently influenced by the spatial distribution of redox-reactive minerals along transport paths that supplied Tc(VII). X-ray computed tomography and autoradiography were performed to identify the spatial locations of Tc(VII) reduction and transport paths in the sediments, and results generally confirmed the newly found behavior of reaction rate changes from batch to column. The results from this study implied that Tc(VII) migration can be reductively retarded at Hanford site with a retardation degree dependent on reactive Fe(II) content and its distribution in sediments. This study also demonstrated that an effective reaction rate may be faster in transport systems than that in well-mixed reactors.

Redox reaction rates in shallow aquifers: Implications for nitrate transport in groundwater and streams

USGS Publications Warehouse

Tesoriero, Anthony J.

2012-01-01

Groundwater age and water chemistry data along flow paths from recharge areas to streams were used to evaluate the trends and transformations of agricultural chemicals. Results from this analysis indicate that median nitrate recharge concentrations in these agricultural areas have increased markedly over the last 50 years from 4 mg N/L in samples collected prior to 1983 to 7.5 mg N/L in samples collected since 1983. The effect that nitrate accumulation in shallow aquifers will have on drinking water quality and stream ecosystems is dependent on the rate of redox reactions along flow paths and on the age distribution of nitrate discharging to supply wells and streams.

Catalytic hydrodeoxygenation of methyl-substituted phenols: correlations of kinetic parameters with molecular properties.

PubMed

Massoth, F E; Politzer, P; Concha, M C; Murray, J S; Jakowski, J; Simons, Jack

2006-07-27

The hydrodeoxygenation of methyl-substituted phenols was carried out in a flow microreactor at 300 degrees C and 2.85 MPa hydrogen pressure over a sulfided CoMo/Al(2)O(3) catalyst. The primary reaction products were methyl-substituted benzene, cyclohexene, cyclohexane, and H(2)O. Analysis of the results suggests that two independent reaction paths are operative, one leading to aromatics and the other to partially or completely hydrogenated cyclohexanes. The reaction data were analyzed using Langmuir-Hinshelwood kinetics to extract the values of the reactant-to-catalyst adsorption constant and of the rate constants characterizing the two reaction paths. The adsorption constant was found to be the same for both reactions, suggesting that a single catalytic site center is operative in both reactions. Ab initio electronic structure calculations were used to evaluate the electrostatic potentials and valence orbital ionization potentials for all of the substituted phenol reactants. Correlations were observed between (a) the adsorption constant and the two reaction rate constants measured for various methyl-substitutions and (b) certain moments of the electrostatic potentials and certain orbitals' ionization potentials of the isolated phenol molecules. On the basis of these correlations to intrinsic reactant-molecule properties, a reaction mechanism is proposed for each pathway, and it is suggested that the dependencies of adsorption and reaction rates upon methyl-group substitution are a result of the substituents' effects on the electrostatic potential and orbitals rather than geometric (steric) effects.

Tetramer model of leukoemeraldine-emeraldine electrochemistry in the presence of trihalogenoacetic acids. DFT approach.

PubMed

Barbosa, Nuno Almeida; Grzeszczuk, Maria; Wieczorek, Robert

2015-01-15

First results of the application of the DFT computational approach to the reversible electrochemistry of polyaniline are presented. A tetrameric chain was used as the simplest model of the polyaniline polymer species. The system under theoretical investigation involved six tetramer species, two electrons, and two protons, taking part in 14 elementary reactions. Moreover, the tetramer species were interacting with two trihalogenoacetic acid molecules. Trifluoroacetic, trichloroacetic, and tribromoacetic acids were found to impact the redox transformation of polyaniline as shown by cyclic voltammetry. The theoretical approach was considered as a powerful tool for investigating the main factors of importance for the experimental behavior. The DFT method provided molecular structures, interaction energies, and equilibrium energies of all of the tetramer-acid complexes. Differences between the energies of the isolated tetramer species and their complexes with acids are discussed in terms of the elementary reactions, that is, ionization potentials and electron affinities, equilibrium constants, electrode potentials, and reorganization energies. The DFT results indicate a high impact of the acid on the reorganization energy of a particular elementary electron-transfer reaction. The ECEC oxidation path was predicted by the calculations. The model of the reacting system must be extended to octamer species and/or dimeric oligomer species to better approximate the real polymer situation.

Bifurcations on Potential Energy Surfaces of Organic Reactions

PubMed Central

Ess, Daniel H.; Wheeler, Steven E.; Iafe, Robert G.; Xu, Lai; Çelebi-Ölçüm, Nihan; Houk, K. N.

2009-01-01

A single transition state may lead to multiple intermediates or products if there is a post-transition state reaction path bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects control selectivity rather than transition state energetics. This minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions. PMID:18767086

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.

Production of Solar-Grade Silicon by the SiF4 and Mg Reaction

NASA Astrophysics Data System (ADS)

Xie, Xiaobing; Bao, Jianer; Sanjurjo, Angel

2016-12-01

Over 90 pct of the solar cells currently produced and installed are Si based, and this industrial dominance is expected to persist for the foreseeable future. The crystalline Si substrate accounts for a significant portion of the total cost of solar cells. In order to further reduce the cost of solar panels, there has been significant effort in producing inexpensive solar-grade Si, mainly through three paths: (1) modification of the Siemens process to lower production costs, (2) upgrading metallurgical-grade Si to reach solar-grade purity, and (3) by means of new metallurgical processes such as the reduction of a silicon halide, e.g., SiF4 or SiCl4, by a reactive metal such as Na or Zn. In this paper, we describe an alternative path that uses Mg to react with SiF4 to produce low-cost solar grade Si. Experimental conditions for complete reaction and separation of the products, Si and MgF2, as well as aspects of the reaction mechanism are described. The reaction involves both a heterogeneous liquid-gas phase reaction and a homogeneous gas-gas phase reaction. When pure Mg was used, the Si product obtained had sub-ppm levels of B and P impurities and is expected to be suitable for solar cell applications.

Hyporheic zone denitrification: controls on effective reaction depth and contribution to whole-stream mass balance

USGS Publications Warehouse

Harvey, Judson W.; Böhlke, John Karl; Voytek, Mary A.; Scott, Durelle; Tobias, Craig R.

2013-01-01

Stream denitrification is thought to be enhanced by hyporheic transport but there is little direct evidence from the field. To demonstrate at a field site, we injected 15NO3−, Br (conservative tracer), and SF6 (gas exchange tracer) and compared measured whole-stream denitrification with in situ hyporheic denitrification in shallow and deeper flow paths of contrasting geomorphic units. Hyporheic denitrification accounted for between 1 and 200% of whole-stream denitrification. The reaction rate constant was positively related to hyporheic exchange rate (greater substrate delivery), concentrations of substrates DOC and nitrate, microbial denitrifier abundance (nirS), and measures of granular surface area and presence of anoxic microzones. The dimensionless product of the reaction rate constant and hyporheic residence time, λhzτhz define a Damköhler number, Daden-hz that was optimal in the subset of hyporheic flow paths where Daden-hz ≈ 1. Optimal conditions exclude inefficient deep pathways transport where substrates are used up and also exclude inefficient shallow pathways that require repeated hyporheic entries and exits to complete the reaction. The whole-stream reaction significance, Rs (dimensionless), was quantified by multiplying Daden-hz by the proportion of stream discharge passing through the hyporheic zone. Together these two dimensionless metrics, one flow-path scale and the other reach-scale, quantify the whole-stream significance of hyporheic denitrification. One consequence is that the effective zone of significant denitrification often differs from the full depth of the hyporheic zone, which is one reason why whole-stream denitrification rates have not previously been explained based on total hyporheic-zone metrics such as hyporheic-zone size or residence time.

The relationship between social support and posttraumatic stress symptoms among youth exposed to a natural disaster.

PubMed

Lai, Betty S; Osborne, Melissa C; Piscitello, Jennifer; Self-Brown, Shannon; Kelley, Mary Lou

2018-01-01

Background : Children are a vulnerable population following a natural disaster, due to their age and dependence on adults. The primary presenting problem children report after disasters is posttraumatic stress symptoms (PTSS). Prior research suggests that PTSS is inversely related to social support, which is often disrupted after a disaster. Objective : This study examined the relationship between social support (from parents, teachers, and peers) and PTSS in children affected by Hurricane Katrina. The research contributes to the literature by examining the mechanisms that drive this relationship over time. Methods : In this study, 426 children were followed over four timepoints, beginning 3-7 months after Hurricane Katrina and concluding 25-27 months post-hurricane. Three path models analysed the relationship between social support (from parents, teachers, and peers, measured by the Social Support Scale for Children) and PTSS (measured by the UCLA PTSD Reaction Index). Covariates included child age, minority status, gender, perceived life threat, and actual life threat. Nonsignificant paths were trimmed from the final models. Global fit indices were examined to determine model fit. Results : In the parent and peer social support models, PTSS exhibited statistically significant effects on social support from one wave to the next. In the teacher model, this was only true between Waves 2 and 3. Social support showed a statistically significant effect on PTSS between Wave 2 and Wave 3 in the peer model (standardized estimate = -0.26, p  < .0001). No paths from social support to PTSS were significant in the parent and teacher models. Conclusion : Findings support a social selection model in which PTSS undermine social support, particularly in the first two years post-disaster. If these findings are replicated, this suggests that, in cases of limited funding, PTSS should be prioritized, given their cascading effects on social support.

A new, double-inversion mechanism of the F- + CH3Cl SN2 reaction in aqueous solution.

PubMed

Liu, Peng; Wang, Dunyou; Xu, Yulong

2016-11-23

Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F - + CH 3 Cl S N 2 reaction in the gas phase [Nat. Commun., 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution. However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent. More importantly, the relationship between the two double-inversion transition states is not clear in the gas phase, but, here we revealed a novel intermediate complex serving as a "connecting link" between the two transition states of the abstraction-induced inversion and the Walden-inversion mechanisms. A detailed reaction path was constructed to show the atomic-level evolution of this novel double reaction mechanism in aqueous solution. The potentials of mean force were calculated and the obtained Walden-inversion barrier height agrees well with the available experimental value.

Constraining Path-Dependent Processes During Basalt-CO2 Interactions with Observations From Flow-Through and Batch Experiments

NASA Astrophysics Data System (ADS)

Thomas, D.; Garing, C.; Zahasky, C.; Harrison, A. L.; Bird, D. K.; Benson, S. M.; Oelkers, E. H.; Maher, K.

2017-12-01

Predicting the timing and magnitude of CO2 storage in basaltic rocks relies partly on quantifying the dependence of reactivity on flow path and mineral distribution. Flow-through experiments that use intact cores are advantageous because the spatial heterogeneity of pore space and reactive phases is preserved. Combining aqueous geochemical analyses and petrologic characterization with non-destructive imaging techniques (e.g. micro-computed tomography) constrains the relationship between irreversible reactions, pore connectivity and accessible surface area. Our work enhances these capabilities by dynamically imaging flow through vesicular basalts with Positron Emission Tomography (PET) scanning. PET highlights the path a fluid takes by detecting photons produced during radioactive decay of an injected radiotracer (FDG). We have performed single-phase, CO2-saturated flow-through experiments with basaltic core from Iceland at CO2 sequestration conditions (50 °C; 76-90 bar Ptot). Constant flow rate and continuous pressure measurements at the inlet and outlet of the core constrain permeability. We monitor geochemical evolution through cation and anion analysis of outlet fluid sampled periodically. Before and after reaction, we perform PET scans and characterize the core using micro-CT. The PET scans indicate a discrete, localized flow path that appears to be a micro-crack connecting vesicles, suggesting that vesicle-lining minerals are immediately accessible and important reactants. Rapid increases in aqueous cation concentration, pH and HCO3- indicate that the rock reacts nearly immediately after CO2 injection. After 24 hours the solute release decreases, which may reflect a transition to reaction with phases with slower kinetic dissolution rates (e.g. zeolites and glasses to feldspar), a decrease in available reactive surface area or precipitation. We have performed batch experiments using crushed material of the same rock to elucidate the effect of flow path geometry and mineral accessibility on geochemical evolution. Interestingly, surface area-normalized dissolution rates as evinced by SiO2 release in all experiments approach similar values ( 10-15 mol/cm2/s). Our experiments show how imaging techniques are helpful in interpreting path-dependent processes in open systems.

Theoretical Study of the Mechanism of Oxoiron(IV) Formation from H2O2 and a Nonheme Iron(II) Complex: O–O Cleavage Involving Proton-Coupled Electron Transfer

PubMed Central

Hirao, Hajime; Li, Feifei; Que, Lawrence; Morokuma, Keiji

2011-01-01

It has recently been shown that the nonheme oxoiron(IV) species supported by the 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane ligand (TMC) can be generated in near-quantitative yield by reacting [FeII(TMC)(OTf)2] with a stoichiometric amount of H2O2 in CH3CN in the presence of 2,6-lutidine (Li, F.; England, J.; Que L., Jr. J. Am. Chem. Soc. 2010, 132, 2134–2135). This finding has major implications for O–O bond cleavage events in both Fenton chemistry and nonheme iron enzymes. To understand the mechanism of this process, especially the intimate details of the O–O bond cleavage step, a series of density functional theory (DFT) calculations and analyses have been carried out. Two distinct reaction paths (A and B) were identified. Path A consists of two principal steps: (1) coordination of H2O2 to Fe(II) and (2) a combination of partial homolytic O–O bond cleavage and proton-coupled electron transfer (PCET). The latter combination renders the rate-limiting O–O cleavage effectively a heterolytic process. Path B proceeds via a simultaneous homolytic O–O bond cleavage of H2O2 and Fe–O bond formation. This is followed by H-abstraction from the resultant Fe(III)–OH species by an •OH radical. Calculations suggest that path B is plausible in the absence of base. However, once 2,6-lutidine is added to the reacting system, the reaction barrier is lowered and more importantly the mechanistic path switches to path A, where 2,6-lutidine plays an essential role as an acid-base catalyst in a manner similar to how the distal histidine or glutamate residue assists in Compound I formation in heme peroxidases. The reaction was found to proceed predominantly on the quintet spin state surface, and a transition to the triplet state, the experimentally known ground state for the TMC-oxoiron(IV) species, occurs in the last stage of the oxoiron(IV) formation process. PMID:21678930

Inverse geochemical modeling of groundwater evolution with emphasis on arsenic in the Mississippi River Valley alluvial aquifer, Arkansas (USA)

USGS Publications Warehouse

Sharif, M.U.; Davis, R.K.; Steele, K.F.; Kim, B.; Kresse, T.M.; Fazio, J.A.

2008-01-01

Inverse geochemical modeling (PHREEQC) was used to identify the evolution of groundwater with emphasis on arsenic (As) release under reducing conditions in the shallow (25-30 m) Mississippi River Valley Alluvial aquifer, Arkansas, USA. The modeling was based on flow paths defined by high-precision (??2 cm) water level contour map; X-ray diffraction (XRD), scanning electron microscopic (SEM), and chemical analysis of boring-sediments for minerals; and detailed chemical analysis of groundwater along the flow paths. Potential phases were constrained using general trends in chemical analyses data of groundwater and sediments, and saturation indices data (MINTEQA2) of minerals in groundwater. Modeling results show that calcite, halite, fluorite, Fe oxyhydroxide, organic matter, H2S (gas) were dissolving with mole transfers of 1.40E - 03, 2.13E - 04, 4.15E - 06, 1.25E + 01, 3.11, and 9.34, respectively along the dominant flow line. Along the same flow line, FeS, siderite, and vivianite were precipitating with mole transfers of 9.34, 3.11, and 2.64E - 07, respectively. Cation exchange reactions of Ca2+ (4.93E - 04 mol) for Na+ (2.51E - 04 mol) on exchange sites occurred along the dominant flow line. Gypsum dissolution reactions were dominant over calcite dissolution in some of the flow lines due to the common ion effect. The concentration of As in groundwater ranged from <0.5 to 77 ??g/L. Twenty percent total As was complexed with Fe and Mn oxyhydroxides. The redox environment, chemical data of sediments and groundwater, and the results of inverse geochemical modeling indicate that reductive dissolution of Fe oxyhydroxide is the dominant process of As release in the groundwater. The relative rate of reduction of Fe oxyhydroxide over SO42 - with co-precipitation of As into sulfide is the limiting factor controlling dissolved As in groundwater. ?? 2007 Elsevier B.V. All rights reserved.

Demonstration of Synaptic Behaviors and Resistive Switching Characterizations by Proton Exchange Reactions in Silicon Oxide

PubMed Central

Chang, Yao-Feng; Fowler, Burt; Chen, Ying-Chen; Zhou, Fei; Pan, Chih-Hung; Chang, Ting-Chang; Lee, Jack C.

2016-01-01

We realize a device with biological synaptic behaviors by integrating silicon oxide (SiOx) resistive switching memory with Si diodes. Minimal synaptic power consumption due to sneak-path current is achieved and the capability for spike-induced synaptic behaviors is demonstrated, representing critical milestones for the use of SiO2–based materials in future neuromorphic computing applications. Biological synaptic behaviors such as long-term potentiation (LTP), long-term depression (LTD) and spike-timing dependent plasticity (STDP) are demonstrated systematically using a comprehensive analysis of spike-induced waveforms, and represent interesting potential applications for SiOx-based resistive switching materials. The resistive switching SET transition is modeled as hydrogen (proton) release from (SiH)2 to generate the hydrogen bridge defect, and the RESET transition is modeled as an electrochemical reaction (proton capture) that re-forms (SiH)2. The experimental results suggest a simple, robust approach to realize programmable neuromorphic chips compatible with large-scale CMOS manufacturing technology. PMID:26880381

Demonstration of Synaptic Behaviors and Resistive Switching Characterizations by Proton Exchange Reactions in Silicon Oxide

NASA Astrophysics Data System (ADS)

Chang, Yao-Feng; Fowler, Burt; Chen, Ying-Chen; Zhou, Fei; Pan, Chih-Hung; Chang, Ting-Chang; Lee, Jack C.

2016-02-01

We realize a device with biological synaptic behaviors by integrating silicon oxide (SiOx) resistive switching memory with Si diodes. Minimal synaptic power consumption due to sneak-path current is achieved and the capability for spike-induced synaptic behaviors is demonstrated, representing critical milestones for the use of SiO2-based materials in future neuromorphic computing applications. Biological synaptic behaviors such as long-term potentiation (LTP), long-term depression (LTD) and spike-timing dependent plasticity (STDP) are demonstrated systematically using a comprehensive analysis of spike-induced waveforms, and represent interesting potential applications for SiOx-based resistive switching materials. The resistive switching SET transition is modeled as hydrogen (proton) release from (SiH)2 to generate the hydrogen bridge defect, and the RESET transition is modeled as an electrochemical reaction (proton capture) that re-forms (SiH)2. The experimental results suggest a simple, robust approach to realize programmable neuromorphic chips compatible with large-scale CMOS manufacturing technology.

Estimating 14C groundwater ages in a methanogenic aquifer

USGS Publications Warehouse

Aravena, Ramon; Wassenaar, Leonard I; Plummer, Niel

1995-01-01

This paper addresses the problem of 14C age dating of groundwaters in a confined regional aquifer affected by methanogenesis. Increasing CH4 concentrations along the groundwater flow system and 13C and 14C isotopic data for dissolved inorganic carbon, dissolved organic carbon, and CH4 clearly show the effect of methanogenesis on groundwater chemistry. Inverse reaction path modeling using NETPATH indicates the predominant geochemical reactions controlling the chemical evolution of groundwater in the aquifer are incongruent dissolution of dolomite, ion exchange, methanogenesis, and oxidation of sedimentary organic matter. Modeling of groundwater 14C ages using NETPATH indicates that a significant part of groundwater in the Alliston aquifer is less than 13,000 years old; however, older groundwater in the range of 15,000–23,000 years is also present in the aquifer. This paper demonstrates that 14C ages calculated using NETPATH, incorporating the effects of methanogenesis on the carbon pools, provide reasonable groundwater ages that were not possible by other isotopic methods.

Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis

NASA Astrophysics Data System (ADS)

Wang, Ting; Plecháč, Petr

2017-12-01

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

New portal to the 15O(α ,γ )19Ne resonance triggering CNO-cycle breakout

NASA Astrophysics Data System (ADS)

Wrede, C.; Glassman, B. E.; Pérez-Loureiro, D.; Allen, J. M.; Bardayan, D. W.; Bennett, M. B.; Brown, B. A.; Chipps, K. A.; Febbraro, M.; Fry, C.; Hall, M. R.; Hall, O.; Liddick, S. N.; O'Malley, P.; Ong, W.-J.; Pain, S. D.; Schwartz, S. B.; Shidling, P.; Sims, H.; Thompson, P.; Zhang, H.

2017-09-01

The 15O(α ,γ )19Ne reaction is expected to trigger the initial path for breakout from the CNO hydrogen-burning cycles to the rapid proton capture (r p ) process in type I x-ray bursts on accreting neutron stars. The thermonuclear reaction rate has a major impact on models of type I x-ray burst observables and it depends on the small α -particle branching ratio, Γα/Γ , of the 4.03 MeV state in 19Ne. Attempts to measure Γα/Γ by populating the 4.03 MeV state using nuclear reactions have only led to strong upper limits. In the present work, we report the first experimental evidence that the 4.03 MeV 19Ne state is populated in 20Mg β -delayed proton emission. This new channel has the potential to provide the necessary sensitivity to detect a finite value of Γα/Γ .

The activation of phosphoramide mustard anticancer drugs from ab initio simulations.

NASA Astrophysics Data System (ADS)

Allesch, Markus; Schwegler, Eric; Colvin, Mike; Gygi, Francois; Galli, Giulia

2007-03-01

The nitrogen mustard based DNA alkylating agents were the first nonhormonal drugs to be used effectively in the treatment of cancer and remain one of the most important drugs for the chemotherapeutic management of many common malignancies today. An understanding of the activation of these compounds is, in itself, of scientific interest, but also critical in designing improved analogs of greater selectivity and efficacy. We have investigated the activation pathways of one of the most active metabolites, phosphoramide mustard (PM), and its methylated ester (PMME). In particular, we have examined the activation barrier and reaction free energy for the intramolecular cyclization reaction using first principles molecular dynamics simulations with explicit and continuum solvation models. Structural, dynamical and electronic properties along the reaction path have been computed mainly to address the question why de-esterification is required to activate these drugs. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48.

The dissociative chemisorption of methane on Ni(100) and Ni(111): Classical and quantum studies based on the reaction path Hamiltonian

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mastromatteo, Michael; Jackson, Bret, E-mail: jackson@chem.umass.edu

Electronic structure methods based on density functional theory are used to construct a reaction path Hamiltonian for CH{sub 4} dissociation on the Ni(100) and Ni(111) surfaces. Both quantum and quasi-classical trajectory approaches are used to compute dissociative sticking probabilities, including all molecular degrees of freedom and the effects of lattice motion. Both approaches show a large enhancement in sticking when the incident molecule is vibrationally excited, and both can reproduce the mode specificity observed in experiments. However, the quasi-classical calculations significantly overestimate the ground state dissociative sticking at all energies, and the magnitude of the enhancement in sticking with vibrationalmore » excitation is much smaller than that computed using the quantum approach or observed in the experiments. The origin of this behavior is an unphysical flow of zero point energy from the nine normal vibrational modes into the reaction coordinate, giving large values for reaction at energies below the activation energy. Perturbative assumptions made in the quantum studies are shown to be accurate at all energies studied.« less

N-nitrosodimethylamine (NDMA) as a product of potassium permanganate reaction with aqueous solutions of dimethylamine (DMA).

PubMed

Andrzejewski, Przemysław; Nawrocki, Jacek

2009-03-01

The reactivity of permanganate with dimethylamine, as possible path of NDMA formation, has been investigated. The results have shown that potassium permanganate reaction with aqueous solutions of dimethylamine (DMA) leads to the formation of N-nitrosodimethylamine (NDMA). The contact time, the molar ratio of permanganate and DMA, pH and presence of nitrite are the key factors influencing the efficiency of NDMA formation. Significant conversion rates of DMA to NDMA were observed only for the high doses of permanganate, which were many times higher than those typically used in water treatment. This reaction however is of importance for water treatment technology, since it shows the possibility of NDMA formation as a result of oxidation of DMA. It is likely that nitrosation is the main path of the reaction. An important role of MnO2 suspension, formed as a result of permanganate reduction in NDMA formation is emphasized. Significant influence of MnO2 suspension on NDMA formation should draw our attention to the potential impact of MnO2 activated filtration beds on NDMA formation.

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

NASA Astrophysics Data System (ADS)

Vanden-Eijnden, Eric; Venturoli, Maddalena

2009-05-01

An improved and simplified version of the finite temperature string (FTS) method [W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005)] is proposed. Like the original approach, the new method is a scheme to calculate the principal curves associated with the Boltzmann-Gibbs probability distribution of the system, i.e., the curves which are such that their intersection with the hyperplanes perpendicular to themselves coincides with the expected position of the system in these planes (where perpendicular is understood with respect to the appropriate metric). Unlike more standard paths such as the minimum energy path or the minimum free energy path, the location of the principal curve depends on global features of the energy or the free energy landscapes and thereby may remain appropriate in situations where the landscape is rough on the thermal energy scale and/or entropic effects related to the width of the reaction channels matter. Instead of using constrained sampling in hyperplanes as in the original FTS, the new method calculates the principal curve via sampling in the Voronoi tessellation whose generating points are the discretization points along this curve. As shown here, this modification results in greater algorithmic simplicity. As a by-product, it also gives the free energy associated with the Voronoi tessellation. The new method can be applied both in the original Cartesian space of the system or in a set of collective variables. We illustrate FTS on test-case examples and apply it to the study of conformational transitions of the nitrogen regulatory protein C receiver domain using an elastic network model and to the isomerization of solvated alanine dipeptide.

Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase.

PubMed

Engel, Hamutal; Doron, Dvir; Kohen, Amnon; Major, Dan Thomas

2012-04-10

The inclusion of nuclear quantum effects such as zero-point energy and tunneling is of great importance in studying condensed phase chemical reactions involving the transfer of protons, hydrogen atoms, and hydride ions. In the current work, we derive an efficient quantum simulation approach for the computation of the momentum distribution in condensed phase chemical reactions. The method is based on a quantum-classical approach wherein quantum and classical simulations are performed separately. The classical simulations use standard sampling techniques, whereas the quantum simulations employ an open polymer chain path integral formulation which is computed using an efficient Monte Carlo staging algorithm. The approach is validated by applying it to a one-dimensional harmonic oscillator and symmetric double-well potential. Subsequently, the method is applied to the dihydrofolate reductase (DHFR) catalyzed reduction of 7,8-dihydrofolate by nicotinamide adenine dinucleotide phosphate hydride (NADPH) to yield S-5,6,7,8-tetrahydrofolate and NADP(+). The key chemical step in the catalytic cycle of DHFR involves a stereospecific hydride transfer. In order to estimate the amount of quantum delocalization, we compute the position and momentum distributions for the transferring hydride ion in the reactant state (RS) and transition state (TS) using a recently developed hybrid semiempirical quantum mechanics-molecular mechanics potential energy surface. Additionally, we examine the effect of compression of the donor-acceptor distance (DAD) in the TS on the momentum distribution. The present results suggest differential quantum delocalization in the RS and TS, as well as reduced tunneling upon DAD compression.

Formation mechanism of the secondary building unit in a chromium terephthalate metal-organic framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cantu Cantu, David; McGrail, B. Peter; Glezakou, Vassiliki Alexandra

2014-09-18

Based on density functional theory calculations and simulation, a detailed mechanism is presented on the formation of the secondary building unit (SBU) of MIL-101, a chromium terephthalate metal-organic framework (MOF). SBU formation is key to MOF nucleation, the rate-limiting step in the formation process of many MOFs. A series of reactions that lead to the formation of the SBU of MIL-101 is proposed in this work. Initial rate-limiting reactions form the metal cluster with three chromium (III) atoms linked to a central bridging oxygen. Terephthalate linkers play a key role as chromium (III) atoms are joined to linker carboxylate groupsmore » prior to the placement of the central bridging oxygen. Multiple linker addition reactions, which follow in different paths due to structural isomers, are limited by the removal of water molecules in the first chromium coordination shell. The least energy path is identified were all linkers on one face of the metal center plane are added first. A simple kinetic model based on transition state theory shows the rate of secondary building unit formation similar to the rate metal-organic framework nucleation. The authors are thankful to Dr. R. Rousseau for a critical reading of the manuscript. This research would not have been possible without the support of the Office of Fossil Energy, U.S. Department of Energy. This research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and the PNNL Institutional Computing (PIC) program located at Pacific Northwest National Laboratory.« less

Extended charge banking model of dual path shocks for implantable cardioverter defibrillators

PubMed Central

Dosdall, Derek J; Sweeney, James D

2008-01-01

Background Single path defibrillation shock methods have been improved through the use of the Charge Banking Model of defibrillation, which predicts the response of the heart to shocks as a simple resistor-capacitor (RC) circuit. While dual path defibrillation configurations have significantly reduced defibrillation thresholds, improvements to dual path defibrillation techniques have been limited to experimental observations without a practical model to aid in improving dual path defibrillation techniques. Methods The Charge Banking Model has been extended into a new Extended Charge Banking Model of defibrillation that represents small sections of the heart as separate RC circuits, uses a weighting factor based on published defibrillation shock field gradient measures, and implements a critical mass criteria to predict the relative efficacy of single and dual path defibrillation shocks. Results The new model reproduced the results from several published experimental protocols that demonstrated the relative efficacy of dual path defibrillation shocks. The model predicts that time between phases or pulses of dual path defibrillation shock configurations should be minimized to maximize shock efficacy. Discussion Through this approach the Extended Charge Banking Model predictions may be used to improve dual path and multi-pulse defibrillation techniques, which have been shown experimentally to lower defibrillation thresholds substantially. The new model may be a useful tool to help in further improving dual path and multiple pulse defibrillation techniques by predicting optimal pulse durations and shock timing parameters. PMID:18673561

Fracture sealing caused by mineral precipitation: The role of aperture and mineral heterogeneity on precipitation-induced permeability loss

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).

Upscaling of reaction rates in reactive transport using pore-scale reactive transport model

NASA Astrophysics Data System (ADS)

Yoon, H.; Dewers, T. A.; Arnold, B. W.; Major, J. R.; Eichhubl, P.; Srinivasan, S.

2013-12-01

Dissolved CO2 during geological CO2 storage may react with minerals in fractured rocks, confined aquifers, or faults, resulting in mineral precipitation and dissolution. The overall rate of reaction can be affected by coupled processes among hydrodynamics, transport, and reactions at the (sub) pore-scale. In this research pore-scale modeling of coupled fluid flow, reactive transport, and heterogeneous reaction at the mineral surface is applied to account for permeability alterations caused by precipitation-induced pore-blocking. This work is motivated by the observed CO2 seeps from a natural analog to geologic CO2 sequestration at Crystal Geyser, Utah. A key observation is the lateral migration of CO2 seep sites at a scale of ~ 100 meters over time. A pore-scale model provides fundamental mechanistic explanations of how calcite precipitation alters flow paths by pore plugging under different geochemical compositions and pore configurations. In addition, response function of reaction rates will be constructed from pore-scale simulations which account for a range of reaction regimes characterized by the Damkohler and Peclet numbers. Newly developed response functions will be used in a continuum scale model that may account for large-scale phenomena mimicking lateral migration of surface CO2 seeps. Comparison of field observations and simulations results will provide mechanistic explanations of the lateral migration and enhance our understanding of subsurface processes associated with the CO2 injection. This work is 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. 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.

SU-E-J-149: Secondary Emission Detection for Improved Proton Relative Stopping Power Identification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saunders, J; Musall, B; Erickson, A

Purpose: This research investigates application of secondary prompt gamma (PG) emission spectra, resulting from nuclear reactions induced by protons, to characterize tissue composition along the particle path. The objective of utilizing the intensity of discrete high-energy peaks of PG is to improve the accuracy of relative stopping power (RSP) values available for proton therapy treatment planning on a patient specific basis and to reduce uncertainty in dose depth calculations. Methods: In this research, MCNP6 was used to simulate PG emission spectra generated from proton induced nuclear reactions in medium of varying composition of carbon, oxygen, calcium and nitrogen, the predominantmore » elements found in human tissue. The relative peak intensities at discrete energies predicted by MCNP6 were compared to the corresponding atomic composition of the medium. Results: The results have shown a good general agreement with experimentally measured values reported by other investigators. Unexpected divergence from experimental spectra was noted in the peak intensities for some cases depending on the source of the cross-section data when using compiled proton table libraries vs. physics models built into MCNP6. While the use of proton cross-section libraries is generally recommended when available, these libraries lack data for several less abundant isotopes. This limits the range of their applicability and forces the simulations to rely on physics models for reactions with natural atomic compositions. Conclusion: Current end-of-range proton imaging provides an average RSP for the total estimated track length. The accurate identification of tissue composition along the incident particle path using PG detection and characterization allows for improved determination of the tissue RSP on the local level. While this would allow for more accurate depth calculations resulting in tighter treatment margins, precise understanding of proton beam behavior in tissue of various compositions is necessary requiring detailed simulations with a high degree of accuracy.« less

Listvenite formation from peridotite: Insights from Oman Drilling Project hole BT1B and preliminary reaction path model approach.

NASA Astrophysics Data System (ADS)

de Obeso, J. C.; Kelemen, P. B.; Manning, C. E.; Michibayashi, K.; Harris, M.

2017-12-01

Oman Drilling Project hole BT1B drilled 300 meters through the basal thrust of the Samail ophiolite. The first 200 meters of this hole are dominated by listvenites (completely carbonated peridotites) and serpentinites. Below 200 meters the hole is mainly composed of metasediments and metavolcanics. This core provides a unique record of interaction between (a) mantle peridotite in the leading edge of the mantle wedge and (b) hydrous, CO2 rich fluids derived from subducting lithologies similar to those in the metamorphic sole. We used EQ3/6 to simulate a reaction path in which hydrous fluid in equilibrium with qtz + calcite + feldspar + chlorite or smectite reacts with initially fresh peridotite at 100°C (the estimated temperature of alteration, Falk & Kelemen GCA 2015) and 5 kb. Water was first equilibrated with minerals observed during core description in the metamorphic sole at 100°C and 5kb. This fluid is then reacted with olivine enstatite and diopside (Mg#90) approximating the average composition of residual mantle peridotite (harzburgite) in Oman. Secondary minerals resulting from complete reaction are then reacted again with the initial fluid in an iterative process, up to water/rock > 1000. Water/rock close to 1 results in complete serpentinization of the peridotite, with chrysotile, brucite and magnetite as the only minerals. Water/rock >10 produces carbonates, chlorite and talc. Further increasing water/rock to > 100 produces assemblages dominated by carbonates and quartz with minor muscovite, similar to listvenites of hole BT1B that contain qtz + carbonates + Fe-oxyhydroxides + relict spinel ± chromian muscovite and fuchsite. The results of this preliminary model are consistent with the complex veining history of core from BT1B, with carbonate/iron oxide veins in both listvenites and serpentinites interpreted to be the earliest record of peridotite carbonation after initial serpentinization.

Multiple Paths of Deuterium Fractionation in Protoplanetary Disks

NASA Astrophysics Data System (ADS)

Aikawa, Yuri; Furuya, Kenji; Hincelin, Ugo; Herbst, Eric

2018-03-01

We investigate deuterium chemistry coupled with the nuclear spin-state chemistry of H2 and {{{H}}}3+ in protoplanetary disks. Multiple paths of deuterium fractionation are found; exchange reactions with D atoms, such as HCO+ + D, are effective in addition to those with HD. In a disk model with grain sizes appropriate for dark clouds, the freeze-out of molecules is severe in the outer midplane, while the disk surface is shielded from UV radiation. Gaseous molecules, including DCO+, thus become abundant at the disk surface, which tends to make their column density distribution relatively flat. If the dust grains have grown to millimeter size, the freeze-out rate of neutral species is reduced and the abundances of gaseous molecules, including DCO+ and N2D+, are enhanced in the cold midplane. Turbulent diffusion transports D atoms and radicals at the disk surface to the midplane, and stable ice species in the midplane to the disk surface. The effects of turbulence on chemistry are thus multifold; while DCO+ and N2D+ abundances increase or decrease depending on the regions, HCN and DCN in the gas and ice are greatly reduced at the innermost radii, compared to the model without turbulence. When cosmic rays penetrate the disk, the ortho-to-para ratio (OPR) of H2 is found to be thermal in the disk, except in the cold (≲10 K) midplane. We also analyze the OPR of {{{H}}}3+ and H2D+, as well as the main reactions of H2D+, DCO+, and N2D+, in order to analytically derive their abundances in the cold midplane.

Effects of Alloyed Metal on the Catalysis Activity of Pt for Ethanol Partial Oxidation: Adsorption and Dehydrogenation on Pt3M (M=Pt, Ru, Sn, Re, Rh, and Pd)

PubMed Central

Xu, Zhen-Feng; Wang, Yixuan

2011-01-01

The adsorption and dehydrogenation reactions of ethanol over bimetallic clusters, Pt3M (M = Pt, Ru, Sn, Re, Rh, and Pd), have been extensively investigated with density functional theory. Both the α-hydrogen and hydroxyl adsorptions on Pt as well as on the alloyed transition metal M sites of PtM were considered as initial reaction steps. The adsorptions of ethanol on Pt and M sites of some PtM via the α-hydrogen were well established. Although the α-hydrogen adsorption on Pt site is weaker than the hydroxyl, the potential energy profiles show that the dehydrogenation via the α-hydrogen path has much lower energy barrier than that via the hydroxyl path. Generally for the α-hydrogen path the adsorption is a rate-determining-step because of rather low dehydrogenation barrier for the α-hydrogen adsorption complex (thermodynamic control), while the hydroxyl path is determined by its dehydrogenation step (kinetic control). The effects of alloyed metal on the catalysis activity of Pt for ethanol partial oxidation, including adsorption energy, energy barrier, electronic structure, and eventually rate constant were discussed. Among all of the alloyed metals only Sn enhances the rate constant of the dehydrogenation via the α-hydrogen path on the Pt site of Pt3Sn as compared with Pt alone, which interprets why the PtSn is the most active to the oxidation of ethanol. PMID:22102920

Toward a complete theory for predicting inclusive deuteron breakup away from stability

NASA Astrophysics Data System (ADS)

Potel, G.; Perdikakis, G.; Carlson, B. V.; Atkinson, M. C.; Dickhoff, W. H.; Escher, J. E.; Hussein, M. S.; Lei, J.; Li, W.; Macchiavelli, A. O.; Moro, A. M.; Nunes, F. M.; Pain, S. D.; Rotureau, J.

2017-09-01

We present an account of the current status of the theoretical treatment of inclusive ( d, p) reactions in the breakup-fusion formalism, pointing to some applications and making the connection with current experimental capabilities. Three independent implementations of the reaction formalism have been recently developed, making use of different numerical strategies. The codes also originally relied on two different but equivalent representations, namely the prior (Udagawa-Tamura, UT) and the post (Ichimura-Austern-Vincent, IAV) representations. The different implementations have been benchmarked for the first time, and then applied to the Ca isotopic chain. The neutron-Ca propagator is described in the Dispersive Optical Model (DOM) framework, and the interplay between elastic breakup (EB) and non-elastic breakup (NEB) is studied for three Ca isotopes at two different bombarding energies. The accuracy of the description of different reaction observables is assessed by comparing with experimental data of ( d, p) on 40,48Ca. We discuss the predictions of the model for the extreme case of an isotope (60Ca) currently unavailable experimentally, though possibly available in future facilities (nominally within production reach at FRIB). We explore the use of ( d, p) reactions as surrogates for (n,γ ) processes, by using the formalism to describe the compound nucleus formation in a (d,pγ ) reaction as a function of excitation energy, spin, and parity. The subsequent decay is then computed within a Hauser-Feshbach formalism. Comparisons between the (d,pγ ) and (n,γ ) induced gamma decay spectra are discussed to inform efforts to infer neutron captures from (d,pγ ) reactions. Finally, we identify areas of opportunity for future developments, and discuss a possible path toward a predictive reaction theory.

Fluid-induced transition from banded kyanite- to bimineralic eclogite and implications for the evolution of cratons

NASA Astrophysics Data System (ADS)

Sommer, H.; Jacob, D. E.; Stern, R. A.; Petts, D.; Mattey, D. P.; Pearson, D. G.

2017-06-01

Heterogeneous, modally banded kyanite-bearing and bimineralic eclogites from the lithospheric mantle, collected at the Roberts Victor Diamond mine (South Africa), show a reaction texture in which kyanite is consumed. Geothermobarometric calculations using measured mineral compositions in Perple_X allowed the construction of a P-T path showing a steep, cool prograde metamorphic gradient of 2 °C/km to reach peak conditions of 5.8 GPa and 890 °C for the kyanite eclogite. The kyanite-out reaction formed bimineralic eclogite and is probably an integral part of the mineralogical evolution of most archetypal bimineralic eclogites at Roberts Victor and potentially elsewhere. The kyanite-out reaction occured at close to peak pressure (5.3 GPa) and was associated with a rise in temperature to 1380 °C. Mass balance calculations show that upon breakdown, the kyanite component is fully accommodated in garnet and omphacite via a reaction system with low water fugacity that required restricted fluid influx from metasomatic sources. The δ18O values of garnets are consistently higher than normal mantle values. Each sample has its characteristic trend of δ18O variance between garnets in the kyanite-bearing sections and those in the bimineralic parts covering a range between 5.1‰ and 6.8‰. No systematic change in O-isotope signature exists across the sample population. Differences in garnet trace element signatures between differing lithologies in the eclogites are significant. Grossular-rich garnets coexisting with kyanite have strong positive Eu-anomalies and low Gd/Yb ratios, while more pyrope-rich garnets in the bimineralic sections have lost their positive Eu-anomaly, have higher Gd/Yb ratios and generally higher heavy rare earth element contents. Garnets in the original kyanite-bearing portions thus reflect the provenance of the rocks as metamorphosed gabbros/troctolites. The kyanite-out reaction was most likely triggered by a heating event in the subcratonic lithosphere. As kyanite contains around 100 ppm of H2O it is suggested that the kyanite-out reaction, once initiated by heating and restricted metasomatic influx, was promoted by the release of water contained in the kyanite. The steep (high-P low-T) prograde P-T path defining rapid compression at low heating rates is atypical for subduction transport of eclogites into the lithospheric mantle. Such a trajectory is best explained in a model where strong lateral compression forces eclogites downward to higher pressures, supporting models of cratonic lithosphere formation by lateral collision and compression.

Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.

PubMed

Templeton, Clark; Chen, Szu-Hua; Fathizadeh, Arman; Elber, Ron

2017-10-21

The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system.

Helicopter Pitch-Control Mechanism Reduces Vibration

NASA Technical Reports Server (NTRS)

Lemont, H.

1986-01-01

Large forces accommodated without increasing weight of helicopter structure. New mechanism yields stiffer control and improves accuracy of pitch changes under load. As result, heavy casting not for gearbox, nor extra reinforcing members needed for fuselage bulkheads, stringers, skin, and other parts. In new mechanism, reaction forces developed in rotor hub. Long load paths to gearbox and fuselage elminated. Reaction member rigidly attached to hub and rotates with it. At lower end of reaction member, bearing forms bridge to fuselage through stationary beam and antirotation link. Beam connected to reaction plate through rods.

An integrated biomechanical modeling approach to the ergonomic evaluation of drywall installation.

PubMed

Yuan, Lu; Buchholz, Bryan; Punnett, Laura; Kriebel, David

2016-03-01

Three different methodologies: work sampling, computer simulation and biomechanical modeling, were integrated to study the physical demands of drywall installation. PATH (Posture, Activity, Tools, and Handling), a work-sampling based method, was used to quantify the percent of time that the drywall installers were conducting different activities with different body segment (trunk, arm, and leg) postures. Utilizing Monte-Carlo simulation to convert the categorical PATH data into continuous variables as inputs for the biomechanical models, the required muscle contraction forces and joint reaction forces at the low back (L4/L5) and shoulder (glenohumeral and sternoclavicular joints) were estimated for a typical eight-hour workday. To demonstrate the robustness of this modeling approach, a sensitivity analysis was conducted to examine the impact of some quantitative assumptions that have been made to facilitate the modeling approach. The results indicated that the modeling approach seemed to be the most sensitive to both the distribution of work cycles for a typical eight-hour workday and the distribution and values of Euler angles that are used to determine the "shoulder rhythm." Other assumptions including the distribution of trunk postures did not appear to have a significant impact on the model outputs. It was concluded that the integrated approach might provide an applicable examination of physical loads during the non-routine construction work, especially for those operations/tasks that have certain patterns/sequences for the workers to follow. Copyright © 2015 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Integration of On-Column Chemical Reactions in Protein Characterization by Liquid Chromatography/Mass Spectrometry: Cross-Path Reactive Chromatography.

PubMed

Pawlowski, Jake W; Carrick, Ian; Kaltashov, Igor A

2018-01-16

Profiling of complex proteins by means of mass spectrometry (MS) frequently requires that certain chemical modifications of their covalent structure (e.g., reduction of disulfide bonds), be carried out prior to the MS or MS/MS analysis. Traditionally, these chemical reactions take place in the off-line mode to allow the excess reagents (the majority of which interfere with the MS measurements and degrade the analytical signal) to be removed from the protein solution prior to MS measurements. In addition to a significant increase in the analysis time, chemical reactions may result in a partial or full loss of the protein if the modifications adversely affect its stability, e.g,, making it prone to aggregation. In this work we present a new approach to solving this problem by carrying out the chemical reactions online using the reactive chromatography scheme on a size exclusion chromatography (SEC) platform with MS detection. This is achieved by using a cross-path reaction scheme, i.e., by delaying the protein injection onto the SEC column (with respect to the injection of the reagent plug containing a disulfide-reducing agent), which allows the chemical reactions to be carried out inside the column for a limited (and precisely controlled) period of time, while the two plugs overlap inside the column. The reduced protein elutes separately from the unconsumed reagents, allowing the signal suppression in ESI to be avoided and enabling sensitive MS detection. The new method is used to measure fucosylation levels of a plasma protein haptoglobin at the whole protein level following online reduction of disulfide-linked tetrameric species to monomeric units. The feasibility of top-down fragmentation of disulfide-containing proteins is also demonstrated using β 2 -microglobulin and a monoclonal antibody (mAb). The new online technique is both robust and versatile, as the cross-path scheme can be readily expanded to include multiple reactions in a single experiment (as demonstrated in this work by oxidatively labeling mAb on the column, followed by reduction of its disulfide bonds and MS analysis of the extent of oxidation within each chain of the molecule).

Neck Muscle Moment Arms Obtained In-Vivo from MRI: Effect of Curved and Straight Modeled Paths.

PubMed

Suderman, Bethany L; Vasavada, Anita N

2017-08-01

Musculoskeletal models of the cervical spine commonly represent neck muscles with straight paths. However, straight lines do not best represent the natural curvature of muscle paths in the neck, because the paths are constrained by bone and soft tissue. The purpose of this study was to estimate moment arms of curved and straight neck muscle paths using different moment arm calculation methods: tendon excursion, geometric, and effective torque. Curved and straight muscle paths were defined for two subject-specific cervical spine models derived from in vivo magnetic resonance images (MRI). Modeling neck muscle paths with curvature provides significantly different moment arm estimates than straight paths for 10 of 15 neck muscles (p < 0.05, repeated measures two-way ANOVA). Moment arm estimates were also found to be significantly different among moment arm calculation methods for 11 of 15 neck muscles (p < 0.05, repeated measures two-way ANOVA). In particular, using straight lines to model muscle paths can lead to overestimating neck extension moment. However, moment arm methods for curved paths should be investigated further, as different methods of calculating moment arm can provide different estimates.

Nonequilibrium umbrella sampling in spaces of many order parameters

NASA Astrophysics Data System (ADS)

Dickson, Alex; Warmflash, Aryeh; Dinner, Aaron R.

2009-02-01

We recently introduced an umbrella sampling method for obtaining nonequilibrium steady-state probability distributions projected onto an arbitrary number of coordinates that characterize a system (order parameters) [A. Warmflash, P. Bhimalapuram, and A. R. Dinner, J. Chem. Phys. 127, 154112 (2007)]. Here, we show how our algorithm can be combined with the image update procedure from the finite-temperature string method for reversible processes [E. Vanden-Eijnden and M. Venturoli, "Revisiting the finite temperature string method for calculation of reaction tubes and free energies," J. Chem. Phys. (in press)] to enable restricted sampling of a nonequilibrium steady state in the vicinity of a path in a many-dimensional space of order parameters. For the study of transitions between stable states, the adapted algorithm results in improved scaling with the number of order parameters and the ability to progressively refine the regions of enforced sampling. We demonstrate the algorithm by applying it to a two-dimensional model of driven Brownian motion and a coarse-grained (Ising) model for nucleation under shear. It is found that the choice of order parameters can significantly affect the convergence of the simulation; local magnetization variables other than those used previously for sampling transition paths in Ising systems are needed to ensure that the reactive flux is primarily contained within a tube in the space of order parameters. The relation of this method to other algorithms that sample the statistics of path ensembles is discussed.

Dual path mechanism in the thermal reduction of graphene oxide.

PubMed

Larciprete, Rosanna; Fabris, Stefano; Sun, Tao; Lacovig, Paolo; Baraldi, Alessandro; Lizzit, Silvano

2011-11-02

Graphene is easily produced by thermally reducing graphene oxide. However, defect formation in the C network during deoxygenation compromises the charge carrier mobility in the reduced material. Understanding the mechanisms of the thermal reactions is essential for defining alternative routes able to limit the density of defects generated by carbon evolution. Here, we identify a dual path mechanism in the thermal reduction of graphene oxide driven by the oxygen coverage: at low surface density, the O atoms adsorbed as epoxy groups evolve as O(2) leaving the C network unmodified. At higher coverage, the formation of other O-containing species opens competing reaction channels, which consume the C backbone. We combined spectroscopic tools and ab initio calculations to probe the species residing on the surface and those released in the gas phase during heating and to identify reaction pathways and rate-limiting steps. Our results illuminate the current puzzling scenario of the low temperature gasification of graphene oxide.

Formation of alternating interfacial layers in Au-12Ge/Ni joints

PubMed Central

Lin, Shih-kang; Tsai, Ming-yueh; Tsai, Ping-chun; Hsu, Bo-hsun

2014-01-01

Au-Ge alloys are promising materials for high-power and high-frequency packaging, and Ni is frequently used as diffusion barriers. This study investigates interfacial reactions in Au-12Ge/Ni joints at 300°C and 400°C. For the reactions at 300°C, typical interfacial morphology was observed and the diffusion path was (Au) + (Ge)/NiGe/Ni5Ge3/Ni. However, an interesting phenomenon – the formation of (Au,Ni,Ge)/NiGe alternating layers – was observed for the reactions at 400°C. The diffusion path across the interface was liquid/(Au,Ni,Ge)/NiGe/···/(Au,Ni,Ge)/NiGe/Ni2Ge/Ni. The periodic thermodynamic instability at the NiGe/Ni2Ge interface caused the subsequent nucleation of new (Au,Ni,Ge)/NiGe pairs. The thermodynamic foundation and mechanism of formation of the alternating layers are elaborated in this paper. PMID:24690992

A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

NASA Astrophysics Data System (ADS)

Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

2015-03-01

We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH2OO and anti/syn-CH3C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH2OO and anti-CH3C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH3C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C-H bonds. For syn-CH3C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH3 group by the terminal O atom producing CH2C(H)O-OH. At 298 K, the intramolecular insertion process in CH2OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

Exploring mechanisms of a tropospheric archetype: CH{sub 3}O{sub 2} + NO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Launder, Andrew M.; Agarwal, Jay; Schaefer, Henry F., E-mail: ccq@uga.edu

Methylperoxy radical (CH{sub 3}O{sub 2}) and nitric oxide (NO) contribute to the propagation of photochemical smog in the troposphere via the production of methoxy radical (CH{sub 3}O) and nitrogen dioxide (NO{sub 2}). This reaction system also furnishes trace quantities of methyl nitrate (CH{sub 3}ONO{sub 2}), a sink for reactive NO{sub x} species. Here, the CH{sub 3}O{sub 2} + NO reaction is examined with highly reliable coupled-cluster methods. Specifically, equilibrium geometries for the reactants, products, intermediates, and transition states of the ground-state potential energy surface are characterized. Relative reaction enthalpies at 0 K (ΔH{sub 0K}) are reported; these values are comprisedmore » of electronic energies extrapolated to the complete basis set limit of CCSDT(Q) and zero-point vibrational energies computed at CCSD(T)/cc-pVTZ. A two-part mechanism involving CH{sub 3}O and NO{sub 2} production followed by radical recombination to CH{sub 3}ONO{sub 2} is determined to be the primary channel for formation of CH{sub 3}ONO{sub 2} under tropospheric conditions. Constrained optimizations of the reaction paths at CCSD(T)/cc-pVTZ suggest that the homolytic bond dissociations involved in this reaction path are barrierless.« less

Importance of geometric phase effects in ultracold chemistry

DOE PAGES

Hazra, Jisha; Kendrick, Brian K.; Balakrishnan, Naduvalath

2015-08-28

Here, it is demonstrated that the inclusion of the geometric phase has an important effect on ultracold chemical reaction rates. The effect appears in rotationally and vibrationally resolved integral cross sections as well as cross sections summed over all product quantum states. The effect arises from interference between scattering amplitudes of two reaction pathways: a direct path and a looping path that encircle the conical intersection between the two lowest adiabatic electronic potential energy surfaces. It is magnified when the two scattering amplitudes have comparable magnitude and they scatter into the same angular region which occurs in the isotropic scatteringmore » characteristic of the ultracold regime (s-wave scattering). Results are presented for the O + OH → H + O 2 reaction for total angular momentum quantum number J = 0–5. Large geometric phase effects occur for collision energies below 0.1 K, but the effect vanishes at higher energies when contributions from different partial waves are included. It is also qualitatively demonstrated that the geometric phase effect can be modulated by applying an external electric field allowing the possibility of quantum control of chemical reactions in the ultracold regime. In this case, the geometric phase plays the role of a “quantum switch” which can turn the reaction “on” or “off”.« less

Arsenic release and geochemical evolution of groundwater in an alluvial aquitard, West Bengal, India.

NASA Astrophysics Data System (ADS)

Desbarats, A. J.; Pal, T.; Mukherjee, P. K.; Beckie, R. D.

2017-12-01

According to the World Health Organization, contamination of groundwater by geogenic arsenic (As) represents the largest mass poisoning in history. At a field site in West Bengal, India, the source of As affecting a shallow aquifer was traced to silty sediments filling an abandoned river meander. Along with As-bearing phases, these sediments also contain 0.46 % organic carbon. The release of As within the channel fill is investigated using a geochemical mass balance model supported by detailed field observations of aqueous chemistry, sequential extraction analyses of sediment chemistry, and analyses of sediment mineralogy. The model explores the evolution of groundwater chemistry along a flow path extending from its recharge point in an abandoned channel pond, through the channel-fill sequence, to the underlying aquifer. Variations in groundwater composition within the host sediments are explained in terms of mineral weathering driven by organic carbon decay. The model yields reaction coefficients expressing amounts of minerals (and gases) reacting or precipitating along the flow path. Arsenic and phosphorus cycles appear closely linked as these species are hosted by goethite, Fe-rich chlorite, and vivianite. Arsenic is released through the rapid reductive dissolution of goethite and the slower weathering of chlorite. Concomitantly, some As is sequestered in precipitating vivianite. These competing processes reach equilibrium deeper in the channel-fill sequence as groundwater As concentrations stabilize. Using groundwater residence time in channel fill obtained from a numerical flow model and the calculated reaction coefficients, rates of organic carbon oxidation, goethite dissolution, and net As release are estimated at 1.15 mmol C L-1 a-1, 0.18 mmol L-1 a-1, and 4.57 10-4 mmol L-1 a-1, respectively. Fine-grained yet slightly permeable deposits such as channel-fill silts containing reactive organic carbon and As-bearing goethite and phyllosilicates are localized centers of intense chemical weathering conducive to As mobilization.

Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions

PubMed Central

Johnson, Margaret E.; Hummer, Gerhard

2012-01-01

We explore the theoretical foundation of different string methods used to find dominant reaction pathways in high-dimensional configuration spaces. Pathways are assessed by the amount of reactive flux they carry and by their orientation relative to the committor function. By examining the effects of transforming between different collective coordinates that span the same underlying space, we unmask artificial coordinate dependences in strings optimized to follow the free energy gradient. In contrast, strings optimized to follow the drift vector produce reaction pathways that are significantly less sensitive to reparameterizations of the collective coordinates. The differences in these paths arise because the drift vector depends on both the free energy gradient and the diffusion tensor of the coarse collective variables. Anisotropy and position dependence of diffusion tensors arise commonly in spaces of coarse variables, whose generally slow dynamics are obtained by nonlinear projections of the strongly coupled atomic motions. We show here that transition paths constructed to account for dynamics by following the drift vector will (to a close approximation) carry the maximum reactive flux both in systems with isotropic position dependent diffusion, and in systems with constant but anisotropic diffusion. We derive a simple method for calculating the committor function along paths that follow the reactive flux. Lastly, we provide guidance for the practical implementation of the dynamic string method. PMID:22616575

A motivational model for environmentally responsible behavior.

PubMed

Tabernero, Carmen; Hernández, Bernardo

2012-07-01

This paper presents a study examining whether self-efficacy and intrinsic motivation are related to environmentally responsible behavior (ERB). The study analysed past environmental behavior, self-regulatory mechanisms (self-efficacy, satisfaction, goals), and intrinsic and extrinsic motivation in relation to ERBs in a sample of 156 university students. Results show that all the motivational variables studied are linked to ERB. The effects of self-efficacy on ERB are mediated by the intrinsic motivation responses of the participants. A theoretical model was created by means of path analysis, revealing the power of motivational variables to predict ERB. Structural equation modeling was used to test and fit the research model. The role of motivational variables is discussed with a view to creating adequate learning contexts and experiences to generate interest and new sensations in which self-efficacy and affective reactions play an important role.

ELASTIC NET FOR COX'S PROPORTIONAL HAZARDS MODEL WITH A SOLUTION PATH ALGORITHM.

PubMed

Wu, Yichao

2012-01-01

For least squares regression, Efron et al. (2004) proposed an efficient solution path algorithm, the least angle regression (LAR). They showed that a slight modification of the LAR leads to the whole LASSO solution path. Both the LAR and LASSO solution paths are piecewise linear. Recently Wu (2011) extended the LAR to generalized linear models and the quasi-likelihood method. In this work we extend the LAR further to handle Cox's proportional hazards model. The goal is to develop a solution path algorithm for the elastic net penalty (Zou and Hastie (2005)) in Cox's proportional hazards model. This goal is achieved in two steps. First we extend the LAR to optimizing the log partial likelihood plus a fixed small ridge term. Then we define a path modification, which leads to the solution path of the elastic net regularized log partial likelihood. Our solution path is exact and piecewise determined by ordinary differential equation systems.

An avionics sensitivity study. Volume 1: Operational considerations

NASA Technical Reports Server (NTRS)

Scott, R. W.; Mcconkey, E. D.

1976-01-01

Equipment and operational concepts affecting aircraft in the terminal area are reported. Curved approach applications and modified climb and descent procedures for minimum fuel consumption are considered. The curved approach study involves the application of MLS guidance to enable execution of the current visual approach to Washington National Airport under instrument flight conditions. The operational significance and the flight path control requirements involved in the application of curved approach paths to this situation are considered. Alternative flight path control regimes are considered to achieve minimum fuel consumption subject to constraints related to air traffic control requirements, flight crew and passenger reactions, and airframe and powerplant limitations.

Probing the N˜Z line via β decay

NASA Astrophysics Data System (ADS)

Oinonen, Markku

1999-11-01

This contribution reports several beta-decay studies performed at ISOLDE On-line Mass Separator at CERN recently for nuclei close to N=Z line. Beta decay of 58Zn provides a possibility to compare Gamow-Teller strength extracted from complementary beta-decay studies and charge-exchange reactions. Measurement on beta-decay half-life of 70Kr shows importance of experimental information in modelling the path of the astrophysical rp process. Decay of 71Kr is an example of a mirror beta decay and extends the systematics of these particular decays towards highly deformed region close to A=80.

Unravelling the impact of reaction paths on mechanical degradation of intercalation cathodes for lithium-ion batteries

DOE PAGES

Li, Juchuan; Zhang, Qinglin; Xiao, Xingcheng; ...

2015-10-18

The intercalation compounds are generally considered as ideal electrode materials for lithium-ion batteries thanks to their minimum volume expansion and fast lithium ion diffusion. However, cracking still occurs in those compounds and has been identified as one of the critical issues responsible for their capacity decay and short cycle life, although the diffusion-induced stress and volume expansion are much smaller than those in alloying-type electrodes. Here, we designed a thin-film model system that enables us to tailor the cation ordering in LiNi 0.5Mn 1.5O 4 spinels and correlate the stress patterns, phase evolution, and cycle performances. Surprisingly, we found thatmore » distinct reaction paths cause negligible difference in the overall stress patterns but significantly different cracking behaviors and cycling performances: 95% capacity retention for disordered LiNi 0.5Mn 1.5O 4 and 48% capacity retention for ordered LiNi 0.5Mn 1.5O 4 after 2000 cycles. We were able to pinpoint that the extended solid-solution region with suppressed phase transformation attributed to the superior electrochemical performance of disordered spinel. Furthermore, this work envisions a strategy for rationally designing stable cathodes for lithium-ion batteries through engineering the atomic structure that extends the solid-solution region and suppresses phase transformation.« less

Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation.

PubMed

Banyasz, Akos; Ketola, Tiia; Martínez-Fernández, Lara; Improta, Roberto; Markovitsi, Dimitra

2018-04-17

There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical. The adenine radicals, thus identified in the time-resolved spectra, disappear with a lifetime of 2.5 ms, giving rise to a reaction product that absorbs at 350 nm. In parallel, the fingerprint of reaction intermediates other than radicals, formed directly from singlet excited states and assigned to AT/TA dimers, is detected at shorter wavelengths. PCM/TD-DFT calculations are carried out to map the pathways leading to such species and to characterize their absorption spectra; we find that, in addition to the path leading to the well-known TA* photoproduct, an AT photo-dimerization path may be operative in duplexes.

Mode pumping experiments on biomolecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Austin, R.H.; Erramilli, S.; Xie, A.

1995-12-31

We will explore several aspects of protein dynamics and energy transfer that can be explored by using the intense, picosecond, tunable mid-IR output of the FEL. In order of appearance they are: (1) Saturation recovery and inter-level coupling of the low temperature amide-I band in acetanilide. This is a continuation of earlier experiments to test soliton models in crystalline hydrogen bonded solids. In this experiment we utilize the sub-picosecond time resolution and low repetition rate of the Stanford SCLA FEL to do both T{sub 1} and T{sub 2} relaxation measurements at 1650 cm{sup -1}. (2) Probing the influence of collectivemore » dynamics in sensory rhodopsin. In this experiment we use the FIR output of the Stanford FIREFLY FEL to determine the lifetime of collective modes in the photo-active protein sensory rhodopsin, and begin experiments on the influence of collective modes on retinal reaction dynamics. (3) Probing the transition states of enzymes. This experiment, in the initial stages, attempts to use the intense IR output of the FEL to probe and influence the reaction path of a transition state analog for the protein nucleoside hydrolase. The transition state of the inosine substrate is believed to have critical modes softened by the protein so that bond-breaking paths show absorption at approximately 800 cm{sup -1}. A form of action spectrum using FEL excitation will be used to probe this state.« less

Improving density functional tight binding predictions of free energy surfaces for peptide condensation reactions in solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for chemistry that is fast relative to DFT simulation times (<10 ps), but the effects on slow chemistry and the free energy surface are not well-known. We present a force matching approach to increase the accuracy of DFTB predictions for free energy surfaces. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials without a priori knowledge of transition states. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT results for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Coupling Fluid Dynamics and Multiphase Disequilibria: Applications to Eutectic and Peritectic Systems

NASA Astrophysics Data System (ADS)

Tweed, L. E. L.; Spiegelman, M. W.; Kelemen, P. B.

2017-12-01

Computational thermodynamics has yielded great insights into petrological processes. However, on its own it cannot capture the inherently dynamic nature of many of these processes which depend on the interaction between time-dependent processes including advection, diffusion and chemical reaction. To understand this interplay, and to move away from a purely equilibrium view, requires the integration of computational thermodynamics and fluid mechanics. A key aspect of doing this is the treatment of chemical reactions as time-dependent, irreversible processes. Such a development is integral to understanding a host of petrological questions from the open system evolution of magma chambers to the dynamics of melt migration beneath mid-ocean ridges and flux melting of the mantle wedge in subduction zones. A simple thermodynamically consistent reactive model is developed that can be integrated with conservation equations for mass, momentum and energy. The model rests on the thermodynamic characterization of an independent set of reactions and has the advantage of being completely general and easily extensible to systems comprising multiple solid and liquid phases. The underlying theory is described in detail in another contribution in this session. Here we apply the framework to experimentally constrained simple systems of petrological interest including the fo-qz binary and the fo-qz-k2o ternary. These systems contain a variety of phase topologies including eutectic and peritectic reactions. As the model allows for the seamless exhaustion and stabilization of phases, we can explore the effect that these discontinuous changes have on the compositional and dynamic evolution of the system. To do this we track how the systems respond to sudden changes in intensive variables that perturb them from equilibrium. Such changes are rife in crustal magmatic systems. Simulations for decompression melting are also run to explore the interplay between reactive and advective fluxes. Buffering between the multiple reactions can result in surprising reaction paths highlighting that micro-mechanics could play a significant role in magmatic evolution. By building up the complexity of the problems gradually, we develop an intuition for the effect of model choices including the kinetic law and the set of reactions used.

Supersonic molecular beam experiments on surface chemical reactions.

PubMed

Okada, Michio

2014-10-01

The interaction of a molecule and a surface is important in various fields, and in particular in complex systems like biomaterials and their related chemistry. However, the detailed understanding of the elementary steps in the surface chemistry, for example, stereodynamics, is still insufficient even for simple model systems. In this Personal Account, I review our recent studies of chemical reactions on single-crystalline Cu and Si surfaces induced by hyperthermal oxygen molecular beams and by oriented molecular beams, respectively. Studies of oxide formation on Cu induced by hyperthermal molecular beams demonstrate a significant role of the translational energy of the incident molecules. The use of hyperthermal molecular beams enables us to open up new chemical reaction paths specific for the hyperthermal energy region, and to develop new methods for the fabrication of thin films. On the other hand, oriented molecular beams also demonstrate the possibility of understanding surface chemical reactions in detail by varying the orientation of the incident molecules. The steric effects found on Si surfaces hint at new ways of material fabrication on Si surfaces. Controlling the initial conditions of incoming molecules is a powerful tool for finely monitoring the elementary step of the surface chemical reactions and creating new materials on surfaces. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450

PubMed Central

Oláh, Julianna; Mulholland, Adrian J.; Harvey, Jeremy N.

2011-01-01

Cytochrome P450 enzymes play key roles in the metabolism of the majority of drugs. Improved models for prediction of likely metabolites will contribute to drug development. In this work, two possible metabolic routes (aromatic carbon oxidation and O-demethylation) of dextromethorphan are compared using molecular dynamics (MD) simulations and density functional theory (DFT). The DFT results on a small active site model suggest that both reactions might occur competitively. Docking and MD studies of dextromethorphan in the active site of P450 2D6 show that the dextromethorphan is located close to heme oxygen in a geometry apparently consistent with competitive metabolism. In contrast, calculations of the reaction path in a large protein model [using a hybrid quantum mechanical–molecular mechanics (QM/MM) method] show a very strong preference for O-demethylation, in accordance with experimental results. The aromatic carbon oxidation reaction is predicted to have a high activation energy, due to the active site preventing formation of a favorable transition-state structure. Hence, the QM/MM calculations demonstrate a crucial role of many active site residues in determining reactivity of dextromethorphan in P450 2D6. Beyond substrate binding orientation and reactivity of Compound I, successful metabolite predictions must take into account the detailed mechanism of oxidation in the protein. These results demonstrate the potential of QM/MM methods to investigate specificity in drug metabolism. PMID:21444768

Coupling photochemical reaction detection based on singlet oxygen sensitization to capillary electrochromatography

PubMed

Dickson; Odom; Ducheneaux; Murray; Milofsky

2000-07-15

Despite the impressive separation efficiency afforded by capillary electrochromatography (CEC), the detection of UV-absorbing compounds following separation in capillary dimensions remains limited by the short path length (5-75 microm) through the column. Moreover, analytes that are poor chromophores present an additional challenge with respect to sensitive detection in CEC. This paper illustrates a new photochemical reaction detection scheme for CEC that takes advantage of the catalytic nature of type II photooxidation reactions. The sensitive detection scheme is selective toward molecules capable of photosensitizing the formation of singlet molecular oxygen (1O2). Following separation by CEC, UV-absorbing analytes promote groundstate 3O2 to an excited state (1O2) which reacts rapidly with tert-butyl-3,4,5-trimethylpyrrolecarboxylate, which is added to the running buffer. Detection is based on the loss of pyrrole. The reaction is catalytic in nature since one analyte molecule may absorb light many times, producing large amounts of 1O2. The detection limit for 9-acetylanthracene, following separation by CEC, is approximately 6 x 10(-9) M (S/N = 3). Optimization of the factors effecting the S/N for four model compounds is discussed.

Density functional theory study of ethylene partial oxidation on Ag 7 clusters

NASA Astrophysics Data System (ADS)

Yu, Hua-Gen

2006-11-01

The partial oxidation reaction of ethylene on neutral and anionic Ag 7 clusters has been studied using the BPW91 hybrid DFT method with the Stuttgart RSC97 relativistic pseudopotential for the 28-electron ionic core of Ag. The atomic oxygen reaction mechanism is mainly addressed. Results show that the reaction occurs via a stable oxametallacycle intermediate ( AgOCH4p, p = 0 or -1), but it involves small reaction barriers along the reaction path. The ZPE-corrected barrier heights are obtained as 0.7-6.5 kcal/mole. In addition, the structure and anionic effects of Ag 7 clusters are also discussed.

Two paths to blame: Intentionality directs moral information processing along two distinct tracks.

PubMed

Monroe, Andrew E; Malle, Bertram F

2017-01-01

There is broad consensus that features such as causality, mental states, and preventability are key inputs to moral judgments of blame. What is not clear is exactly how people process these inputs to arrive at such judgments. Three studies provide evidence that early judgments of whether or not a norm violation is intentional direct information processing along 1 of 2 tracks: if the violation is deemed intentional, blame processing relies on information about the agent's reasons for committing the violation; if the violation is deemed unintentional, blame processing relies on information about how preventable the violation was. Owing to these processing commitments, when new information requires perceivers to switch tracks, they must reconfigure their judgments, which results in measurable processing costs indicated by reaction time (RT) delays. These findings offer support for a new theory of moral judgment (the Path Model of Blame) and advance the study of moral cognition as hierarchical information processing. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Dissociative Ionization of Benzene by Electron Impact

NASA Technical Reports Server (NTRS)

Huo, Winifred; Dateo, Christopher; Kwak, Dochan (Technical Monitor)

2002-01-01

We report a theoretical study of the dissociative ionization (DI) of benzene from the low-lying ionization channels. Our approach makes use of the fact that electron motion is much faster than nuclear motion and DI is treated as a two-step process. The first step is electron-impact ionization resulting in an ion with the same nuclear geometry as the neutral molecule. In the second step the nuclei relax from the initial geometry and undergo unimolecular dissociation. For the ionization process we use the improved binary-encounter dipole (iBED) model. For the unimolecular dissociation step, we study the steepest descent reaction path to the minimum of the ion potential energy surface. The path is used to analyze the probability of unimolecular dissociation and to determine the product distributions. Our analysis of the dissociation products and the thresholds of the productions are compared with the result dissociative photoionization measurements of Feng et al. The partial oscillator strengths from Feng et al. are then used in the iBED cross section calculations.

Pyrolysis Products Of Dimethyldichlorosilane

NASA Technical Reports Server (NTRS)

Cagliostro, D. E.; Riccitiello, S. R.; Carswell, M. G.

1990-01-01

Report describes experimental study of chemical reactions and chemical products of chemical-vapor deposition of silicon carbide from dimethyldichlorosilane. Topic important because it relates to current interest in lightweight refractory materials for use in advanced aircraft and spacecraft. Analyses showed that at temperature of 700 to 1,100 degrees C and contact time of about 1 minute, SiC forms by two chemical-reaction paths.

(d ,n ) proton-transfer reactions on 9Be, 11B, 13C, N,1514, and 19F and spectroscopic factors at Ed=16 MeV

NASA Astrophysics Data System (ADS)

Febbraro, M.; Becchetti, F. D.; Torres-Isea, R. O.; Riggins, J.; Lawrence, C. C.; Kolata, J. J.; Howard, A. M.

2017-08-01

The (d ,n ) reaction has been studied with targets of 9Be, 11B, 13C, N,1514, and 19F at Ed=16 MeV using a deuterated liquid-scintillator array. Advanced spectral unfolding techniques with accurately measured scintillator response functions were employed to extract neutron energy spectra without the need for long-path neutron time-of-flight. An analysis of the proton-transfer data at forward angles to the ground states of the final nuclei, using finite-range distorted-wave Born approximation analysis with common bound-state, global, and local optical-model parameter sets, yields a set of self-consistent spectroscopic factors. These are compared with the results of several previous time-of-flight measurements, most done many years ago for individual nuclei at lower energy and often analyzed using zero-range transfer codes. In contrast to some of the earlier published data, our data generally compare well with simple shell-model predictions, with little evidence for uniform quenching (reduction from shell-model values) that has previously been reported from analysis of nucleon knock-out reactions. Data for low-lying excited states in 14N from 13C(d ,n ) also is analyzed and spectroscopic information relevant to nuclear astrophysics obtained. A preliminary study of the radioactive ion beam induced reaction 7Be(d ,n ) , E (7Be)=30 MeV was carried out and indicates further improvements are needed for such measurements, which require detection of neutrons with En<2 MeV .

Reaction path of energetic materials using THOR code

NASA Astrophysics Data System (ADS)

Duraes, L.; Campos, J.; Portugal, A.

1997-07-01

The method of predicting reaction path, using a thermochemical computer code, named THOR, allows for isobar and isochor adiabatic combustion and CJ detonation regimes, the calculation of the composition and thermodynamic properties of reaction products of energetic materials. THOR code assumes the thermodynamic equilibria of all possible products, for the minimum Gibbs free energy, using a thermal equation of state (EoS). The used HL EoS is a new EoS developed in previous works. HL EoS is supported by a Boltzmann EoS, taking α =13.5 to the exponent of the intermolecular potential and θ=1.4 to the adimensional temperature. This code allows now the possibility of estimating various sets of reaction products, obtained successively by the decomposition of the original reacting compound, as a function of the released energy. Two case studies of thermal decomposition procedure were selected, described, calculated and discussed - Ammonium Nitrate based explosives and Nitromethane - because they are very known explosives and their equivalence ratio is respectively near and greater than the stoicheiometry. Predictions of detonation properties of other condensed explosives, as a function of energy release, present results in good correlation with experimental values.

Two-phase vesicles: a study on evolutionary and stationary models.

PubMed

Sahebifard, MohammadMahdi; Shahidi, Alireza; Ziaei-Rad, Saeed

2017-05-01

In the current article, the dynamic evolution of two-phase vesicles is presented as an extension to a previous stationary model and based on an equilibrium of local forces. In the simplified model, ignoring the effects of membrane inertia, a dynamic equilibrium between the membrane bending potential and local fluid friction is considered in each phase. The equilibrium equations at the domain borders are completed by extended introduction of membrane section reactions. We show that in some cases, the results of stationary and evolutionary models are in agreement with each other and also with experimental observations, while in others the two models differ markedly. The value of our approach is that we can account for unresponsive points of uncertainty using our equations with the local velocity of the lipid membranes and calculating the intermediate states (shapes) in the consequent evolutionary, or response, path.

Path integration of head direction: updating a packet of neural activity at the correct speed using axonal conduction delays.

PubMed

Walters, Daniel; Stringer, Simon; Rolls, Edmund

2013-01-01

The head direction cell system is capable of accurately updating its current representation of head direction in the absence of visual input. This is known as the path integration of head direction. An important question is how the head direction cell system learns to perform accurate path integration of head direction. In this paper we propose a model of velocity path integration of head direction in which the natural time delay of axonal transmission between a linked continuous attractor network and competitive network acts as a timing mechanism to facilitate the correct speed of path integration. The model effectively learns a "look-up" table for the correct speed of path integration. In simulation, we show that the model is able to successfully learn two different speeds of path integration across two different axonal conduction delays, and without the need to alter any other model parameters. An implication of this model is that, by learning look-up tables for each speed of path integration, the model should exhibit a degree of robustness to damage. In simulations, we show that the speed of path integration is not significantly affected by degrading the network through removing a proportion of the cells that signal rotational velocity.

Path Integration of Head Direction: Updating a Packet of Neural Activity at the Correct Speed Using Axonal Conduction Delays

PubMed Central

Walters, Daniel; Stringer, Simon; Rolls, Edmund

2013-01-01

The head direction cell system is capable of accurately updating its current representation of head direction in the absence of visual input. This is known as the path integration of head direction. An important question is how the head direction cell system learns to perform accurate path integration of head direction. In this paper we propose a model of velocity path integration of head direction in which the natural time delay of axonal transmission between a linked continuous attractor network and competitive network acts as a timing mechanism to facilitate the correct speed of path integration. The model effectively learns a “look-up” table for the correct speed of path integration. In simulation, we show that the model is able to successfully learn two different speeds of path integration across two different axonal conduction delays, and without the need to alter any other model parameters. An implication of this model is that, by learning look-up tables for each speed of path integration, the model should exhibit a degree of robustness to damage. In simulations, we show that the speed of path integration is not significantly affected by degrading the network through removing a proportion of the cells that signal rotational velocity. PMID:23526976

Integrated modelling of nitrogen transport and turnover in lowland catchements of northern Germany

NASA Astrophysics Data System (ADS)

Wriedt, G.

2003-04-01

Nitrogen loads in surface water often do not reflect the actual input situation. This retention of nitrogen can be explained by chemical transformations in the soil and groundwater (e.g. denitrification) and hydrological factors (e.g. transition time, mixing) in soil and groundwater and depends strongly on the geological and chemical patterns within the catchment areas (e.g. reactive substances, conductivities). In order to facilitate modelling studies on the relation between nitrogen transport and catchment characteristics we developed a modelling approach, that allows simulation of the complete nitrogen transport path from the soil input until the exfiltration into the surface water system. This approach is based on the loose coupling of a soil water model and an analytical soil nitrogen model (mRISK-N) with a groundwater flow model (MODFLOW) and a multi-species reactive transport model (RT3D). Groundwater nitrogen turnover is represented by a closed reaction scheme that explicitly includes oxidation of organic matter and pyrite oxidation by several electron acceptors as the main reactive pathways, in order to link nitrogen turnover directly to the availability of the substances involved in the chemical reactions. This reaction module has been implemented into the modelling system as a user defined reaction module within the RT3D-environment. The soil submodel was tested against lysimeter data. It was found, that soil water balance was represented quite well. Nitrogen leaching rates however, can only be interpreted for larger time scales, whereas considerable deviations from measured values do occur in single years. Nevertheless, model performance is comparable to other, more complex soil water and nitrogen models currently available. It was found, that the high uncertainty of model parameters and input data as well as limited knowledge on processes limit the accuracy of soil nitrogen models in general. The next step of the project is the model application in the study area “Schaugraben catchment”. The study area is located near Osterburg/Altmark in the north of Sachsen-Anhalt, its size is about 25 km2. The geology is determined by pleistocene deposits, mainly glacial till in the plateau areas and glaciofluvial sandy deposits in the valleys. A dense drainage network, a high groundwater table and intensive agricultural use provide a high risk for both, groundwater and surface water quality. Model application focuses on the analysis of the interactions between catchment characteristics (hydrological and geological), spatial input patterns and the fate of nitrogen within the catchment. This is done by applying sensitivity analysis, uncertainty analysis and scenario simulation. A three dimensional groundwater flow model for the Schaugraben area has been set up and calibrated in order to analyse the regional flow paths, transition times and groundwater catchments. More detailed modelling studies including the reactive groundwater transport are performed on selected cutouts and transects, defining specific hydrogeological settings, e.g. riparian areas, buffer stripes, hydrological windows etc. Under special consideration is also the influence of spatial input patterns of nitrate and organic matter leaching to the groundwater. Results of the modelling studies are expect until March ‘03. The modelling approach developed here is a tool for the assessment of transport-turnover interaction and may help to improve experimental studies and measurement strategies and to provide useful information for managing purposes.

Kinetics of the hydrogen atom abstraction reactions from 1-butanol by hydroxyl radical: theory matches experiment and more.

PubMed

Seal, Prasenjit; Oyedepo, Gbenga; Truhlar, Donald G

2013-01-17

In the present work, we study the H atom abstraction reactions by hydroxyl radical at all five sites of 1-butanol. Multistructural variational transition state theory (MS-VTST) was employed to estimate the five thermal rate constants. MS-VTST utilizes a multifaceted dividing surface that accounts for the multiple conformational structures of the transition state, and we also include all the structures of the reactant molecule. The vibrational frequencies and minimum energy paths (MEPs) were computed using the M08-HX/MG3S electronic structure method. The required potential energy surfaces were obtained implicitly by direct dynamics employing interpolated variational transition state theory with mapping (IVTST-M) using a variational reaction path algorithm. The M08-HX/MG3S electronic model chemistry was then used to calculate multistructural torsional anharmonicity factors to complete the MS-VTST rate constant calculations. The results indicate that torsional anharmonicity is very important at higher temperatures, and neglecting it would lead to errors of 26 and 32 at 1000 and 1500 K, respectively. Our results for the sums of the site-specific rate constants agree very well with the experimental values of Hanson and co-workers at 896-1269 K and with the experimental results of Campbell et al. at 292 K, but slightly less well with the experiments of Wallington et al., Nelson et al., and Yujing and Mellouki at 253-372 K; nevertheless, the calculated rates are within a factor of 1.61 of all experimental values at all temperatures. This gives us confidence in the site-specific values, which are currently inaccessible to experiment.

Nonequilibrium thermodynamics and a fluctuation theorem for individual reaction steps in a chemical reaction network

NASA Astrophysics Data System (ADS)

Pal, Krishnendu; Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

2015-09-01

We have introduced an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of the individual elementary reactions and the corresponding reverse reactions. The method is a microscopic formulation of the dissipation function in terms of the relative entropy or Kullback-Leibler distance which is based on the analogy of phase space trajectory with the path of elementary reactions in a network of chemical process. We have introduced here a fluctuation theorem valid for each opposite pair of elementary reactions which is useful in determining the contribution of each sub-reaction on the nonequilibrium thermodynamics of overall reaction. The methodology is applied to an oligomeric enzyme kinetics at a chemiostatic condition that leads the reaction to a nonequilibrium steady state for which we have estimated how each step of the reaction is energy driven or entropy driven to contribute to the overall reaction.

Mathematical Modeling of the Origins of Life

NASA Technical Reports Server (NTRS)

Pohorille, Andrew

2006-01-01

The emergence of early metabolism - a network of catalyzed chemical reactions that supported self-maintenance, growth, reproduction and evolution of the ancestors of contemporary cells (protocells) was a critical, but still very poorly understood step on the path from inanimate to animate matter. Here, it is proposed and tested through mathematical modeling of biochemically plausible systems that the emergence of metabolism and its initial evolution towards higher complexity preceded the emergence of a genome. Even though the formation of protocellular metabolism was driven by non-genomic, highly stochastic processes the outcome was largely deterministic, strongly constrained by laws of chemistry. It is shown that such concepts as speciation and fitness to the environment, developed in the context of genomic evolution, also held in the absence of a genome.

How to Compute Electron Ionization Mass Spectra from First Principles.

PubMed

Bauer, Christoph Alexander; Grimme, Stefan

2016-06-02

The prediction of electron ionization (EI) mass spectra (MS) from first principles has been a major challenge for quantum chemistry (QC). The unimolecular reaction space grows rapidly with increasing molecular size. On the one hand, statistical models like Eyring's quasi-equilibrium theory and Rice-Ramsperger-Kassel-Marcus theory have provided valuable insight, and some predictions and quantitative results can be obtained from such calculations. On the other hand, molecular dynamics-based methods are able to explore automatically the energetically available regions of phase space and thus yield reaction paths in an unbiased way. We describe in this feature article the status of both methodologies in relation to mass spectrometry for small to medium sized molecules. We further present results obtained with the QCEIMS program developed in our laboratory. Our method, which incorporates stochastic and dynamic elements, has been a significant step toward the reliable routine calculation of EI mass spectra.

A quantum chemical study for the multichannel reaction PH 2 + PH 2

NASA Astrophysics Data System (ADS)

Pimentel, André S.; Viana, Rommel B.

2007-04-01

The PH 2 + PH 2 multichannel reaction path was proposed in this study. The transition state that connects the reactants to cis-P 2H 2 isomer was found for the first time ever. This process is not allowed to occur at ordinary conditions because of its high energy barrier, 70 kcal mol -1. The PH 2 + PH 2 disproportionation to form the triplet PH 3 radical is an exothermic and spontaneous reaction. The PH 2 + PH 2 reaction may also form the P 2H 4 molecule in the absence of surfaces.

Pulled Motzkin paths

NASA Astrophysics Data System (ADS)

Janse van Rensburg, E. J.

2010-08-01

In this paper the models of pulled Dyck paths in Janse van Rensburg (2010 J. Phys. A: Math. Theor. 43 215001) are generalized to pulled Motzkin path models. The generating functions of pulled Motzkin paths are determined in terms of series over trinomial coefficients and the elastic response of a Motzkin path pulled at its endpoint (see Orlandini and Whittington (2004 J. Phys. A: Math. Gen. 37 5305-14)) is shown to be R(f) = 0 for forces pushing the endpoint toward the adsorbing line and R(f) = f(1 + 2cosh f))/(2sinh f) → f as f → ∞, for forces pulling the path away from the X-axis. In addition, the elastic response of a Motzkin path pulled at its midpoint is shown to be R(f) = 0 for forces pushing the midpoint toward the adsorbing line and R(f) = f(1 + 2cosh (f/2))/sinh (f/2) → 2f as f → ∞, for forces pulling the path away from the X-axis. Formal combinatorial identities arising from pulled Motzkin path models are also presented. These identities are the generalization of combinatorial identities obtained in directed paths models to their natural trinomial counterparts.

Thermodynamic Predictions vs. Measured Fluid Chemistry: Lessons from Low-Temperature, Serpentinizing Fluids

NASA Astrophysics Data System (ADS)

Leong, J. M.; Howells, A. H.; Robinson, K. J.; Shock, E. L.

2018-05-01

A combination of reaction-path, mixing, and sensitivity calculations was used to reconcile deviations between thermodynamic predictions and actual measurements of low-temperature serpentinizing fluid chemistry.

ELASTIC NET FOR COX’S PROPORTIONAL HAZARDS MODEL WITH A SOLUTION PATH ALGORITHM

PubMed Central

Wu, Yichao

2012-01-01

For least squares regression, Efron et al. (2004) proposed an efficient solution path algorithm, the least angle regression (LAR). They showed that a slight modification of the LAR leads to the whole LASSO solution path. Both the LAR and LASSO solution paths are piecewise linear. Recently Wu (2011) extended the LAR to generalized linear models and the quasi-likelihood method. In this work we extend the LAR further to handle Cox’s proportional hazards model. The goal is to develop a solution path algorithm for the elastic net penalty (Zou and Hastie (2005)) in Cox’s proportional hazards model. This goal is achieved in two steps. First we extend the LAR to optimizing the log partial likelihood plus a fixed small ridge term. Then we define a path modification, which leads to the solution path of the elastic net regularized log partial likelihood. Our solution path is exact and piecewise determined by ordinary differential equation systems. PMID:23226932

An automated integration-free path-integral method based on Kleinert's variational perturbation theory

NASA Astrophysics Data System (ADS)

Wong, Kin-Yiu; Gao, Jiali

2007-12-01

Based on Kleinert's variational perturbation (KP) theory [Path Integrals in Quantum Mechanics, Statistics, Polymer Physics, and Financial Markets, 3rd ed. (World Scientific, Singapore, 2004)], we present an analytic path-integral approach for computing the effective centroid potential. The approach enables the KP theory to be applied to any realistic systems beyond the first-order perturbation (i.e., the original Feynman-Kleinert [Phys. Rev. A 34, 5080 (1986)] variational method). Accurate values are obtained for several systems in which exact quantum results are known. Furthermore, the computed kinetic isotope effects for a series of proton transfer reactions, in which the potential energy surfaces are evaluated by density-functional theory, are in good accordance with experiments. We hope that our method could be used by non-path-integral experts or experimentalists as a "black box" for any given system.

Unusual solvent effect on a SN2 reaction. A quantum-mechanical and kinetic study of the Menshutkin reaction between 2-amino-1-methylbenzimidazole and iodomethane in the gas phase and in acetonitrile.

PubMed

Melo, André; Alfaia, António J I; Reis, João Carlos R; Calado, António R T

2006-02-02

The quaternization reaction between 2-amino-1-methylbenzimidazole and iodomethane was investigated in the gas phase and in liquid acetonitrile. Both experimental and theoretical techniques were used in this study. In the experimental part of this work, accurate second-order rate constants were obtained for this reaction in acetonitrile from conductivity data in the 293-323 K temperature range and at ambient pressure. From two different empirical equations describing the effect of temperature on reaction rates, thermodynamic functions of activation were calculated. In the theoretical part of this work, the mechanism of this reaction was investigated in the gas phase and in acetonitrile. Two different quantum levels (B3LYP/[6-311++G(3df,3pd)/LanL2DZ]//B3LYP/[6-31G(d)/LanL2DZ] and B3LYP/[6-311++G(3df,3pd)/LanL2DZ]//B3LYP/[6-31+G(d)/LanL2DZ]) were used in the calculations, and the acetonitrile environment was modeled using the polarized continuum model (PCM). In addition, an atoms in molecules (AIM) analysis was made aiming to characterize possible hydrogen bonding. The results obtained by both techniques are in excellent agreement and lead to new insight into the mechanism of the reaction under examination. These include the identification and thermodynamic characterization of the relevant stationary species, the rationalization of the mechanistic role played by the solvent and the amine group adjacent to the nucleophile nitrogen atom, the proposal of alternative paths on the modeled potential energy surfaces, and the origin of the marked non-Arrhenius behavior of the kinetic data in solvent acetonitrile. In particular, the AIM analysis confirmed the operation of intermolecular hydrogen bonds between reactants and between products, both in the gas phase and in solution. It is also concluded that the unusual solvent effect on this Menshutkin reaction stems from the conjunction of a nucleophile possessing a relatively complex chemical structure with a dipolar aprotic solvent that is protophobic.

Modeling the Migration of Fluids in Subduction Zones

NASA Astrophysics Data System (ADS)

Wilson, C. R.; Spiegelman, M.; Van Keken, P. E.; Vrijmoed, J. C.; Hacker, B. R.

2011-12-01

Fluids play a major role in the formation of arc volcanism and the generation of continental crust. Progressive dehydration reactions in the downgoing slab release fluids to the hot overlying mantle wedge, causing flux melting and the migration of melts to the volcanic front. While the qualitative concept is well established, the quantitative details of fluid release and especially that of fluid migration and generation of hydrous melting in the wedge is still poorly understood. Here we present new models of the fluid migration through the mantle wedge for subduction zones. We use an existing set of high resolution metamorphic models (van Keken et al, 2010) to predict the regions of water release from the sediments, upper and lower crust, and upper most mantle. We use this water flux as input for the fluid migration calculation based on new finite element models built on advanced computational libraries (FEniCS/PETSc) for efficient and flexible solution of coupled multi-physics problems. The first generation of one-way coupled models solves for the evolution of porosity and fluid-pressure/flux throughout the slab and wedge given solid flow, viscosity and thermal fields from separate solutions to the incompressible Stokes and energy equations in the mantle wedge. These solutions are verified by comparing to previous benchmark studies (van Keken et al, 2008) and global suites of thermal subduction models (Syracuse et al, 2010). Fluid flow depends on both permeability and the rheology of the slab-wedge system as interaction with rheological variability can induce additional pressure gradients that affect the fluid flow pathways. These non-linearities have been shown to explain laboratory-scale observations of melt band orientation in labratory experiments and numerical simulations of melt localization in shear bands (Katz et al 2006). Our second generation of models dispense with the pre-calculation of incompressible mantle flow and fully couple the now compressible system of mantle and fluid flow equations, introducing complex feedbacks between the rheology, temperature, permeability, strain rate and porosity. Using idealized subduction zone geometries we investigate the effects of this non-linearity and explore the sensitivity of fluid flow paths for a range of fluid flow parameters with emphasis on variability of the location of the volcanic arc with respect to flow paths. We also estimate the expected degrees of hydrous melting using a variety of wet-melting parameterizations (e.g., Katz et al, 2003, Kelley et al, 2010). The current models only include dehydration reactions but work continues on the next generation of models which will include both dehydration and hydration reactions as well as parameterized flux melting in a consistent reactive-flow framework.

Dynamic structural disorder in supported nanoscale catalysts

NASA Astrophysics Data System (ADS)

Rehr, J. J.; Vila, F. D.

2014-04-01

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

A nine-dimensional ab initio global potential energy surface for the H2O+ + H2 → H3O+ + H reaction

NASA Astrophysics Data System (ADS)

Li, Anyang; Guo, Hua

2014-06-01

An accurate full-dimensional global potential energy surface (PES) is developed for the title reaction. While the long-range interactions in the reactant asymptote are represented by an analytical expression, the interaction region of the PES is fit to more than 81 000 of ab initio points at the UCCSD(T)-F12b/AVTZ level using the permutation invariant polynomial neural network approach. Fully symmetric with respect to permutation of all four hydrogen atoms, the PES provides a faithful representation of the ab initio points, with a root mean square error of 1.8 meV or 15 cm-1. The reaction path for this exoergic reaction features an attractive and barrierless entrance channel, a submerged saddle point, a shallow H4O+ well, and a barrierless exit channel. The rate coefficients for the title reaction and kinetic isotope effect have been determined on this PES using quasi-classical trajectories, and they are in good agreement with available experimental data. It is further shown that the H2O+ rotational enhancement of reactivity observed experimentally can be traced to the submerged saddle point. Using our recently proposed Sudden Vector Projection model, we demonstrate that a rotational degree of freedom of the H2O+ reactant is strongly coupled with the reaction coordinate at this saddle point, thus unraveling the origin of the pronounced mode specificity in this reaction.

Uses of Agent-Based Modeling for Health Communication: the TELL ME Case Study.

PubMed

Barbrook-Johnson, Peter; Badham, Jennifer; Gilbert, Nigel

2017-08-01

Government communication is an important management tool during a public health crisis, but understanding its impact is difficult. Strategies may be adjusted in reaction to developments on the ground and it is challenging to evaluate the impact of communication separately from other crisis management activities. Agent-based modeling is a well-established research tool in social science to respond to similar challenges. However, there have been few such models in public health. We use the example of the TELL ME agent-based model to consider ways in which a non-predictive policy model can assist policy makers. This model concerns individuals' protective behaviors in response to an epidemic, and the communication that influences such behavior. Drawing on findings from stakeholder workshops and the results of the model itself, we suggest such a model can be useful: (i) as a teaching tool, (ii) to test theory, and (iii) to inform data collection. We also plot a path for development of similar models that could assist with communication planning for epidemics.

PathCase-SB architecture and database design

PubMed Central

2011-01-01

Background Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Description PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. Conclusions PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. PMID:22070889

Final Technical Report: Mathematical Foundations for Uncertainty Quantification in Materials Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plechac, Petr; Vlachos, Dionisios G.

We developed path-wise information theory-based and goal-oriented sensitivity analysis and parameter identification methods for complex high-dimensional dynamics and in particular of non-equilibrium extended molecular systems. The combination of these novel methodologies provided the first methods in the literature which are capable to handle UQ questions for stochastic complex systems with some or all of the following features: (a) multi-scale stochastic models such as (bio)chemical reaction networks, with a very large number of parameters, (b) spatially distributed systems such as Kinetic Monte Carlo or Langevin Dynamics, (c) non-equilibrium processes typically associated with coupled physico-chemical mechanisms, driven boundary conditions, hybrid micro-macro systems,more » etc. A particular computational challenge arises in simulations of multi-scale reaction networks and molecular systems. Mathematical techniques were applied to in silico prediction of novel materials with emphasis on the effect of microstructure on model uncertainty quantification (UQ). We outline acceleration methods to make calculations of real chemistry feasible followed by two complementary tasks on structure optimization and microstructure-induced UQ.« less

Microstructural analysis of the 2195 aluminum-lithium alloy welds

NASA Technical Reports Server (NTRS)

Talia, George E.

1993-01-01

The principal objective of this research was to explain a tendency of 2195 Al-Li alloy to crack at elevated temperature during welding. Therefore, a study was made on the effect of welding and thermal treatment on the microstructure of Al-Li Alloy 2195. The critical roles of precipitates, boundaries, phases, and other features of the microstructure were inferred from the crack propagation paths and the morphology of fracture surface of the alloy with different microstructures. Particular emphasis was placed on the microstructures generated by the welding process and the mechanisms of crack propagation in such structures. Variation of the welding parameters and thermal treatments were used to alter the micro/macro structures, and they were characterized by optical and scanning electron microscopy. A theoretical model is proposed to explain changes in the microstructure of welded material. This model proposes a chemical reaction in which gases from the air (i.e., nitrogen) release hydrogen inside the alloy. Such a reaction could generate large internal stresses capable to induce porosity and crack-like delamination in the material.

Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions

PubMed Central

Dzierlenga, M.W.; Varga, M.J.

2016-01-01

The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate the full dynamical properties of enzymatic systems. This can lead to misleading results in cases where enzyme motion plays a significant role in the reaction coordinate, which is especially relevant in particle transfer reactions where nuclear tunneling may occur. In this chapter, we outline previous methods, as well as discuss newly developed dynamical methods to interrogate mechanisms of enzymatic particle transfer reactions. These new methods allow for the calculation of free energy barriers and kinetic isotope effects (KIEs) with the incorporation of quantum effects through centroid molecular dynamics (CMD) and the full complement of enzyme dynamics through transition path sampling (TPS). Recent work, summarized in this chapter, applied the method for calculation of free energy barriers to reaction in lactate dehydrogenase (LDH) and yeast alcohol dehydrogenase (YADH). It was found that tunneling plays an insignificant role in YADH but plays a more significant role in LDH, though not dominant over classical transfer. Additionally, we summarize the application of a TPS algorithm for the calculation of reaction rates in tandem with CMD to calculate the primary H/D KIE of YADH from first principles. It was found that the computationally obtained KIE is within the margin of error of experimentally determined KIEs, and corresponds to the KIE of particle transfer in the enzyme. These methods provide new ways to investigate enzyme mechanism with the inclusion of protein and quantum dynamics. PMID:27497161

Characterizing Reactive Flow Paths in Fractured Cement

NASA Astrophysics Data System (ADS)

Wenning, Q. C.; Huerta, N. J.; Hesse, M. A.; Bryant, S. L.

2011-12-01

Geologic carbon sequestration can be a viable method for reducing anthropogenic CO2 flux into the atmosphere. However, the technology must be economically feasible and pose acceptable risk to stakeholders. One key risk is CO2 leakage out of the storage reservoir. Potential driving forces for leakage are the overpressure due to CO2 injection and the buoyancy of free phase CO2. Potential hazards of leakage are contamination of Underground Sources of Drinking Water or the atmosphere and would be deemed an unacceptable risk. Wells potentially provide a fast path for leakage from the reservoir. While the well's cement casing is reactive with CO2 and CO2-saturated brine, the low cement matrix permeability and slow diffusion rate make it unlikely that CO2 will escape through a properly constructed wellbore. However, highly permeable fractures with micrometer scale apertures can occur in cement casings. Reactions that occur in the flow in these fractures can either be self-limiting or self-enhancing. Therefore, understanding the reactive flow is critical to understanding of leakage evolution through these fractures. The goal of our work is to characterize the modification of the flow paths in the fracture due to reaction with acidic brine. With this aim we have characterized both the initial flow path of un-reactive flow and the final flow path after introduction of low-pH acid along the same fracture. Class H cement cores 3-6 cm in length and 2.5 cm diameter are created and a single natural and unique fracture is produced in each core using the Brazilian method. Our experimental fluid is injected at a constant rate into the cement core housed in a Hassler Cell under confining pressure. A solution of red dye and deionized water is pumped through the fracture to stain the un-reactive flow paths. Deionized water is then pumped through the core to limit diffusion of the dye into non-flowing portions of the fracture. After staining the initial flow path, low pH water due to hydrochloric acid (HCL), is pumped through the core at the same rate as the dye. The low pH water is used as a proxy for acidic CO2-saturated brine. Both staining from the un-reactive dye and acid produce visible permanent color alterations on the cement fracture plane. Results show that nearly the entire fracture width is stained by the red dye, with only a few asperities un-dyed. However the low pH HCl forms restricted reacted channels that are a subset of the area open to un-reactive flow, occupying only 10-50% of the entire fracture width. Low pH HCl is believed to be the driving force for the reaction that causes channeling. As acid flows through the fracture, calcium is stripped from the low pH high velocity flow front and precipitates along of the edges of the channel where pH is higher due to the lower flow velocities outside the channel. It is hypothesized that this mineral precipitation restricts the flow into localized channels within the plane of fractures having apertures of tens of micrometers. Reactions restrict the flow path to a smaller fraction of the surface, which may be an indication of self-limiting behavior.

Interfacial reactions between metal and gallium arsenide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, J.C.; Schulz, K.J.; Hsieh, K.C.

1989-10-01

The phase formation sequence for GaAs/metal ternary diffusion couples is discussed. The diffusion path concept is introduced and is used with the phase diagram to understand interfacial reactions between GaAs and metal. The correlation between growth kinetics and interface morphology is discussed. Studies of bulk and thin film couples in two systems, GaAs/Pd and GaAs/Pt, are given to illustrate these concepts.

Formation and decay of tetrazane derivatives--a Car-Parrinello molecular dynamics study.

PubMed

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.

Theoretical insights into the sites and mechanisms for base catalyzed esterification and aldol condensation reactions over Cu.

PubMed

Neurock, Matthew; Tao, Zhiyuan; Chemburkar, Ashwin; Hibbitts, David D; Iglesia, Enrique

2017-04-28

Condensation and esterification are important catalytic routes in the conversion of polyols and oxygenates derived from biomass to fuels and chemical intermediates. Previous experimental studies show that alkanal, alkanol and hydrogen mixtures equilibrate over Cu/SiO 2 and form surface alkoxides and alkanals that subsequently promote condensation and esterification reactions. First-principle density functional theory (DFT) calculations were carried out herein to elucidate the elementary paths and the corresponding energetics for the interconversion of propanal + H 2 to propanol and the subsequent C-C and C-O bond formation paths involved in aldol condensation and esterification of these mixtures over model Cu surfaces. Propanal and hydrogen readily equilibrate with propanol via C-H and O-H addition steps to form surface propoxide intermediates and equilibrated propanal/propanol mixtures. Surface propoxides readily form via low energy paths involving a hydrogen addition to the electrophilic carbon center of the carbonyl of propanal or via a proton transfer from an adsorbed propanol to a vicinal propanal. The resulting propoxide withdraws electron density from the surface and behaves as a base catalyzing the activation of propanal and subsequent esterification and condensation reactions. These basic propoxides can readily abstract the acidic C α -H of propanal to produce the CH 3 CH (-) CH 2 O* enolate, thus initiating aldol condensation. The enolate can subsequently react with a second adsorbed propanal to form a C-C bond and a β-alkoxide alkanal intermediate. The β-alkoxide alkanal can subsequently undergo facile hydride transfer to form the 2-formyl-3-pentanone intermediate that decarbonylates to give the 3-pentanone product. Cu is unique in that it rapidly catalyzes the decarbonylation of the C 2n intermediates to form C 2n-1 3-pentanone as the major product with very small yields of C 2n products. This is likely due to the absence of Brønsted acid sites, present on metal oxide catalysts, that rapidly catalyze dehydration of the hemiacetal or hemiacetalate over decarbonylation. The basic surface propoxide that forms on Cu can also attack the carbonyl of a surface propanal to form propyl propionate. Theoretical results indicate that the rates for both aldol condensation and esterification are controlled by reactions between surface propoxide and propanal intermediates. In the condensation reaction, the alkoxide abstracts the weakly acidic hydrogen of the C α -H of the adsorbed alkanal to form the surface enolate whereas in the esterification reaction the alkoxide nucleophilically attacks the carbonyl group of a vicinal bound alkanal. As both condensation and esterification involve reactions between the same two species in the rate-limiting step, they result in the same rate expression which is consistent with experimental results. The theoretical results indicate that the barriers between condensation and esterification are within 3 kJ mol -1 of one another with esterification being slightly more favored. Experimental results also report small differences in the activation barriers but suggest that condensation is slightly preferred.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Fan; Parker, Jack C.; Brooks, Scott C

This study investigated sorption of uranium and technetium onto aluminum and iron hydroxides during titration of a contaminated groundwater using both Na hydroxide and carbonate as titrants. The contaminated groundwater has a low pH of 3.8 and high concentrations of NO3-, SO42-, Al, Ca, Mg, Mn, trace metals such as Ni and Co, and radionuclides such as U and Tc. During titration, most Al and Fe were precipitated out at pH above ~4.5. U as well as Tc was found to be removed from aqueous phase at pH below ~5.5, but to some extent released at higher pH values. Anmore » earlier geochemical equilibrium reaction path model that considered aqueous complexation and precipitation/dissolution reactions predicted mineral precipitation and adequately described concentration variations of Al, Fe and some other metal cations, but failed to predict sulfate, U and Tc concentrations during titration. Previous studies have shown that Fe- and Al-oxyhydroxides strongly sorb dissolved sulfate, U and Tc species. Therefore, an anion exchange model was developed for the sorption of sulfate, U and Tc onto Al and Fe hydroxides. With the additional consideration of the anion exchange reactions, concentration profiles of sulfate, U and Tc were more accurately predicted. Results of this study indicate that consideration of complex reactions such as sorption/desorption on mixed mineral phases, in addition to hydrolysis and precipitation, could improve the prediction of various contaminants during pre- and post-groundwater treatment practices.« less

Free Energy Contribution Analysis Using Response Kernel Approximation: Insights into the Acylation Reaction of a Beta-Lactamase.

PubMed

Asada, Toshio; Ando, Kanta; Bandyopadhyay, Pradipta; Koseki, Shiro

2016-09-08

A widely applicable free energy contribution analysis (FECA) method based on the quantum mechanical/molecular mechanical (QM/MM) approximation using response kernel approaches has been proposed to investigate the influences of environmental residues and/or atoms in the QM region on the free energy profile. This method can evaluate atomic contributions to the free energy along the reaction path including polarization effects on the QM region within a dramatically reduced computational time. The rate-limiting step in the deactivation of the β-lactam antibiotic cefalotin (CLS) by β-lactamase was studied using this method. The experimentally observed activation barrier was successfully reproduced by free energy perturbation calculations along the optimized reaction path that involved activation by the carboxylate moiety in CLS. It was found that the free energy profile in the QM region was slightly higher than the isolated energy and that two residues, Lys67 and Lys315, as well as water molecules deeply influenced the QM atoms associated with the bond alternation reaction in the acyl-enzyme intermediate. These facts suggested that the surrounding residues are favorable for the reactant complex and prevent the intermediate from being too stabilized to proceed to the following deacylation reaction. We have demonstrated that the free energy contribution analysis should be a useful method to investigate enzyme catalysis and to facilitate intelligent molecular design.

Thermal Decomposition Mechanism of CL-20 at Different Temperatures by ReaxFF Reactive Molecular Dynamics Simulations.

PubMed

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 .

Limitations to maximum running speed on flat curves.

PubMed

Chang, Young-Hui; Kram, Rodger

2007-03-01

Why is maximal running speed reduced on curved paths? The leading explanation proposes that an increase in lateral ground reaction force necessitates a decrease in peak vertical ground reaction force, assuming that maximum leg extension force is the limiting factor. Yet, no studies have directly measured these forces or tested this critical assumption. We measured maximum sprint velocities and ground reaction forces for five male humans sprinting along a straight track and compared them to sprints along circular tracks of 1, 2, 3, 4 and 6 m radii. Circular track sprint trials were performed either with or without a tether that applied centripetal force to the center of mass. Sprinters generated significantly smaller peak resultant ground reaction forces during normal curve sprinting compared to straight sprinting. This provides direct evidence against the idea that maximum leg extension force is always achieved and is the limiting factor. Use of the tether increased sprint speed, but not to expected values. During curve sprinting, the inside leg consistently generated smaller peak forces compared to the outside leg. Several competing biomechanical constraints placed on the stance leg during curve sprinting likely make the inside leg particularly ineffective at generating the ground reaction forces necessary to attain maximum velocities comparable to straight path sprinting. The ability of quadrupeds to redistribute function across multiple stance legs and decouple these multiple constraints may provide a distinct advantage for turning performance.

Evolution of Secondary Phases Formed upon Solidification of a Ni-Based Alloy

NASA Astrophysics Data System (ADS)

Zuo, Qiang; Liu, Feng; Wang, Lei; Chen, Changfeng

2013-07-01

The solidification of UNS N08028 alloy subjected to different cooling rates was studied, where primary austenite dendrites occur predominantly and different amounts of sigma phase form in the interdendritic regions. The solidification path and elemental segregation upon solidification were simulated using the CALPHAD method, where THERMO-CALC software packages and two classical segregation models were employed to predict the real process. It is thus revealed that the interdendritic sigma phase is formed via eutectic reaction at the last stage of solidification. On this basis, an analytical model was developed to predict the evolution of nonequilibrium eutectic phase, while the isolated morphology of sigma phase can be described using divorced eutectic theory. Size, fraction, and morphology of the sigma phase were quantitatively studied by a series of experiments; the results are in good agreement with the model prediction.

PHITS-2.76, Particle and Heavy Ion Transport code System

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-08-01

Version 03 PHITS can deal with the transport of almost all particles (nucleons, nuclei, mesons, photons, and electrons) over wide energy ranges, using several nuclear reaction models and nuclear data libraries. Geometrical configuration of the simulation can be set with GG (General Geometry) or CG (Combinatorial Geometry). Various quantities such as heat deposition, track length and production yields can be deduced from the simulation, using implemented estimator functions called "tally". The code also has a function to draw 2D and 3D figures of the calculated results as well as the setup geometries, using a code ANGEL. The physical processes includedmore » in PHITS can be divided into two categories, transport process and collision process. In the transport process, PHITS can simulate motion of particles under external fields such as magnetic and gravity. Without the external fields, neutral particles move along a straight trajectory with constant energy up to the next collision point. However, charge particles interact many times with electrons in the material losing energy and changing direction. PHITS treats ionization processes not as collision but as a transport process, using the continuous-slowing-down approximation. The average stopping power is given by the charge density of the material and the momentum of the particle taking into account the fluctuations of the energy loss and the angular deviation. In the collision process, PHITS can simulate the elastic and inelastic interactions as well as decay of particles. The total reaction cross section, or the life time of the particle is an essential quantity in the determination of the mean free path of the transport particle. According to the mean free path, PHITS chooses the next collision point using the Monte Carlo method. To generate the secondary particles of the collision, we need the information of the final states of the collision. For neutron induced reactions in low energy region, PHITS employs the cross sections from evaluated nuclear data libraries JENDL-4.0 (Shibata et al 2011). For high energy neutrons and other particles, we have incorporated several models such as JAM (Nara et al 1999), INCL (Cugnon et al 2011), INCL-ELF (Sawada et al 2012) and JQMD (Niita et al 1995) to simulate nuclear reactions up to 100 GeV/u. The special features of PHITS are the event generator mode (Iwamoto et al 2007) and the microdosimetric function (Sato et al 2009). Owing to the event generator mode, PHITS can determine the profiles of all secondary particles generated from a single nuclear interaction even using nuclear data libraries, taking the momentum and energy conservations into account. The microdosimetric function gives the probability densities of deposition energy in microscopic sites such as lineal energy y and specific energy z, using the mathematical model developed based on the results of the track structure simulation. These features are very important for various purposes such as the estimations of soft-error rates of semi-conductor devices induced by neutrons, and relative biological effectiveness of charged particles. From version 2.64, Prompt gamma spectrum and isomer production rates can be precisely estimated, owing to the implementation of EBITEM (ENSDF-Based Isomeric Transition and isomEr production Model). The photo-nuclear reaction model was improved up to 140 MeV. From version 2.76, electron and photon transport algorithm based on EGS5 (Hirayama et al. 2005) was incorporated. Models for describing photo-nuclear reaction above 140 MeV and muon-nuclear reaction were implemented. Event-generator mode version 2 was developed. Relativistic theory can be considered in the JQMD model.« less

Path Flow Estimation Using Time Varying Coefficient State Space Model

NASA Astrophysics Data System (ADS)

Jou, Yow-Jen; Lan, Chien-Lun

2009-08-01

The dynamic path flow information is very crucial in the field of transportation operation and management, i.e., dynamic traffic assignment, scheduling plan, and signal timing. Time-dependent path information, which is important in many aspects, is nearly impossible to be obtained. Consequently, researchers have been seeking estimation methods for deriving valuable path flow information from less expensive traffic data, primarily link traffic counts of surveillance systems. This investigation considers a path flow estimation problem involving the time varying coefficient state space model, Gibbs sampler, and Kalman filter. Numerical examples with part of a real network of the Taipei Mass Rapid Transit with real O-D matrices is demonstrated to address the accuracy of proposed model. Results of this study show that this time-varying coefficient state space model is very effective in the estimation of path flow compared to time-invariant model.

Predictions of diagenetic reactions in the presence of organic acids

NASA Astrophysics Data System (ADS)

Harrison, Wendy J.; Thyne, Geoffrey D.

1992-02-01

Stability constants have been estimated for cation complexes with anions of monofunctional and difunctional acids (combinations of Ca, Mg, Fe, Al, Sr, Mn, U, Th, Pb, Cu, Zn with formate, acetate, propionate, oxalate, malonate, succinate, and salicylate) between 0 and 200°C. Difunctional acid anions form much more stable complexes than monofunctional acid anions with aluminum; the importance of the aluminum-acetate complex is relatively minor in comparison to aluminum oxalate and malonate complexes. Divalent metal cations such as Mg, Ca, and Fe form more stable complexes with acetate than with difunctional acid anions. Aluminum-oxalate can dominate the species distribution of aluminum under acidic pH conditions, whereas the divalent cation-acetate and oxalate complexes rarely account for more than 60% of the total dissolved cation, and then only in more alkaline waters. Mineral thermodynamic affinities were calculated using the reaction path model EQ3/6 for waters having variable organic acid anion (OAA) contents under conditions representative of those found during normal burial diagenesis. The following scenarios are possible: 1) K-feldspar and albite are stable, anorthite dissolves 2) All feldpars are stable 3) Carbonates can be very unstable to slightly unstable, but never increase in stability. Organic acid anions are ineffective at neutral to alkaline pH in modifying stabilities of aluminosilicate minerals whereas the anions are variably effective under a wide range of pH in modifying carbonate mineral stabilities. Reaction path calculations demonstrate that the sequence of mineral reactions occurring in an arkosic sandstone-fluid system is only slightly modified by the presence of OAA. A spectrum of possible sandstone alteration mineralogies can be obtained depending on the selected boundary conditions: EQ3/6 predictions include quartz overgrowth, calcite replacement of plagioclase, albitization of plagioclase, and the formation of porosity-occluding calcite cement, smectite, and illite, all of which are commonly documented in rocks. Under some circumstances, OAA-bearing waters are less effective at producing porosity in an arkosic sandstone than are OAA-free waters. In the scenarios modeled in this study the role of OAA in fluid-rock interactions is to contribute to the total alteration assemblage but not necessarily to dominate it, except under exceptional circumstances that might include, for example, hydrocarbon contaminant plumes in aquifers, wetland environments, and within hydrocarbon source-rocks.

Nucleation of intragranular ferrite in Fe-Ni-P alloys

NASA Astrophysics Data System (ADS)

Narayan, C.; Goldstein, J. I.

1984-05-01

The nucleation of intragranular ferrite from austenite in Fe-Ni-P alloys was investigated in order to understand the development of the Widmanstätten pattern in iron meteorites. Alloys containing 5 to 10 wt pct Ni and 0 to 1 wt pct P were used to simulate iron meteorite compositions. In the isothermal and controlled cooling experiments the reaction path γ → α + γ serves only to nucleate ferrite along austenite grain boundaries. It is necessary for (FeNi)3P to be present within y grains in order to nucleate intragranular ferrite. The reaction path γ → γ + phosphide → α + γ + phosphide yields rod shaped ferrite nuclei that bear a near Kurdjumov-Sachs orientation relationship with the surrounding matrix. The precipitation of ferrite, both along grain boundaries and within the austenite grains, is suppressed in the absence of P.

The effects of aging on postural control and selective attention when stepping down while performing a concurrent auditory response task.

PubMed

Tsang, William W N; Lam, Nazca K Y; Lau, Kit N L; Leung, Harry C H; Tsang, Crystal M S; Lu, Xi

2013-12-01

To investigate the effects of aging on postural control and cognitive performance in single- and dual-tasking. A cross-sectional comparative design was conducted in a university motion analysis laboratory. Young adults (n = 30; age 21.9 ± 2.4 years) and older adults (n = 30; age 71.9 ± 6.4 years) were recruited. Postural control after stepping down was measured with and without performing a concurrent auditory response task. Measurement included: (1) reaction time and (2) error rate in performing the cognitive task; (3) total sway path and (4) total sway area after stepping down. Our findings showed that the older adults had significantly longer reaction times and higher error rates than the younger subjects in both the single-tasking and dual-tasking conditions. The older adults had significantly longer reaction times and higher error rates when dual-tasking compared with single-tasking, but the younger adults did not. The older adults demonstrated significantly less total sway path, but larger total sway area in single-leg stance after stepping down than the young adults. The older adults showed no significant change in total sway path and area between the dual-tasking and when compared with single-tasking conditions, while the younger adults showed significant decreases in sway. Older adults prioritize postural control by sacrificing cognitive performance when faced with dual-tasking.

Experiment and simulation study on the effects of cement minerals on the water-rock-CO2 interaction during CO2 geological storage

NASA Astrophysics Data System (ADS)

Liu, N.; Cheng, J.

2016-12-01

The CO2 geological storage is one of the most promising technology to mitigate CO2 emission. The fate of CO2 underground is dramatically affected by the CO2-water-rock interaction, which are mainly dependent on the initial aquifer mineralogy and brine components. The cement minerals are common materials in sandstone reservoir but few attention has been paid for its effects on CO2-water-rock interaction. Five batch reactions, in which 5% cement minerals were assigned to be quartz, calcite, dolomite, chlorite and Ca-montmorillonite, respectively, were conducted to understanding the cement minerals behaviors and its corresponding effects on the matrix minerals alterations during CO2 geological storage. Pure mineral powders were selected to mix and assemble the 'sandstone rock' with different cement components meanwhile keeping the matrix minerals same for each group as 70% quartz, 20% K-feldspar and 5% albite. These `rock' reacted with 750ml deionized water and CO2 under 180° and 18MPa for 15 days, during which the water chemistry evolution and minerals surface micromorphology changes has been monitored. The minerals saturation indexes calculation and phase diagram as well as the kinetic models were made by PHREEQC to uncover the minerals reaction paths. The experiment results indicated that the quartz got less eroded, on the contrary, K-feldspar and albite continuously dissolved to favor the gibbsite and kaolinite precipitations. The carbonates cement minerals quickly dissolved to reach equilibrium with the pH buffered and in turn suppressed the alkali feldspar dissolutions. No carbonates minerals precipitations occurred until the end of reactions for all groups. The simulation results were basically consistent with the experiment record but failed to simulate the non-stoichiometric reactions and the minerals kinetic rates seemed underestimated at the early stage of reactions. The cement minerals significantly dominated the reaction paths during CO2 geological storage and its effects on the CO2-water-rock interaction should be focused no matter for the benefit of injection sustainability or carbon sequestration capability. And more cement minerals such as ankerite should be included and the reservoir quality changes should also be taken consideration in the further study.

A kinetic rate model for crystalline basalt dissolution at temperature and pressure conditions relevant for geologic CO2 sequestration

NASA Astrophysics Data System (ADS)

Pollyea, R.; Rimstidt, J. D.

2016-12-01

Geologic carbon sequestration in terrestrial basalt reservoirs is predicated on permanent CO2 trapping through CO2-water-rock dissolution reactions followed by carbonate precipitation. Bench-scale experiments have shown these reaction paths to be rapid, occurring on a timescale 100 - 102 years. Moreover, recent results from the CarbFix basalt sequestration pilot project in Iceland demonstrate >95% CO2 isolation two years after a small-scale injection. In order to assess the viability of basalt sequestration worldwide (e.g., Deccan Traps, Columbia Plateau, etc.), flexible simulation tools are required that distill the dissolution reactions into a user-friendly format that is readily transmissible to existing reactive transport numerical simulators. In the present research, we combine experimental results extant in the literature for Icelandic basalt to develop kinetic rate models describing the pH-dependent dissolution of (1) basaltic glass and (2) an aggregate mineral assemblage for crystalline basalt comprising olivine, pyroxene, and plagioclase phases. In order to utilize these kinetic rate models with numerical simulation, a thermodynamic solubility model for each phase is developed for use with the reactive transport simulation code, TOUGHREACT. We use reactive transport simulation in a simple 1-D reactor to compare dissolution of the aggregate crystalline basalt phase with the traditional formulation comprising individual mineral phases for the crystalline basalt. Simulation results are in general agreement, illustrating the efficacy of this simplified approach for modeling basalt dissolution at temperature and pressure conditions typical of geologic CO2 reservoirs. Moreover, this approach may be of value to investigators seeking dissolution models for crystalline basalt in other mafic provinces.

Nuclear Masses in the A=80 Region of Nuclei

NASA Astrophysics Data System (ADS)

Cuka, N.; Gadala-Maria, A.; Aprahamian, A.

1996-05-01

Nucleosynthesis in explosive hydrogen burning at high temperatures above 8x10^8 K is characterized by the rp-process. A recent study^1 of the reaction flow and their associated time scales showed that the reaction path may in fact proceed well beyond the A=80 region of nuclei. An accurate simulation of the nucleosynthesis and energy generation of this process strongly depends on reliable nuclear physics input parameters such as masses, lifetimes, and reaction rates. We have extended the use of the simple P-parametrization^2,3 that had been applied to the characterization of the structure contributions to the nuclear masses in the actinides to include the A=80 region. The results will be presented along with predictions of masses for presently unknown masses of nuclei along the rp-process path. ^1 R. Wallace and S. Woosley, Ap. J. Suppl. 45, 389 (81). ^2 R. F. Casten, D.S. Brenner and P.E. Haustein, Phys. Rev. Lett. 58, 658 (87). ^3 P. Haustein, D.S. Brenner and R.F. Casten, Phys. Rev. C 38, 467 (88).

Using a Family of Dividing Surfaces Normal to the Minimum EnergyPath for Quantum Instanton Rate Constants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yimin; Miller, Wlliam H.

2006-02-22

One of the outstanding issues in the quantum instanton (QI) theory (or any transition state-type theory) for thermal rate constants of chemical reactions is the choice of an appropriate ''dividing surface'' (DS) that separates reactants and products. (In the general version of the QI theory, there are actually two dividing surfaces involved.) This paper shows one simple and general way for choosing DS's for use in QI Theory, namely using the family of (hyper) planes normal to the minimum energy path (MEP) on the potential energy surface at various distances s along it. Here the reaction coordinate is not onemore » of the dynamical coordinates of the system (which will in general be the Cartesian coordinates of the atoms), but rather simply a parameter which specifies the DS. It is also shown how this idea can be implemented for an N-atom system in 3d space in a way that preserves overall translational and rotational invariance. Numerical application to a simple system (the colliner H + H{sub 2} reaction) is presented to illustrate the procedure.« less

A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Trong-Nghia; Department of Physical Chemistry, Hanoi University of Science and Technology, Hanoi; Putikam, Raghunath

2015-03-28

We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} groupmore » by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.« less

Theoretical survey of the reaction between osmium and acetaldehyde

NASA Astrophysics Data System (ADS)

Dai, Guo-Liang; Wang, Chuan-Feng

2012-05-01

The mechanism of the reaction of osmium atom with acetaldehyde has been investigated with a DFT approach. All the stationary points are determined at the UB3LYP/ sdd/6-311++G** level of the theory. Both ground and excited state potential energy surfaces are investigated in detail. The present results show that the title reaction start with the formation of a CH3CHO-metal complex followed by C-C, aldehyde C-H, C-O, and methyl C-H activation. These reactions can lead to four different products (HOsCH3 + CO, OsCO + CH4, OsCOCH3 + H, and OsO + C2H4). The minimum energy reaction path is found to involve the spin inversion in the initial reaction step. This potential energy curve-crossing dramatically affects reaction exothermic. The present results may be helpful in understanding the mechanism of the title reaction and further experimental investigation of the reaction.

Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.

PubMed

Banerjee, Rahul; Cukier, Robert I

2014-03-20

Conformational states and their interconversion pathways of the zwitterionic form of the pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular dynamics (MD) trajectory is used to construct a Markov state model (MSM) based on dihedral space clustering of the trajectory, and transition path theory (TPT) is applied to identify pathways between open and closed conformers. In the MD trajectory, only four of the eight backbone dihedrals exhibit bistable behavior. Defining a conformer as the string XXXX with X = "+" or "-" denoting, respectively, positive or negative values of a given dihedral angle and obtaining the populations of these conformers shows that only four conformers are highly populated, implying a strong correlation among these dihedrals. Clustering in dihedral space to construct the MSM finds the same four bistable dihedral angles. These state populations are very similar to those found directly from the MD trajectory. TPT is used to obtain pathways, parametrized by committor values, in dihedral state space that are followed in transitioning from closed to open states. Pathway costs are estimated by introducing a kinetics-based procedure that orders pathways from least (shortest) to greater cost paths. The least costly pathways in dihedral space are found to only involve the same XXXX set of dihedral angles, and the conformers accessed in the closed to open transition pathways are identified. For these major pathways, a correlation between reaction path progress (committors) and the end-to-end distance is identified. A dihedral space principal component analysis of the MD trajectory shows that the first three modes capture most of the overall fluctuation, and pick out the same four dihedrals having essentially all the weight in those modes. A MSM based on root-mean-square backbone clustering was also carried out, with good agreement found with dihedral clustering for the static information, but with results that differ significantly for the pathway analysis.

Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods.

PubMed

Gozem, Samer; Melaccio, Federico; Lindh, Roland; Krylov, Anna I; Granovsky, Alexander A; Angeli, Celestino; Olivucci, Massimo

2013-10-08

The photoisomerization of the retinal chromophore of visual pigments proceeds along a complex reaction coordinate on a multidimensional surface that comprises a hydrogen-out-of-plane (HOOP) coordinate, a bond length alternation (BLA) coordinate, a single bond torsion and, finally, the reactive double bond torsion. These degrees of freedom are coupled with changes in the electronic structure of the chromophore and, therefore, the computational investigation of the photochemistry of such systems requires the use of a methodology capable of describing electronic structure changes along all those coordinates. Here, we employ the penta-2,4-dieniminium (PSB3) cation as a minimal model of the retinal chromophore of visual pigments and compare its excited state isomerization paths at the CASSCF and CASPT2 levels of theory. These paths connect the cis isomer and the trans isomer of PSB3 with two structurally and energetically distinct conical intersections (CIs) that belong to the same intersection space. MRCISD+Q energy profiles along these paths provide benchmark values against which other ab initio methods are validated. Accordingly, we compare the energy profiles of MRPT2 methods (CASPT2, QD-NEVPT2, and XMCQDPT2) and EOM-SF-CC methods (EOM-SF-CCSD and EOM-SF-CCSD(dT)) to the MRCISD+Q reference profiles. We find that the paths produced with CASSCF and CASPT2 are topologically and energetically different, partially due to the existence of a "locally excited" region on the CASPT2 excited state near the Franck-Condon point that is absent in CASSCF and that involves a single bond, rather than double bond, torsion. We also find that MRPT2 methods as well as EOM-SF-CCSD(dT) are capable of quantitatively describing the processes involved in the photoisomerization of systems like PSB3.

Analysis of the theory of high energy ion transport

NASA Technical Reports Server (NTRS)

Wilson, J. W.

1977-01-01

Procedures for the approximation of the transport of high-energy ions are discussed on the basis of available data on ion nuclear reactions. A straightahead approximation appears appropriate for space applications. The assumption that the secondary-ion-fragment velocity is equal to that of the fragmenting nucleus is inferior to straightahead theory but is of sufficient accuracy if the primary ions display a broad energy spectrum. An iterative scheme for the solution of the inhomogenous integral transport equations holds promise for practical calculation. A model calculation shows that multiple charged ion fragments penetrate to greater depths in comparison with the free path of a primary heavy ion.

Prebiotic NH3 Formation: Insights from Simulations.

PubMed

Stirling, András; Rozgonyi, Tamás; Krack, Matthias; Bernasconi, Marco

2016-02-15

Simulations of prebiotic NH₃ synthesis from NO₃⁻ and NO₂⁻ on pyrite surfaces under hydrothermal conditions are reported. Ab initio metadynamics calculations have successfully explored the full reaction path which explains earlier experimental observations. We have found that the reaction mechanism can be constructed from stepwise single atom transfers which are compatible with the expected reaction time scales. The roles of the hot-pressurized water and of the pyrite surfaces have been addressed. The mechanistic picture that emerged from the simulations strengthens the theory of chemoautotrophic origin of life by providing plausible reaction pathways for the formation of ammonia within the iron-sulfur-world scenario.

Transition-state optimization by the free energy gradient method: Application to aqueous-phase Menshutkin reaction between ammonia and methyl chloride

NASA Astrophysics Data System (ADS)

Hirao, Hajime; Nagae, Yukihiko; Nagaoka, Masataka

2001-11-01

The transition state (TS) for the Menshutkin reaction H 3N+CH 3Cl→H 3NCH 3++Cl - in aqueous solution was located on the free energy surface (FES) by the free energy gradient (FEG) method. The solute-solvent system was described by a hybrid quantum mechanical and molecular mechanical (QM/MM) method. The reaction path in water was found to deviate largely from that in the gas phase. It was concluded that, in such a reaction including charge separation, TS structure optimization on an FES is inevitable for obtaining valid information about a TS in solution.

Path generation algorithm for UML graphic modeling of aerospace test software

NASA Astrophysics Data System (ADS)

Qu, MingCheng; Wu, XiangHu; Tao, YongChao; Chen, Chao

2018-03-01

Aerospace traditional software testing engineers are based on their own work experience and communication with software development personnel to complete the description of the test software, manual writing test cases, time-consuming, inefficient, loopholes and more. Using the high reliability MBT tools developed by our company, the one-time modeling can automatically generate test case documents, which is efficient and accurate. UML model to describe the process accurately express the need to rely on the path is reached, the existing path generation algorithm are too simple, cannot be combined into a path and branch path with loop, or too cumbersome, too complicated arrangement generates a path is meaningless, for aerospace software testing is superfluous, I rely on our experience of ten load space, tailor developed a description of aerospace software UML graphics path generation algorithm.

Lattice Boltzmann simulation of dissolution-induced changes in permeability and porosity in 3D CO2 reactive transport

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.

A two-component rain model for the prediction of attenuation and diversity improvement

NASA Technical Reports Server (NTRS)

Crane, R. K.

1982-01-01

A new model was developed to predict attenuation statistics for a single Earth-satellite or terrestrial propagation path. The model was extended to provide predictions of the joint occurrences of specified or higher attenuation values on two closely spaced Earth-satellite paths. The joint statistics provide the information required to obtain diversity gain or diversity advantage estimates. The new model is meteorologically based. It was tested against available Earth-satellite beacon observations and terrestrial path measurements. The model employs the rain climate region descriptions of the Global rain model. The rms deviation between the predicted and observed attenuation values for the terrestrial path data was 35 percent, a result consistent with the expectations of the Global model when the rain rate distribution for the path is not used in the calculation. Within the United States the rms deviation between measurement and prediction was 36 percent but worldwide it was 79 percent.

Investigation of in-body path loss in different human subjects for localization of capsule endoscope.

PubMed

Ara, Perzila; Cheng, Shaokoon; Heimlich, Michael; Dutkiewicz, Eryk

2015-01-01

Recent developments in capsule endoscopy have highlighted the need for accurate techniques to estimate the location of a capsule endoscope. A highly accurate location estimation of a capsule endoscope in the gastrointestinal (GI) tract in the range of several millimeters is a challenging task. This is mainly because the radio-frequency signals encounter high loss and a highly dynamic channel propagation environment. Therefore, an accurate path-loss model is required for the development of accurate localization algorithms. This paper presents an in-body path-loss model for the human abdomen region at 2.4 GHz frequency. To develop the path-loss model, electromagnetic simulations using the Finite-Difference Time-Domain (FDTD) method were carried out on two different anatomical human models. A mathematical expression for the path-loss model was proposed based on analysis of the measured loss at different capsule locations inside the small intestine. The proposed path-loss model is a good approximation to model in-body RF propagation, since the real measurements are quite infeasible for the capsule endoscopy subject.

Catalytic reactor for promoting a chemical reaction on a fluid passing therethrough

NASA Technical Reports Server (NTRS)

Roychoudhury, Subir (Inventor); Pfefferle, William C. (Inventor)

2001-01-01

A catalytic reactor with an auxiliary heating structure for raising the temperature of a fluid passing therethrough whereby the catalytic reaction is promoted. The invention is a apparatus employing multiple electrical heating elements electrically isolated from one another by insulators that are an integral part of the flow path. The invention provides step heating of a fluid as the fluid passes through the reactor.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, Albert F., E-mail: wagner@anl.gov; Dawes, Richard; Continetti, Robert E.

The measured H(D)OCO survival fractions of the photoelectron-photofragment coincidence experiments by the Continetti group are qualitatively reproduced by tunneling calculations to H(D) + CO{sub 2} on several recent ab initio potential energy surfaces for the HOCO system. The tunneling calculations involve effective one-dimensional barriers based on steepest descent paths computed on each potential energy surface. The resulting tunneling probabilities are converted into H(D)OCO survival fractions using a model developed by the Continetti group in which every oscillation of the H(D)-OCO stretch provides an opportunity to tunnel. Four different potential energy surfaces are examined with the best qualitative agreement with experimentmore » occurring for the PIP-NN surface based on UCCSD(T)-F12a/AVTZ electronic structure calculations and also a partial surface constructed for this study based on CASPT2/AVDZ electronic structure calculations. These two surfaces differ in barrier height by 1.6 kcal/mol but when matched at the saddle point have an almost identical shape along their reaction paths. The PIP surface is a less accurate fit to a smaller ab initio data set than that used for PIP-NN and its computed survival fractions are somewhat inferior to PIP-NN. The LTSH potential energy surface is the oldest surface examined and is qualitatively incompatible with experiment. This surface also has a small discontinuity that is easily repaired. On each surface, four different approximate tunneling methods are compared but only the small curvature tunneling method and the improved semiclassical transition state method produce useful results on all four surfaces. The results of these two methods are generally comparable and in qualitative agreement with experiment on the PIP-NN and CASPT2 surfaces. The original semiclassical transition state theory method produces qualitatively incorrect tunneling probabilities on all surfaces except the PIP. The Eckart tunneling method uses the least amount of information about the reaction path and produces too high a tunneling probability on PIP-NN surface, leading to survival fractions that peak at half their measured values.« less

Intelligent path loss prediction engine design using machine learning in the urban outdoor environment

NASA Astrophysics Data System (ADS)

Wang, Ruichen; Lu, Jingyang; Xu, Yiran; Shen, Dan; Chen, Genshe; Pham, Khanh; Blasch, Erik

2018-05-01

Due to the progressive expansion of public mobile networks and the dramatic growth of the number of wireless users in recent years, researchers are motivated to study the radio propagation in urban environments and develop reliable and fast path loss prediction models. During last decades, different types of propagation models are developed for urban scenario path loss predictions such as the Hata model and the COST 231 model. In this paper, the path loss prediction model is thoroughly investigated using machine learning approaches. Different non-linear feature selection methods are deployed and investigated to reduce the computational complexity. The simulation results are provided to demonstratethe validity of the machine learning based path loss prediction engine, which can correctly determine the signal propagation in a wireless urban setting.

Metabolic Plasticity and Inter-Compartmental Interactions in Rice Metabolism: An Analysis from Reaction Deletion Study.

PubMed

Shaw, Rahul; Kundu, Sudip

2015-01-01

More than 20% of the total caloric intake of human population comes from rice. The expression of rice genes and hence, the concentration of enzymatic proteins might vary due to several biotic and abiotic stresses. It in turn, can influence the overall metabolism and survivability of rice plant. Thus, understanding the rice cellular metabolism, its plasticity and potential readjustments under different perturbations can help rice biotechnologists to design efficient rice cultivars. Here, using the flux balance analysis (FBA) method, with the help of in-silico reaction deletion strategy, we study the metabolic plasticity of genome-scale metabolic model of rice leaf. A set of 131 reactions, essential for the production of primary biomass precursors is identified; deletion of any of them can inhibit the overall biomass production. Usability Index (IU) for the rest of the reactions are estimated and based on this parameter, they are classified into three categories-maximally-favourable, quasi-favourable and unfavourable for the primary biomass production. The lower value of 1 - IU of a reaction suggests that the cell cannot easily bypass it for biomass production. While some of the alternative paths are energetically equally efficient, others demand for higher photon. The variations in (i) ATP/NADPH ratio, (ii) exchange of metabolites through chloroplastic transporters and (iii) total biomass production are also presented here. Mutual metabolic dependencies of different cellular compartments are also demonstrated.

Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution.

PubMed

Liu, Peng; Wang, Qiong; Niu, Meixing; Wang, Dunyou

2017-08-10

Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.

Think-Aloud Process Superior to Thought-Listing in Increasing Children's Critical Processing of Advertising

ERIC Educational Resources Information Center

Rozendaal, Esther; Buijzen, Moniek; Valkenburg, Patti M.

2012-01-01

This study develops and tests a model of children's critical processing of advertising. Within this model, 2 paths to reduced advertising susceptibility (i.e., attitude toward the advertised brand) were hypothesized: a cognitive path and an affective path. The secondary aim was to compare these paths for different thought verbalization processes:…

Nonadiabatic effects in C-Br bond scission in the photodissociation of bromoacetyl chloride

NASA Astrophysics Data System (ADS)

Valero, Rosendo; Truhlar, Donald G.

2006-11-01

Bromoacetyl chloride photodissociation has been interpreted as a paradigmatic example of a process in which nonadiabatic effects play a major role. In molecular beam experiments by Butler and co-workers [J. Chem. Phys. 95, 3848 (1991); J. Chem. Phys. 97, 355 (1992)], BrCH2C(O )Cl was prepared in its ground electronic state (S0) and excited with a laser at 248nm to its first excited singlet state (S1). The two main ensuing photoreactions are the ruptures of the C-Cl bond and of the C-Br bond. A nonadiabatic model was proposed in which the C-Br scission is strongly suppressed due to nonadiabatic recrossing at the barrier formed by the avoided crossing between the S1 and S2 states. Recent reduced-dimensional dynamical studies lend support to this model. However, another interpretation that has been given for the experimental results is that the reduced probability of C-Br scission is a consequence of incomplete intramolecular energy redistribution. To provide further insight into this problem, we have studied the energetically lowest six singlet electronic states of bromoacetyl chloride by using an ab initio multiconfigurational perturbative electronic structure method. Stationary points (minima and saddle points) and minimum energy paths have been characterized on the S0 and S1 potential energy surfaces. The fourfold way diabatization method has been applied to transform five adiabatic excited electronic states to a diabatic representation. The diabatic potential energy matrix of the first five excited singlet states has been constructed along several cuts of the potential energy hypersurfaces. The thermochemistry of the photodissociation reactions and a comparison with experimental translational energy distributions strongly suggest that nonadiabatic effects dominate the C-Br scission, but that the reaction proceeds along the energetically allowed diabatic pathway to excited-state products instead of being nonadiabatically suppressed. This conclusion is also supported by the low values of the diabatic couplings on the C-Br scission reaction path. The methodology established in the present study will be used for the construction of global potential energy surfaces suitable for multidimensional dynamics simulations to test these preliminary interpretations.

Foundations and latest advances in replica exchange transition interface sampling.

PubMed

Cabriolu, Raffaela; Skjelbred Refsnes, Kristin M; Bolhuis, Peter G; van Erp, Titus S

2017-10-21

Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations.

Foundations and latest advances in replica exchange transition interface sampling

NASA Astrophysics Data System (ADS)

Cabriolu, Raffaela; Skjelbred Refsnes, Kristin M.; Bolhuis, Peter G.; van Erp, Titus S.

2017-10-01

Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations.

Impact of (α, n) reactions on weak r-process in neutrino-driven winds

NASA Astrophysics Data System (ADS)

Bliss, J.; Arcones, A.; Montes, F.; Pereira, J.

2017-05-01

After a successful core-collapse supernova, a neutrino-driven wind develops where it is possible to synthesize lighter heavy elements (30 < Z < 45). In the early galaxy, the origin of these elements is associated with the r-process and to an additional process. Here we assume that the additional process corresponds to the weak r-process (sometimes referred to as alpha-process) taking place in neutrino-driven winds. Based on a trajectory obtained from hydrodynamical simulations we study the astrophysics and nuclear physics uncertainties of a weak r-process with our main focus on the (α, n) reactions. These reactions are critical to redistribute the matter and allow it to move from light to heavy elements after nuclear statistical equilibrium freezes out. In this first sensitivity study, we vary all (α, n) reactions by given constant factors which are justified based on the uncertainties of the statistical model and its nuclear physics input, mainly alpha optical potentials for weak r-process conditions. Our results show that (α, n) rate uncertainties are indeed crucial to predict abundances. Therefore, further studies will follow to identify individual critical reactions. Since the nucleosynthesis path is close to stability, these reactions can be measured in the near future. Since much of the other nuclear data for the weak r-process are known, the reduction in nuclear physics uncertainties provided by these experiments will allow astronomical observations to directly constrain the astronomical conditions in the wind.

O/S-1/ interactions - The product channels. [collisional electron quenching and chemical reaction pathway frequencies

NASA Technical Reports Server (NTRS)

Slanger, T. G.; Black, G.

1978-01-01

The first measurements are reported of the reaction pathways for the interaction between oxygen atoms in the 4.19 eV S-1 state, and four molecules, N2O, CO2, H2O, and NO. Distinction is made between three possible paths - quenching to O(D-1), quenching to O(P-3), and chemical reaction. With N2O, the most reasonable interpretation of the data indicates that there no reaction, in sharp contrast with the interaction between O(D-1) and N2O, which proceeds entirely by reaction. Similarly, there is no reaction with CO2. With H2O, the reactive pathway is the dominant one, although electronic quenching is not negligible. With NO, O(D-1) is the preferred product.

Calculating Path-Dependent Travel Time Prediction Variance and Covariance fro a Global Tomographic P-Velocity Model

NASA Astrophysics Data System (ADS)

Ballard, S.; Hipp, J. R.; Encarnacao, A.; Young, C. J.; Begnaud, M. L.; Phillips, W. S.

2012-12-01

Seismic event locations can be made more accurate and precise by computing predictions of seismic travel time through high fidelity 3D models of the wave speed in the Earth's interior. Given the variable data quality and uneven data sampling associated with this type of model, it is essential that there be a means to calculate high-quality estimates of the path-dependent variance and covariance associated with the predicted travel times of ray paths through the model. In this paper, we describe a methodology for accomplishing this by exploiting the full model covariance matrix and show examples of path-dependent travel time prediction uncertainty computed from SALSA3D, our global, seamless 3D tomographic P-velocity model. Typical global 3D models have on the order of 1/2 million nodes, so the challenge in calculating the covariance matrix is formidable: 0.9 TB storage for 1/2 of a symmetric matrix, necessitating an Out-Of-Core (OOC) blocked matrix solution technique. With our approach the tomography matrix (G which includes Tikhonov regularization terms) is multiplied by its transpose (GTG) and written in a blocked sub-matrix fashion. We employ a distributed parallel solution paradigm that solves for (GTG)-1 by assigning blocks to individual processing nodes for matrix decomposition update and scaling operations. We first find the Cholesky decomposition of GTG which is subsequently inverted. Next, we employ OOC matrix multiplication methods to calculate the model covariance matrix from (GTG)-1 and an assumed data covariance matrix. Given the model covariance matrix, we solve for the travel-time covariance associated with arbitrary ray-paths by summing the model covariance along both ray paths. Setting the paths equal and taking the square root yields the travel prediction uncertainty for the single path.

Laboratory studies of stratospheric bromine chemistry: Kinetics of the reactions of bromine monoxide with nitrogen dioxide and atomic oxygen

NASA Astrophysics Data System (ADS)

Thorn, Robert Peyton

A laser flash photolysis - long path absorption - technique has been employed to study the kinetics of the reaction BrO+NO2+M(k(sub 16)) yields products as a function of temperature (248-346 K), pressure (16-800 Torr), and buffer gas identity (N2, CF4). 351 nm photolysis of NO2/Br2/N2 mixtures generated BrO. The BrO decay in the presence of excess NO2 was followed by UV absorption at 338.3 nm. The reaction is in the falloff regime between third and second order over the entire range of conditions investigated. This is the first study where temperature dependent measurements of k(sub 16)(P,T) have been reported at pressures greater than 12 Torr; hence, these results help constrain choices of k(sub 16)(P,T) for use in modeling stratospheric BrO(x) chemistry. The kinetics of the important stratospheric reaction BrO+O(P-3)(k(sub 14)) yields Br+O2 in N2 buffer gas have been studied as a function of temperature (233-328 K) and pressure (25-150 Torr) using a novel dual laser flash photolysis/long path absorption/resonance fluorescence technique. 248 nm pulsed laser photolysis of Br2/O3/N2 mixtures produces O atoms in excess over Br2. After a delay sufficient for BrO to be generated, a 532 nm laser pulse photolysis a small fraction of the O3 to generate O(P-3). The decay of O(P-3) in the presence of an excess, known concentration of BrO, as determined by UV absorption at 338.3 nm and by numerical simulation, is then followed by time-resoved atomic resonance fluorescence spectroscopy. The experimental results have shown the reaction kinetics to be independent of pressure, to increase with decreasing temperature, and to be faster than suggested by the only previous (indirect) measurement. The resulting Anhenius expression for k(sub 14)(T) is k(sub 14)(T) = 1.64 x 10(exp -11) exp(263/T) cm(exp 3) molecule(exp-1)s(exp -1). The absolute accuracy of k(sub 14)(T) at any temperature within the range studied is estimated to be +/- 25%. Possible kinetic interferences from production of vibrationally or electronically excited O2 are discussed. The effect of the faster reaction rate coefficients that are reported for the BrO + NO2 + M and BrO + O(P-3) reactions upon bromine partitioning and ozone depletion in the stratosphere is discussed.

Laboratory Studies of Stratospheric Bromine Chemistry: Kinetics of the Reactions of Bromine Monoxide with Nitrogen Dioxide and Atomic Oxygen.

NASA Astrophysics Data System (ADS)

Thorn, Robert Peyton, Jr.

A laser flash photolysis - long path absorption technique has been employed to study the kinetics of the reaction rm BrO + NO_2 + M{k _{16}atopto} products as a function of temperature (248-346 K), pressure (16 -800 Torr), and buffer gas identity (rm N _2,CF_4). 351 nm photolysis of rm NO_2/Br_2/N_2 mixtures generated BrO. The BrO decay in the presence of excess NO_2 was followed by UV absorption at 338.3 nm. The reaction is in the falloff regime between third and second order over the entire range of conditions investigated. This is the first study where temperature dependent measurements of k_{16} (P,T) have been reported at pressures greater than 12 Torr; hence, these results help constrain choices of k_{16}(P,T) for use in modeling stratospheric BrO_{rm x} chemistry. The kinetics of the important stratospheric reaction rm BrO+O(^3P)_sp{to }{k_{14}}Br+O_2 in N_2 buffer gas have been studied as a function of temperature (233-328 K) and pressure (25 -150 Torr) using a novel dual laser flash photolysis/long path absorption/resonance fluorescence technique. 248 nm pulsed laser photolysis of rm Br_2/O _3/N_2 mixtures produces O atoms in excess over Br_2. After a delay sufficient for BrO to be generated, a 532 nm laser pulse photolyses a small fraction of the O_3 to generate O(^3P). The decay of O(^3P) in the presence of an excess, known concentration of BrO, as determined by UV absorption at 338.3 nm and by numerical simulation, is then followed by time-resolved atomic resonance fluorescence spectroscopy. The experimental results have shown the reaction kinetics to be independent of pressure, to increase with decreasing temperature, and to be faster than suggested by the only previous (indirect) measurement. The resulting Anhenius expression for k_{14}(T) is given below.rm k_{14 }(T) = 1.64times 10^{-11} exp (263/T) cm^3 molecule ^{-1} s^{-1} The absolute accuracy of k_{14 }(T) at any temperature within the range studied is estimated to be +/-25%. Possible kinetic interferences from production of vibrationally or electronically excited O_2 are discussed. The effect of the faster reaction rate coefficients that are reported for the rm BrO + NO_2 + M and BrO + O(^3P) reactions upon bromine partitioning and ozone depletion in the stratosphere is discussed.

Influence of Shear Stiffness Degradation on Crack Paths in Uni-Directional Composite Laminates

NASA Technical Reports Server (NTRS)

Satyanarayana, Arunkumar; Bogert, Phil B.

2017-01-01

Influence of shear stiffness degradation in an element, due to damage, on crack paths in uni-directional laminates has been demonstrated. A new shear stiffness degradation approach to improve crack path prediction has been developed and implemented in an ABAQUS/Explicit frame work using VUMAT. Three progressive failure analysis models, built-in ABAQUS (TradeMark), original COmplete STress Reduction (COSTR) and the modified COSTR damage models have been utilized in this study to simulate crack paths in five unidirectional notched laminates, 15deg, 30deg, 45deg, 60deg and 75deg under uniaxial tension load. Results such as crack paths and load vs. edge displacement curves are documented in this report. Modified COSTR damage model shows better accuracy in predicting crack paths in all the uni-directional laminates compared to the ABAQUS (TradeMark) and the original COSTR damage models.

Using GPS RO L1 data for calibration of the atmospheric path delay model for data reduction of the satellite altimetery observations.

NASA Astrophysics Data System (ADS)

Petrov, L.

2017-12-01

Processing satellite altimetry data requires the computation of path delayin the neutral atmosphere that is used for correcting ranges. The path delayis computed using numerical weather models and the accuracy of its computationdepends on the accuracy of numerical weather models. Accuracy of numerical modelsof numerical weather models over Antarctica and Greenland where there is a very sparse network of ground stations, is not well known. I used the dataset of GPS RO L1 data, computed predicted path delay for ROobservations using the numerical whether model GEOS-FPIT, formed the differences with observed path delay and used these differences for computationof the corrections to the a priori refractivity profile. These profiles wereused for computing corrections to the a priori zenith path delay. The systematic patter of these corrections are used for de-biasing of the the satellite altimetry results and for characterization of the systematic errorscaused by mismodeling atmosphere.

A computer program incorporating Pitzer's equations for calculation of geochemical reactions in brines

USGS Publications Warehouse

Plummer, Niel; Parkhurst, D.L.; Fleming, G.W.; Dunkle, S.A.

1988-01-01

The program named PHRQPITZ is a computer code capable of making geochemical calculations in brines and other electrolyte solutions to high concentrations using the Pitzer virial-coefficient approach for activity-coefficient corrections. Reaction-modeling capabilities include calculation of (1) aqueous speciation and mineral-saturation index, (2) mineral solubility, (3) mixing and titration of aqueous solutions, (4) irreversible reactions and mineral water mass transfer, and (5) reaction path. The computed results for each aqueous solution include the osmotic coefficient, water activity , mineral saturation indices, mean activity coefficients, total activity coefficients, and scale-dependent values of pH, individual-ion activities and individual-ion activity coeffients , and scale-dependent values of pH, individual-ion activities and individual-ion activity coefficients. A data base of Pitzer interaction parameters is provided at 25 C for the system: Na-K-Mg-Ca-H-Cl-SO4-OH-HCO3-CO3-CO2-H2O, and extended to include largely untested literature data for Fe(II), Mn(II), Sr, Ba, Li, and Br with provision for calculations at temperatures other than 25C. An extensive literature review of published Pitzer interaction parameters for many inorganic salts is given. Also described is an interactive input code for PHRQPITZ called PITZINPT. (USGS)

Spectroscopic factors near the r-process path using (d , p) measurements at two energies

NASA Astrophysics Data System (ADS)

Walter, D.; Cizewski, J. A.; Baugher, T.; Ratkiewicz, A.; Manning, B.; Pain, S. D.; Nunes, F. M.; Ahn, S.; Cerizza, G.; Thornsberry, C.; Jones, K. L.

2016-09-01

To determine spectroscopic factors, it is necessary to use a nuclear reaction model that is dependent on the bound-state potential. A poorly constrained potential can drastically increase uncertainties in extracted spectroscopic factors. Mukhamedzhanov and Nunes have proposed a technique to mitigate this uncertainty by combining transfer reaction measurements at two energies. At peripheral reaction energies ( 5 MeV/u), the external contribution of the wave function can be reliably extracted, and then combined with the higher energy reaction ( 40 MeV/u) with a larger contribution from the interior. The two measurements will constrain the single-particle asymptotic normalization coefficient, ANC, and enable spectroscopic factors to be determined with uncertainties dominated by the cross section measurements rather than in the bound-state potential. Published measurements of 86Kr(d , p) at 5.5 MeV/u have been combined with recent results at 35 MeV/u at the NSCL using the ORRUBA and SIDAR arrays of silicon-strip detectors. Preliminary analysis shows that the single-particle ANC can be constrained. The details of the analysis and prospects for measurements with rare isotope beams will be presented. This research by the ORRUBA Collaboration is supported in part by the NSF and the U.S. DOE.

Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Leite, Vitor B. Pereira

The dynamics of solvent polarization plays a major role in the control of charge transfer reactions. The success of Marcus theory describing the solvent influence via a single collective quadratic polarization coordinate has been remarkable. Onuchic and Wolynes have recently proposed (J. Chem Phys 98 (3) 2218, 1993) a simple model demonstrating how a many-dimensional-complex model composed by several dipole moments (representing solvent molecules or polar groups in proteins) can be reduced under the appropriate limits into the Marcus Model. This work presents a dynamical study of the same model, which is characterized by two parameters, an average dipole-dipole interaction as a term associated with the potential energy landscape roughness. It is shown why the effective potential, obtained using a thermodynamic approach, is appropriate for the dynamics of the system. At high temperatures, the system exhibits effective diffusive one-dimensional dynamics, where the Born-Marcus limit is recovered. At low temperatures, a glassy phase appears with a slow non-self-averaging dynamics. At intermediate temperatures, the concept of equivalent diffusion paths and polarization dependence effects are discussed. This approach is extended to treat more realistic solvent models. Real solvents are discussed in terms of simple parameters described above, and an analysis of how different regimes affect the rate of charge transfer is presented. Finally, these ideas are correlated to analogous problems in other areas.

Reaction path in the formation of titanium diboride by a magnesium thermite process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundaram, V.; Logan, K.V.; Speyer, R.F.

1995-12-31

TiB{sub 2} was formed by a thermite reaction amongst Mg, amorphous B{sub 2}O{sub 3} and TiO{sub 2} powders. Mixtures consisting of 2Mg-TiO{sub 2}, 3Mg-B{sub 2}O{sub 3} and 5Mg-TiO{sub 2}-B{sub 2}O{sub 3} were heat treated using DTA and separately via ignition with a nichrome wire; product phases were identified using XRD. MgO and Ti were products from the first mixture reacted in argon, whereas an incomplete transformation forming Mg{sub 3}TiO{sub 4} occurred in air. For the second mixture, a reaction forming Mg{sub 3}B{sub 2}O{sup 6} occurred in air, but no reaction occurred in argon due to deficiency of oxygen. Minor amountsmore » Of Mg{sub 3}B{sub 2}O{sub 6} and Mg{sub 2}TiO{sub 4} were detected in addition to the predicted product phases of MgO and TiB{sub 2} for the third mixture ignited both in air and argon. Based on available evidence, a path for this reaction was deduced; Mg particles in contact with TiO{sub 2} reacted to form Ti, which in turn reacted with B{sub 2}O{sub 3} to form TiB{sub 2}. TiB{sub 2} product particles from the reaction in argon had a more faceted appearance than those formed during the reaction in air. This was interpreted to be the result of glassy B{sub 2}O{sub 3} surface layer formation on TiB{sub 2} particles in air.« less

Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction.

PubMed

Monge-Palacios, M; Rangel, C; Espinosa-Garcia, J

2013-02-28

A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200-2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.

Synergetic interaction between neighbouring platinum monomers in CO2 hydrogenation

NASA Astrophysics Data System (ADS)

Li, Hongliang; Wang, Liangbing; Dai, Yizhou; Pu, Zhengtian; Lao, Zhuohan; Chen, Yawei; Wang, Menglin; Zheng, Xusheng; Zhu, Junfa; Zhang, Wenhua; Si, Rui; Ma, Chao; Zeng, Jie

2018-05-01

Exploring the interaction between two neighbouring monomers has great potential to significantly raise the performance and deepen the mechanistic understanding of heterogeneous catalysis. Herein, we demonstrate that the synergetic interaction between neighbouring Pt monomers on MoS2 greatly enhanced the CO2 hydrogenation catalytic activity and reduced the activation energy relative to isolated monomers. Neighbouring Pt monomers were achieved by increasing the Pt mass loading up to 7.5% while maintaining the atomic dispersion of Pt. Mechanistic studies reveal that neighbouring Pt monomers not only worked in synergy to vary the reaction barrier, but also underwent distinct reaction paths compared with isolated monomers. Isolated Pt monomers favour the conversion of CO2 into methanol without the formation of formic acid, whereas CO2 is hydrogenated stepwise into formic acid and methanol for neighbouring Pt monomers. The discovery of the synergetic interaction between neighbouring monomers may create a new path for manipulating catalytic properties.

Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolter, Tino; Elstner, Marcus; Fischer, Stefan

2014-01-01

Relaxation of the twisted-retinal photoproduct state triggers proton-coupled reaction cycle in retinal proteins. A key open question is whether the retinal relaxation path is governed by the intrinsic torsional properties of the retinal or rather by the interactions of the retinal with protein and water groups, given the crowded protein environments in which the retinal resides. We address this question by performing systematic quantum mechanical/molecular mechanical molecular dynamics computations of retinal dynamics in bacteriorhodopsin at different temperatures, reaction path computations, and assessment of the vibrational fingerprints of the retinal molecule. Our results demonstrate a complex dependence of the retinal dynamicsmore » and preferred geometry on temperature. As the temperature increases, the retinal dihedral angle samples values largely determined by its internal conformational energy. The protein environment shapes the energetics of retinal relaxation and provides hydrogen-bonding partners that stabilize the retinal geometry.« less

Structures, electronic properties and reaction paths from Fe(CO)5 molecule to small Fe clusters

NASA Astrophysics Data System (ADS)

Li, Zhi; Zhao, Zhen

2018-04-01

The geometries, electrical characters and reaction paths from Fe(CO)5 molecule to small Fe clusters were investigated by using all-electron density functional theory. The results show that in the decomposition process of pentacarbonyl-iron, Fe(CO)5 molecule prefers to remove a carbon monoxide and adsorb another Fe(CO)5 molecule to produce nonacarbonyldiiron Fe2(CO)9 then Fe2(CO)9 gradually removes carbon monoxide to produce small Fe clusters. As It can be seen from the highest occupied molecule orbital-lowest unoccupied molecule orbital gap curves, the Fe(CO)n=3, and 5 and Fe2(CO)n=3, 7 and 9 intermediates have higher chemical stability than their neighbors. The local magnetic moment of the carbon monoxide is aligning anti-ferromagnetic. The effect of external magnetic field to the initial decomposition products of Fe(CO)5 can be ignored.

Application of the nudged elastic band method to the point-to-point radio wave ray tracing in IRI modeled ionosphere

NASA Astrophysics Data System (ADS)

Nosikov, I. A.; Klimenko, M. V.; Bessarab, P. F.; Zhbankov, G. A.

2017-07-01

Point-to-point ray tracing is an important problem in many fields of science. While direct variational methods where some trajectory is transformed to an optimal one are routinely used in calculations of pathways of seismic waves, chemical reactions, diffusion processes, etc., this approach is not widely known in ionospheric point-to-point ray tracing. We apply the Nudged Elastic Band (NEB) method to a radio wave propagation problem. In the NEB method, a chain of points which gives a discrete representation of the radio wave ray is adjusted iteratively to an optimal configuration satisfying the Fermat's principle, while the endpoints of the trajectory are kept fixed according to the boundary conditions. Transverse displacements define the radio ray trajectory, while springs between the points control their distribution along the ray. The method is applied to a study of point-to-point ionospheric ray tracing, where the propagation medium is obtained with the International Reference Ionosphere model taking into account traveling ionospheric disturbances. A 2-dimensional representation of the optical path functional is developed and used to gain insight into the fundamental difference between high and low rays. We conclude that high and low rays are minima and saddle points of the optical path functional, respectively.

A New Chemical Pathway Yielding A-Type Vitisins in Red Wines

PubMed Central

Araújo, Paula; Fernandes, Ana; de Freitas, Victor; Oliveira, Joana

2017-01-01

A new chemical pathway yielding A-type vitisins in red wines is proposed herein from the reaction between anthocyanins and oxaloacetic acid (OAA). This new chemical path is thought to occur in the first stages of the wine production even during the fermentation process. This is due to the revealed high reactivity of OAA with anthocyanins compared with the already known precursor (pyruvic acid, PA). In model solutions at wine pH (3.5), when malvidin-3-O-glucoside (mv-3-glc) is in contact with OAA and PA a decrease in the OAA concentration is observed along with the formation of A-type vitisin. Moreover, part of the OAA is also chemically converted into PA in model solutions. The reaction yields were also determined for OAA and PA using different mv-3-glc:organic acid molar ratios (1:0.5, 1:1, 1:5, 1:10; 1:50, and 1:100) and these values were always higher for OAA when compared to PA, even at the lowest molar ratio (1:0.5). The reaction yields were higher at pH 2.6 in comparison to pH 1.5 and 3.5, being less affected at pH 3.5 for OAA. These results support the idea that OAA can be at the origin of A-type vitisins in the first stages of wine production and PA in the subsequent ageing process. PMID:28375190

A New Chemical Pathway Yielding A-Type Vitisins in Red Wines.

PubMed

Araújo, Paula; Fernandes, Ana; de Freitas, Victor; Oliveira, Joana

2017-04-04

A new chemical pathway yielding A-type vitisins in red wines is proposed herein from the reaction between anthocyanins and oxaloacetic acid (OAA). This new chemical path is thought to occur in the first stages of the wine production even during the fermentation process. This is due to the revealed high reactivity of OAA with anthocyanins compared with the already known precursor (pyruvic acid, PA). In model solutions at wine pH (3.5), when malvidin-3- O -glucoside (mv-3-glc) is in contact with OAA and PA a decrease in the OAA concentration is observed along with the formation of A-type vitisin. Moreover, part of the OAA is also chemically converted into PA in model solutions. The reaction yields were also determined for OAA and PA using different mv-3-glc:organic acid molar ratios (1:0.5, 1:1, 1:5, 1:10; 1:50, and 1:100) and these values were always higher for OAA when compared to PA, even at the lowest molar ratio (1:0.5). The reaction yields were higher at pH 2.6 in comparison to pH 1.5 and 3.5, being less affected at pH 3.5 for OAA. These results support the idea that OAA can be at the origin of A-type vitisins in the first stages of wine production and PA in the subsequent ageing process.

Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

PubMed

Gao, J

2016-01-01

Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects. © 2016 Elsevier Inc. All rights reserved.

Gas Phase Dissociation Behavior of Acyl-Arginine Peptides.

PubMed

McGee, William M; McLuckey, Scott A

2013-11-15

The gas phase dissociation behavior of peptides containing acyl-arginine residues is investigated. These acylations are generated via a combination of ion/ion reactions between arginine-containing peptides and N -hydroxysuccinimide (NHS) esters and subsequent tandem mass spectrometry (MS/MS). Three main dissociation pathways of acylated arginine, labeled Paths 1-3, have been identified and are dependent on the acyl groups. Path 1 involves the acyl-arginine undergoing deguanidination, resulting in the loss of the acyl group and dissociation of the guanidine to generate an ornithine residue. This pathway generates selective cleavage sites based on the recently discussed "ornithine effect". Path 2 involves the coordinated losses of H 2 O and NH 3 from the acyl-arginine side chain while maintaining the acylation. We propose that Path 2 is initiated via cyclization of the δ-nitrogen of arginine and the C-terminal carbonyl carbon, resulting in rapid rearrangement from the acyl-arginine side chain and the neutral losses. Path 3 occurs when the acyl group contains α-hydrogens and is observed as a rearrangement to regenerate unmodified arginine while the acylation is lost as a ketene.

Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path

DOE PAGES

Carpenter, Barry K.; Harvey, Jeremy N.; Glowacki, David R.

2014-12-11

Classical molecular dynamics simulations are reported for the deazetisation and ring opening of meso-2,3-difluoro-2,3-dimethyldiazocyclopropane in three solvents: CHCl 3, CHFClBr and CH 3CH(OH)CF 3 (TFIPA). In this study, the achiral reactant leads to enantiomeric allene products, and the question addressed in the study is whether either of the chiral, enantiomerically pure solvents can induce significant enantiomeric excess in the products. The direct dynamics calculations use an empirical valence bond potential for the solute, with empirical parameters optimised against M06-2X/cc-pVTZ density functional results. The results reveal that the exothermic N 2 loss and ring opening promote transient strong solvent–solute interactions withinmore » the first ~100 fs of the reaction. Because of the bifurcating reaction path, these interactions occur at time when the “decision” about which enantiomer of the product to form has yet to be made (at least for many of the trajectories). Hence, it is possible in principle that the solvent could exert a larger-than-normal influence on the course of the reaction. In fact, the results reveal no such effect for CHFClBr but do predict that TFIPA should induce 15.2 ± 2.1% enantiomeric excess. This is roughly an order of magnitude larger than solvent-induced enantiomeric excesses found experimentally in reactions where the conversion of reactant(s) to enantiomeric products occur over separate transition states.« less

Dependence of Internal Friction on Folding Mechanism

PubMed Central

2016-01-01

An outstanding challenge in protein folding is understanding the origin of “internal friction” in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein. PMID:25721133

Dependence of internal friction on folding mechanism.

PubMed

Zheng, Wenwei; De Sancho, David; Hoppe, Travis; Best, Robert B

2015-03-11

An outstanding challenge in protein folding is understanding the origin of "internal friction" in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein.

Capturing poromechanical coupling effects of the reactive fracturing process in porous rock via a DEM-network model

NASA Astrophysics Data System (ADS)

Ulven, Ole Ivar; Sun, WaiChing

2016-04-01

Fluid transport in a porous medium has important implications for understanding natural geological processes. At a sufficiently large scale, a fluid-saturated porous medium can be regarded as a two-phase continuum, with the fluid constituent flowing in the Darcian regime. Nevertheless, a fluid mediated chemical reaction can in some cases change the permeability of the rock locally: Mineral dissolution can cause increased permeability, whereas mineral precipitation can reduce the permeability. This might trigger a complicated hydro-chemo-mechanical coupling effect that causes channeling of fluids or clogging of the system. If the fluid is injected or produced at a sufficiently high rate, the pressure might increase enough to cause the onset and propagation of fractures. Fractures in return create preferential flow paths that enhance permeability, localize fluid flow and chemical reaction, prevent build-up of pore pressure and cause anisotropy of the hydro-mechanical responses of the effective medium. This leads to a complex coupled process of solid deformation, chemical reaction and fluid transport enhanced by the fracture formation. In this work, we develop a new coupled numerical model to study the complexities of feedback among fluid pressure evolution, fracture formation and permeability changes due to a chemical process in a 2D system. We combine a discrete element model (DEM) previously used to study a volume expanding process[1, 2] with a new fluid transport model based on poroelasticity[3] and a fluid-mediated chemical reaction that changes the permeability of the medium. This provides new insights into the hydro-chemo-mechanical process of a transforming porous medium. References [1] Ulven, O. I., Storheim, H., Austrheim, H., and Malthe-Sørenssen, A. "Fracture Initiation During Volume Increasing Reactions in Rocks and Applications for CO2 Sequestration", Earth Planet. Sc. Lett. 389C, 2014a, pp. 132 - 142, doi:10.1016/j.epsl.2013.12.039. [2] Ulven, O. I., Jamtveit, B., and Malthe-Sørenssen, A., "Reaction-driven fracturing of porous rock", J. Geophys. Res. Solid Earth 119, 2014b, doi:10.1002/2014JB011102. [3] Ulven, O. I., and Sun, W.C., "A locally mass-conserving dual-graph lattice model for fluid-driven fracture", in prep.

Distribution path robust optimization of electric vehicle with multiple distribution centers

PubMed Central

Hao, Wei; He, Ruichun; Jia, Xiaoyan; Pan, Fuquan; Fan, Jing; Xiong, Ruiqi

2018-01-01

To identify electrical vehicle (EV) distribution paths with high robustness, insensitivity to uncertainty factors, and detailed road-by-road schemes, optimization of the distribution path problem of EV with multiple distribution centers and considering the charging facilities is necessary. With the minimum transport time as the goal, a robust optimization model of EV distribution path with adjustable robustness is established based on Bertsimas’ theory of robust discrete optimization. An enhanced three-segment genetic algorithm is also developed to solve the model, such that the optimal distribution scheme initially contains all road-by-road path data using the three-segment mixed coding and decoding method. During genetic manipulation, different interlacing and mutation operations are carried out on different chromosomes, while, during population evolution, the infeasible solution is naturally avoided. A part of the road network of Xifeng District in Qingyang City is taken as an example to test the model and the algorithm in this study, and the concrete transportation paths are utilized in the final distribution scheme. Therefore, more robust EV distribution paths with multiple distribution centers can be obtained using the robust optimization model. PMID:29518169

A dual-porous, biophysical void structure model of soil for the understanding of the conditions causing nitrous oxide emission

NASA Astrophysics Data System (ADS)

Matthews, G. Peter; Maurizio Laudone, G.; Whalle, W. Richard; Bird, Nigel; Gregory, Andrew; Cardenas, Laura; Misselbrook, Tom

2010-05-01

Nitrous oxide is the fourth most important greenhouse gas. It is 300 times more potent than carbon dioxide, and two-thirds of anthropogenic nitrous oxide is emitted by agricultural land. This presentation will begin with a brief overview of the laboratory measurements of nitrous oxide emission from carefully characterised soils, presented in more detail by Cardenas et al.. The measurements were made in a twelve-chamber, gas chromatographic apparatus at North Wyke Research (formerly IGER). The presentation will then continue with a description of a void network model of sufficient accuracy and authenticity that it can be used to explain and predict the nitrous oxide production, and the modelling of the biological, chemical and physical processes for the production of nitrous oxide within the constructed network. Finally, conclusions will be drawn from a comparison of the model results with experiment. The void network model Nitrous oxide is produced by microbial activity located in ‘hotspots' within the microstructure of soil, and nutrients and gases flow or diffuse to and from these hotspots through the water or gas-filled macro-porosity. It is clear, therefore, that a network model to describe and explain nitrous oxide production must encompass the full size range of pore space active within the process, which covers 6 orders of magnitude, and must make realistic suppositions about the positional relationship of the hotspots relative to the soil macro-porosity. Previous experimental (Tsakiroglou, C. D. et al, European J.Soil Sci., 2008) and theoretical approaches to the modelling of soil void structure cannot generally meet these two requirements. We have therefore built on the success of the previous uni-porous model of soil (Matthews, G. P. et al, Wat.Resour.Res, 2010), and the concept of a critical percolation path, to develop a dual porous model (Laudone, G. M. et al, European J.Soil Sci., 2010) with the following features: • A porous unit cell, with periodic boundary conditions, and with a critical percolation path with the correct percolation characteristics and void volume of the macro-porosity of the soil. • A solid phase between the pores of the large unit cell, with the correct volume of the fraction of larger soil aggregates (larger 1 mm). • All the remaining pores of the large unit cell, which are not part of the critical percolation path, filled with smaller unit cells, which account for the micro-porosity of the soil sample. We describe the construction of a model that closely matches the following characteristics of a specific example of typical arable soil, taken from the Warren field of the Rothamsted experimental farm at Woburn, although the model can be used for a wide range of soils: (i) macroporosity and microporosity as measured by the water retention curve, (ii) the shape of the water retention characteristic under a wide range of tensions, (iii) the soil texture, and (iv) the extent of irreducible water content. Process model We will describe the insertion of Michaelis-Menten kinetics and Crank-Nicholson diffusion equations into the precisely scaled model, building on previous diffusion modelling (Laudone, G. M. et al, Chem.Eng.Sci., 2008). Comparison with experiment A comparison with experimental results sheds light on (i) the positional relationships of aerobic and anaerobic bacteria relative to the critical percolation path, (ii) the relationship between the critical percolation path and the preferential / critical flow path (Figure 4), (iii) the extent of ignorance about the reaction kinetics of some of the fundamental processes occurring, (iv) the soil conditions that cause nitrous oxide emission, and (v) the effect of soil compaction on the emission. Acknowledgement This presentation is a summary of the some of the work of the BBSRC funded U.K. soil research consortium "Soil Programme for Quality and Resilience" (BB/E001793/1 and others), of which Matthews is principal investigator.

Orbital maneuvering subsystem functional path analysis for performance monitoring fault detection and annunciation

NASA Technical Reports Server (NTRS)

Keesler, E. L.

1974-01-01

The functional paths of the Orbital Maneuver Subsystem (OMS) is defined. The operational flight instrumentation required for performance monitoring, fault detection, and annunciation is described. The OMS is a pressure fed rocket engine propulsion subsystem. One complete OMS shares each of the two auxiliary propulsion subsystem pods with a reaction control subsystem. Each OMS is composed of a pressurization system, a propellant tanking system, and a gimbaled rocket engine. The design, development, and operation of the system are explained. Diagrams of the system are provided.

Novel benzothiophene 1,1-dioxide deoxygenation path for the microwave-assisted synthesis of substituted benzothiophene-fused pyrrole derivatives.

PubMed

Karakuş, Hamza; Dürüst, Yaşar

2017-02-01

The reaction of C-(4-substituted-phenyl)-N-(benzoyl)-N-methylglycines with benzo[b]thiophene 1,1-dioxide unexpectedly gave benzothiophene-fused pyrrole derivatives in toluene under microwave irradiation via a cycloaddition and metal-free Pummerer-type sulfone deoxygenation path. In order to obtain the desired sulfone derivatives, the sulfide group underwent oxidation with m-CPBA to afford sulfones. The structures of all the new products were elucidated by spectroscopic/physical methods and, in two cases, by X-ray diffraction.

NASA Videofile of Solar Eclipse from Jefferson City, Missouri

NASA Image and Video Library

2017-08-21

During the eclipse, 14 states across the U.S. were in the path of totality and experienced more than two minutes of darkness in the middle of the day – with a partial eclipse viewable all across North America. The broadcast – Eclipse Across America: Through the Eyes of NASA – covered locations along the path of totality, from Oregon to South Carolina including public reactions from all ages. During this event, NASA Glenn Research Center celebrates the eclipse at the capital eclipse event in Jefferson City, MO

An improved empirical model for diversity gain on Earth-space propagation paths

NASA Technical Reports Server (NTRS)

Hodge, D. B.

1981-01-01

An empirical model was generated to estimate diversity gain on Earth-space propagation paths as a function of Earth terminal separation distance, link frequency, elevation angle, and angle between the baseline and the path azimuth. The resulting model reproduces the entire experimental data set with an RMS error of 0.73 dB.

Generalized Path Analysis and Generalized Simultaneous Equations Model for Recursive Systems with Responses of Mixed Types

ERIC Educational Resources Information Center

Tsai, Tien-Lung; Shau, Wen-Yi; Hu, Fu-Chang

2006-01-01

This article generalizes linear path analysis (PA) and simultaneous equations models (SiEM) to deal with mixed responses of different types in a recursive or triangular system. An efficient instrumental variable (IV) method for estimating the structural coefficients of a 2-equation partially recursive generalized path analysis (GPA) model and…

Module-oriented modeling of reactive transport with HYTEC

NASA Astrophysics Data System (ADS)

van der Lee, Jan; De Windt, Laurent; Lagneau, Vincent; Goblet, Patrick

2003-04-01

The paper introduces HYTEC, a coupled reactive transport code currently used for groundwater pollution studies, safety assessment of nuclear waste disposals, geochemical studies and interpretation of laboratory column experiments. Based on a known permeability field, HYTEC evaluates the groundwater flow paths, and simulates the migration of mobile matter (ions, organics, colloids) subject to geochemical reactions. The code forms part of a module-oriented structure which facilitates maintenance and improves coding flexibility. In particular, using the geochemical module CHESS as a common denominator for several reactive transport models significantly facilitates the development of new geochemical features which become automatically available to all models. A first example shows how the model can be used to assess migration of uranium from a sub-surface source under the effect of an oxidation front. The model also accounts for alteration of hydrodynamic parameters (local porosity, permeability) due to precipitation and dissolution of mineral phases, which potentially modifies the migration properties in general. The second example illustrates this feature.

A model for the kinetics of a solar-pumped long path laser experiment

NASA Technical Reports Server (NTRS)

Stock, L. V.; Wilson, J. W.; Deyoung, R. J.

1986-01-01

A kinetic model for a solar-simulator pumped iodine laser system is developed and compared to an experiment in which the solar simulator output is dispersed over a large active volume (150 cu cm) with low simulator light intensity (approx. 200 solar constants). A trace foreign gas which quenches the upper level is introduced into the model. Furthermore, a constant representing optical absorption of the stimulated emission is introduced, in addition to a constant representing the scattering at each of the mirrors, via the optical cavity time constant. The non-uniform heating of the gas is treated as well as the pressure change as a function of time within the cavity. With these new phenomena introduced into the kinetic model, a best reasonable fit to the experimental data is found by adjusting the reaction rate coefficients within the range of known uncertainty by numerical methods giving a new bound within this range of uncertainty. The experimental parameters modeled are the lasing time, laser pulse energy, and time to laser threshold.

Cosmic-ray models for early Galactic Lithium, Beryllium, and Boron production

NASA Technical Reports Server (NTRS)

Fields, Brian D.; Olive, Keith A.; Schramm, David N.

1994-01-01

To understand better the early Galactic production of Li, Be, and B by comsmic-ray spallation and fusion reactions, the dependence of these production rates on cosmic-ray models and model parameters is examined. The sensitivity of elemental and isotopic production to the cosmic-ray path length magnitude and energy dependence, source spectrum, spallation kinematics, and cross section uncertainties is studied. Changes in these model features, particularly those features related to confinement, are shown to alter the Be- and B- versus-Fe slopes from a naive quadratic relation. The implications of our results for the diffuse gamma-ray background are examined, and the role of chemical evolution and its relation to our results is noted. It is also noted that the unmeasured high-energy behavior of alpha + alpha fusion can lead to effects as large as a factor of 2 in the resultant yields. Future data should enable Population II Li, Be, and B abundances to constrain cosmic-ray models for the early Galaxy.

Modeling Low-temperature Geochemical Processes

NASA Astrophysics Data System (ADS)

Nordstrom, D. K.

2003-12-01

Geochemical modeling has become a popular and useful tool for a wide number of applications from research on the fundamental processes of water-rock interactions to regulatory requirements and decisions regarding permits for industrial and hazardous wastes. In low-temperature environments, generally thought of as those in the temperature range of 0-100 °C and close to atmospheric pressure (1 atm=1.01325 bar=101,325 Pa), complex hydrobiogeochemical reactions participate in an array of interconnected processes that affect us, and that, in turn, we affect. Understanding these complex processes often requires tools that are sufficiently sophisticated to portray multicomponent, multiphase chemical reactions yet transparent enough to reveal the main driving forces. Geochemical models are such tools. The major processes that they are required to model include mineral dissolution and precipitation; aqueous inorganic speciation and complexation; solute adsorption and desorption; ion exchange; oxidation-reduction; or redox; transformations; gas uptake or production; organic matter speciation and complexation; evaporation; dilution; water mixing; reaction during fluid flow; reaction involving biotic interactions; and photoreaction. These processes occur in rain, snow, fog, dry atmosphere, soils, bedrock weathering, streams, rivers, lakes, groundwaters, estuaries, brines, and diagenetic environments. Geochemical modeling attempts to understand the redistribution of elements and compounds, through anthropogenic and natural means, for a large range of scale from nanometer to global. "Aqueous geochemistry" and "environmental geochemistry" are often used interchangeably with "low-temperature geochemistry" to emphasize hydrologic or environmental objectives.Recognition of the strategy or philosophy behind the use of geochemical modeling is not often discussed or explicitly described. Plummer (1984, 1992) and Parkhurst and Plummer (1993) compare and contrast two approaches for modeling groundwater chemistry: (i) "forward modeling," which predicts water compositions from hypothesized reactions and user assumptions and (ii) "inverse modeling," which uses water, mineral, and isotopic compositions to constrain hypothesized reactions. These approaches simply reflect the amount of information one has to work with. With minimal information on a site, a modeler is forced to rely on forward modeling. Optimal information would include detailed mineralogy on drill cores or well cuttings combined with detailed water analyses at varying depths and sufficient spatial distribution to follow geochemical reactions and mixing of waters along defined flow paths. With optimal information, a modeler will depend on inverse modeling.This chapter outlines the main concepts and key developments in the field of geochemical modeling for low-temperature environments and illustrates their use with examples. It proceeds with a short discussion of what modeling is, continues with concepts and definitions commonly used, and follows with a short history of geochemical models, a discussion of databases, the codes that embody models, and recent examples of how these codes have been used in water-rock interactions. An important new stage of development seems to have been reached in this field with questions of reliability and validity of models. Future work will be obligated to document ranges of certainty and sources of uncertainty, sensitivity of models and codes to parameter errors and assumptions, propagation of errors, and delineation of the range of applicability.

Reaction pathways of propene pyrolysis.

PubMed

Qu, Yena; Su, Kehe; Wang, Xin; Liu, Yan; Zeng, Qingfeng; Cheng, Laifei; Zhang, Litong

2010-05-01

The gas-phase reaction pathways in preparing pyrolytic carbon with propene pyrolysis have been investigated in detail with a total number of 110 transition states and 50 intermediates. The structure of the species was determined with density functional theory at B3PW91/6-311G(d,p) level. The transition states and their linked intermediates were confirmed with frequency and the intrinsic reaction coordinates analyses. The elementary reactions were explored in the pathways of both direct and the radical attacking decompositions. The energy barriers and the reaction energies were determined with accurate model chemistry method at G3(MP2) level after an examination of the nondynamic electronic correlations. The heat capacities and entropies were obtained with statistical thermodynamics. The Gibbs free energies at 298.15 K for all the reaction steps were reported. Those at any temperature can be developed with classical thermodynamics by using the fitted (as a function of temperature) heat capacities. It was found that the most favorable paths are mainly in the radical attacking chain reactions. The chain was proposed with 26 reaction steps including two steps of the initialization of the chain to produce H and CH(3) radicals. For a typical temperature (1200 K) adopted in the experiments, the highest energy barriers were found in the production of C(3) to be 203.4 and 193.7 kJ/mol. The highest energy barriers for the production of C(2) and C were found 174.1 and 181.4 kJ/mol, respectively. These results are comparable with the most recent experimental observation of the apparent activation energy 201.9 +/- 0.6 or 137 +/- 25 kJ/mol. Copyright 2010 Wiley Periodicals, Inc.

Feynman-Kac equations for reaction and diffusion processes

NASA Astrophysics Data System (ADS)

Hou, Ru; Deng, Weihua

2018-04-01

This paper provides a theoretical framework for deriving the forward and backward Feynman-Kac equations for the distribution of functionals of the path of a particle undergoing both diffusion and reaction processes. Once given the diffusion type and reaction rate, a specific forward or backward Feynman-Kac equation can be obtained. The results in this paper include those for normal/anomalous diffusions and reactions with linear/nonlinear rates. Using the derived equations, we apply our findings to compute some physical (experimentally measurable) statistics, including the occupation time in half-space, the first passage time, and the occupation time in half-interval with an absorbing or reflecting boundary, for the physical system with anomalous diffusion and spontaneous evanescence.

Modeling and in Situ Probing of Surface Reactions in Atomic Layer Deposition.

PubMed

Zheng, Yuanxia; Hong, Sungwook; Psofogiannakis, George; Rayner, G Bruce; Datta, Suman; van Duin, Adri C T; Engel-Herbert, Roman

2017-05-10

Atomic layer deposition (ALD) has matured into a preeminent thin film deposition technique by offering a highly scalable and economic route to integrate chemically dissimilar materials with excellent thickness control down to the subnanometer regime. Contrary to its extensive applications, a quantitative and comprehensive understanding of the reaction processes seems intangible. Complex and manifold reaction pathways are possible, which are strongly affected by the surface chemical state. Here, we report a combined modeling and experimental approach utilizing ReaxFF reactive force field simulation and in situ real-time spectroscopic ellipsometry to gain insights into the ALD process of Al 2 O 3 from trimethylaluminum and water on hydrogenated and oxidized Ge(100) surfaces. We deciphered the origin for the different peculiarities during initial ALD cycles for the deposition on both surfaces. While the simulations predicted a nucleation delay for hydrogenated Ge(100), a self-cleaning effect was discovered on oxidized Ge(100) surfaces and resulted in an intermixed Al 2 O 3 /GeO x layer that effectively suppressed oxygen diffusion into Ge. In situ spectroscopic ellipsometry in combination with ex situ atomic force microscopy and X-ray photoelectron spectroscopy confirmed these simulation results. Electrical impedance characterizations evidenced the critical role of the intermixed Al 2 O 3 /GeO x layer to achieve electrically well-behaved dielectric/Ge interfaces with low interface trap density. The combined approach can be generalized to comprehend the deposition and reaction kinetics of other ALD precursors and surface chemistry, which offers a path toward a theory-aided rational design of ALD processes at a molecular level.

Revisiting and Computing Reaction Coordinates with Directional Milestoning

PubMed Central

Kirmizialtin, Serdal; Elber, Ron

2011-01-01

The method of Directional Milestoning is revisited. We start from an exact and more general expression and state the conditions and validity of the memory-loss approximation. An algorithm to compute a reaction coordinate from Directional Milestoning data is presented. The reaction coordinate is calculated as a set of discrete jumps between Milestones that maximizes the flux between two stable states. As an application we consider a conformational transition in solvated Adenosine. We compare a long molecular dynamic trajectory with Directional Milestoning and discuss the differences between the maximum flux path and minimum energy coordinates. PMID:21500798

Gyration-radius dynamics in structural transitions of atomic clusters.

PubMed

Yanao, Tomohiro; Koon, Wang S; Marsden, Jerrold E; Kevrekidis, Ioannis G

2007-03-28

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.

Gyration-radius dynamics in structural transitions of atomic clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang S.; Marsden, Jerrold E.; Kevrekidis, Ioannis G.

2007-03-01

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.

Cartographic modeling of snow avalanche path location within Glacier National Park, Montana

NASA Technical Reports Server (NTRS)

Walsh, Stephen J.; Brown, Daniel G.; Bian, Ling; Butler, David R.

1990-01-01

Geographic information system (GIS) techniques were applied to the study of snow-avalanche path location within Glacier National Park, Montana. Aerial photointerpretation and field surveys confirmed the location of 121 avalanche paths within the selected study area. Spatial and nonspatial information on each path were integrated using the ARC/INFO GIS. Lithologic, structural, hydrographic, topographic, and land-cover impacts on path location were analyzed. All path frequencies within variable classes were normalized by the area of class occurrence relative to the total area of the study area and were added to the morphometric information contained within INFO tables. The normalized values for each GIS coverage were used to cartographically model, by means of composite factor weightings, avalanche path locations.

The effect of CO2-fluid-rock interactions on the porosity and permeability of calcite-bearing sandstone

NASA Astrophysics Data System (ADS)

Lamy-Chappuis, B.; Yardley, B.; Grattoni, C.

2013-12-01

Brine acidification following CO2 dissolution will initiate fluid-rock interactions that could significantly modify porosity, permeability and therefore the capacity and injectivity of a reservoir. We have investigated experimentally the dissolution of calcite in sandstone cores injected with CO2-saturated brine, and the effect this has on permeability. A series of CT (Computerized Tomography) - monitored experiments were conducted on a Jurassic sandstone (porosity = 30%, permeability = 10mD, calcite content = 5% in the form of dispersed shell fragments). Brine saturated with CO2 at pressures up to 1 MPa was injected into 5cm long, 3.75cm diameter cores at a flow rate of 1 ml/min and room temperature. The data showed quasi-instantaneous dissolution of the calcite even at low CO2 concentrations (0.15 Molar) and high fluid interstitial velocities (1mm/s), with the migration of a calcite dissolution front through the core recorded by successive CT scans. The resulting permeability increase was 60 - 80% whereas the predicted permeability change for the observed increase in porosity is only 10 - 20% using the Kozeny-Carman relationship. This result is particularly significant because the effect of porosity increase on permeability is usually modelled with this relationship, irrespective of the mechanism of porosity increase. Micro-CT scans (pixel resolution: 2.5 microns) of unreacted cores were used to generate 3D porosity models with calcite either treated as solid (pre-reaction model) or converted to pores (post-reaction model). FLUENT simulations performed using these models predicted the observed large relative changes in permeability with calcite dissolution but overestimated absolute permeability by an order of magnitude. This was probably due to the scan resolution being too coarse to correctly model pore throats. The observed large change in permeability for a small change in porosity may have resulted from increase in connectivity, focused dissolution at the pore throats or reduction in tortuosity. SEM (Scanning Electron Microscope) imaging demonstrates dissolution of relatively large isolated shell fragments but this had little effect on the overall connectivity. No calcite cement was observed at the pore throats in the unreacted specimens. The micro-CT scans indicate a modest tortuosity decrease from 2.00 to 1.85 when calcite is dissolved, but this change in tortuosity results from the opening of new flow paths as the dissolution of discrete grains opened new flow paths and created shortcuts, not from changes to the sinuosity of existing pathways. We suggest that the marked discrepancy in the effect of calcite dissolution on permeability between our experimental data and standard models arises because of the very different way in which the porosity is increased (new pathways rather than inflation). While our results cast doubt on the general applicability of standard models for porosity-permeability relationships for situations in which porosity changes by grain-specific reactions, it is encouraging that pore scale modelling is able to reproduce the experimental relationships.

Path-Dependent Travel Time Prediction Variance and Covariance for a Global Tomographic P- and S-Velocity Model

NASA Astrophysics Data System (ADS)

Hipp, J. R.; Ballard, S.; Begnaud, M. L.; Encarnacao, A. V.; Young, C. J.; Phillips, W. S.

2015-12-01

Recently our combined SNL-LANL research team has succeeded in developing a global, seamless 3D tomographic P- and S-velocity model (SALSA3D) that provides superior first P and first S travel time predictions at both regional and teleseismic distances. However, given the variable data quality and uneven data sampling associated with this type of model, it is essential that there be a means to calculate high-quality estimates of the path-dependent variance and covariance associated with the predicted travel times of ray paths through the model. In this paper, we describe a methodology for accomplishing this by exploiting the full model covariance matrix and show examples of path-dependent travel time prediction uncertainty computed from our latest tomographic model. Typical global 3D SALSA3D models have on the order of 1/2 million nodes, so the challenge in calculating the covariance matrix is formidable: 0.9 TB storage for 1/2 of a symmetric matrix, necessitating an Out-Of-Core (OOC) blocked matrix solution technique. With our approach the tomography matrix (G which includes a prior model covariance constraint) is multiplied by its transpose (GTG) and written in a blocked sub-matrix fashion. We employ a distributed parallel solution paradigm that solves for (GTG)-1 by assigning blocks to individual processing nodes for matrix decomposition update and scaling operations. We first find the Cholesky decomposition of GTG which is subsequently inverted. Next, we employ OOC matrix multiplication methods to calculate the model covariance matrix from (GTG)-1 and an assumed data covariance matrix. Given the model covariance matrix, we solve for the travel-time covariance associated with arbitrary ray-paths by summing the model covariance along both ray paths. Setting the paths equal and taking the square root yields the travel prediction uncertainty for the single path.

Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye.

PubMed

Dietzek, Benjamin; Brüggemann, Ben; Pascher, Torbjörn; Yartsev, Arkady

2007-10-31

Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.

Anatomy of an Elementary Chemical Reaction

NASA Astrophysics Data System (ADS)

Alexander, Andrew J.; Zare, Richard N.

1998-09-01

The alchemists of old sought the knowledge to transform one material to another-for example, base metals into gold-as a path to the elixir of life. As chemists have concerned themselves with the transformation from compound to compound, so they have become involved in trying to uncover the structures of molecules and the pathways that reactions follow. Classically, the study of reaction mechanisms in chemistry encompasses reaction kinetics, the study of velocities or rates of reactions, and reaction dynamics, the study of the nanoscopic motion and rearrangement of atoms during a reactive event. An essential aim of this article is to bring the reader to a favorable vantage point with a brief introduction to reactive dynamics, and from there to describe some examples of recent strategies that have been employed to promote a fundamental understanding of the anatomy of elementary chemical reactions. In the final section we ponder future directions for this rapidly evolving field of research.

Paper-cutting operations using scissors in Drury's law tasks.

PubMed

Yamanaka, Shota; Miyashita, Homei

2018-05-01

Human performance modeling is a core topic in ergonomics. In addition to deriving models, it is important to verify the kinds of tasks that can be modeled. Drury's law is promising for path tracking tasks such as navigating a path with pens or driving a car. We conducted an experiment based on the observation that paper-cutting tasks using scissors resemble such tasks. The results showed that cutting arc-like paths (1/4 of a circle) showed an excellent fit with Drury's law (R 2  > 0.98), whereas cutting linear paths showed a worse fit (R 2  > 0.87). Since linear paths yielded better fits when path amplitudes were divided (R 2  > 0.99 for all amplitudes), we discuss the characteristics of paper-cutting operations using scissors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effect of electron Monte Carlo collisions on a hybrid simulation of a low-pressure capacitively coupled plasma

NASA Astrophysics Data System (ADS)

Hwang, Seok Won; Lee, Ho-Jun; Lee, Hae June

2014-12-01

Fluid models have been widely used and conducted successfully in high pressure plasma simulations where the drift-diffusion and the local-field approximation are valid. However, fluid models are not able to demonstrate non-local effects related to large electron energy relaxation mean free path in low pressure plasmas. To overcome this weakness, a hybrid model coupling electron Monte Carlo collision (EMCC) method with the fluid model is introduced to obtain precise electron energy distribution functions using pseudo-particles. Steady state simulation results by a one-dimensional hybrid model which includes EMCC method for the collisional reactions but uses drift-diffusion approximation for electron transport in a fluid model are compared with those of a conventional particle-in-cell (PIC) and a fluid model for low pressure capacitively coupled plasmas. At a wide range of pressure, the hybrid model agrees well with the PIC simulation with a reduced calculation time while the fluid model shows discrepancy in the results of the plasma density and the electron temperature.

Theoretical Investigation of the Interfacial Reactions during Hot-Dip Galvanizing of Steel

NASA Astrophysics Data System (ADS)

Mandal, G. K.; Balasubramaniam, R.; Mehrotra, S. P.

2009-03-01

In the modern galvanizing line, as soon as the steel strip enters the aluminum-containing zinc bath, two reactions occur at the strip and the liquid-zinc alloy interface: (1) iron rapidly dissolves from the strip surface, raising the iron concentration in the liquid phase at the strip-liquid interface; and (2) aluminum forms a stable aluminum-iron intermetallic compound layer at the strip-coating interface due to its greater affinity toward iron. The main objective of this study is to develop a simple and realistic mathematical model for better understanding of the kinetics of galvanizing reactions at the strip and the liquid-zinc alloy interface. In the present study, a model is proposed to simulate the effect of various process parameters on iron dissolution in the bath, as well as, aluminum-rich inhibition layer formation at the substrate-coating interface. The transient-temperature profile of the immersed strip is predicted based on conductive and convective heat-transfer mechanisms. The inhibition-layer thickness at the substrate-coating interface is predicted by assuming the cooling path of the immersed strip consists of a series of isothermal holds of infinitesimal time-step. The influence of galvanizing reaction is assessed by considering nucleation and growth mechanisms at each hold time, which is used to estimate the total effect of the immersion time on the formation mechanism of the inhibition layer. The iron- dissolution model is developed based on well established principles of diffusion taking into consideration the area fraction covered by the intermetallic on the strip surface during formation of the inhibition layer. The model can be effectively used to monitor the dross formation in the bath by optimizing the process parameters. Theoretical predictions are compared with the findings of other researchers. Simulated results are in good agreement with the theoretical and experimental observation carried out by other investigators.

Oxygenolysis of flavonoid compounds: DFT description of the mechanism for quercetin.

PubMed

Fiorucci, Sébastien; Golebiowski, Jerôme; Cabrol-Bass, Daniel; Antonczak, Serge

2004-11-12

Flavonoids are naturally occurring phenol derivatives present in substantial amounts in a large variety of plants, fruits and vegetables daily eaten by humans. Most of these compounds exhibit several interesting biological activities, such as antiradical and antioxidant actions. Indeed, by complexation with specific enzymes, flavonoids are notably liable to metabolize molecular dioxygen. On the basis of experimental results describing oxygenolysis of the flavonoid quercetin, activated by the enzyme quercetin 2,3-dioxygenase (2,3-QD),ur attention has focused on the role of metal center in the activation of the substrate quercetin. Thus, in the present study, by means of DFT calculations at the B3LYP/ 6-31(+)G* level on model molecular systems, we describe different mechanisms for dioxygen metabolization by quercetin. Stationary points are described, and energetic and structural analyses along the reaction paths are reported. Our calculations show that the copper cation must act as an oxidant towards the substrate and that the reaction proceeds through a 1,3-cycloaddition.

A study of the dynamics and photochemistry of vibrationally excited ozone in the middle atmosphere

NASA Astrophysics Data System (ADS)

Kaufmann, M.; Gil-Lopez, S.; Imk-Iaa Mipas/Envisat Team

The vibrational states of ozone depart from local thermodynamic equilibrium (LTE) due to radiative absorption, chemical pumping, spontaneous emission, and photochemical reaction. The recombination reaction of O+O_2 is the most important source of highly excited ozone, however the distribution of the energy disposal (nascent distribution) is poorly known. In addition, the collisional relaxation scheme is another significant source of uncertainty in the modeling of ozone infrared radiation. We have built a non-LTE model being part of the Generic RAdiative traNsfer AnD non-LTE population Algorithm (GRANADA) that represents the nascent distribution by means of a linear surprisal model. For the collisional relaxation we extrapolate measured rates of the fundamental bands to hot band transitions by using a Landau-Teller type scaling in combination with a relaxation-path dependent energy-gap model. In this talk we present model results in terms of ozone vibrational temperatures and atmospheric limb radiances in the 4-15 μm region. The modeled limb spectra will be compared with measurements from the MIPAS (Michelson Interferometer for Passive Atmosphere Sounding) instrument on board of the polar orbiter ENVISAT. The high spectral resolution of this instrument gives a unique opportunity to observe ozone non-LTE emissions down to the lower stratosphere where ozone densities are high enough to sense even highly excited vibrational states. These give valuable information for the validation of the non-LTE scheme, and therefore will improve the quality of upper mesospheric ozone retrievals.

Formation of cyanoallene (buta-2, 3-dienenitrile) in the interstellar medium: a quantum chemical and spectroscopic study

NASA Astrophysics Data System (ADS)

Singh, Amresh; Shivani; Misra, Alka; Tandon, Poonam

2014-03-01

The interstellar medium, filling the vast space between stars, is a rich reservoir of molecular material ranging from simple diatomic molecules to more complex, astrobiologically important molecules such as vinylcyanide, methylcyanodiaccetylene, cyanoallene, etc. Interstellar molecular cyanoallene is one of the most stable isomers of methylcynoacetylene. An attempt has been made to explore the possibility of forming cyanoallene in interstellar space by radical-radical and radical-molecule interaction schemes in the gaseous phase. The formation of cyanoallene starting from some simple, neutral interstellar molecules and radicals has been studied using density functional theory. The reaction energies and structures of the reactants and products show that the formation of cyanoallene is possible in the gaseous phase. Both of the considered reaction paths are totally exothermic and barrierless, thus giving rise to a high probability of occurrence. Rate constants for each step in the formation process of cyanoallene in both the reaction paths are estimated. A full vibrational analysis has been attempted for cyanoallene in the harmonic and anharmonic approximations. Anharmonic spectroscopic parameters such as rotational constants, rotation-vibration coupling constants and centrifugal distortion constants have been calculated.

The reactions to macro-economic crises in Nordic health system policies: Denmark, Finland and Sweden, 1980-2013.

PubMed

Lehto, Juhani; Vrangbæk, Karsten; Winblad, Ulrika

2015-01-01

Denmark, Finland and Sweden have experienced two major recessions during the last 25 years. The adjustments to the earlier crisis in the late 1980s (Denmark) and early 1990s (Finland and Sweden) resembled the policies in many other European countries during the present crisis. The analysis of relationship of deep economic crises and growth period between them to the health system policies and institutions in the three countries from the 1980s to 2013 is based on a categorisation of reactions to external shocks as path conforming or path breaking. The results of the empirical long-term trends show that the reactions to deep recessions have been mainly temporary adjustments and acceleration of changes already prepared before economic crisis. The economic crisis in the three countries has not been 'good enough' to enable paradigmatic changes in the Nordic public, decentralised and equity-oriented health systems. Changes such as the slow privatisation in care funding and production and the adoption of new management practices indicate an ongoing paradigmatic change related to longer-term societal, ideological and political developments rather than directly to economic crises or growth.

An experimental and kinetic investigation of premixed furan/oxygen/argon flames

PubMed Central

Tian, Zhenyu; Yuan, Tao; Fournet, Rene; Glaude, Pierre-Alexandre; Sirjean, Baptiste; Battin-Leclerc, Frédérique; Zhang, Kuiwen; Qi, Fei

2013-01-01

The detailed chemical structures of three low-pressure (35 Torr) premixed laminar furan/oxygen/argon flames with equivalence ratios of 1.4, 1.8 and 2.2 have been investigated by using tunable synchrotron vacuum ultraviolet (VUV) photoionization and molecular-beam mass spectrometry. About 40 combustion species including hydrocarbons and oxygenated intermediates have been identified by measurements of photoionization efficiency spectra. Mole fraction profiles of the flame species including reactants, intermediates and products have been determined by scanning burner position with some selected photon energies near ionization thresholds. Flame temperatures have been measured by a Pt-6%Rh/Pt-30%Rh thermocouple. A new mechanism involving 206 species and 1368 reactions has been proposed whose predictions are in reasonable agreement with measured species profiles for the three investigated flames. Rate-of-production and sensitivity analyses have been performed to track the key reaction paths governing furan consumption for different equivalence ratios. Both experimental and modeling results indicate that few aromatics could be formed in these flames. Furthermore, the current model has been validated against previous pyrolysis results of the literature obtained behind shock waves and the agreement is reasonable as well. PMID:23814311

An experimental and kinetic investigation of premixed furan/oxygen/argon flames.

PubMed

Tian, Zhenyu; Yuan, Tao; Fournet, Rene; Glaude, Pierre-Alexandre; Sirjean, Baptiste; Battin-Leclerc, Frédérique; Zhang, Kuiwen; Qi, Fei

2011-04-01

The detailed chemical structures of three low-pressure (35 Torr) premixed laminar furan/oxygen/argon flames with equivalence ratios of 1.4, 1.8 and 2.2 have been investigated by using tunable synchrotron vacuum ultraviolet (VUV) photoionization and molecular-beam mass spectrometry. About 40 combustion species including hydrocarbons and oxygenated intermediates have been identified by measurements of photoionization efficiency spectra. Mole fraction profiles of the flame species including reactants, intermediates and products have been determined by scanning burner position with some selected photon energies near ionization thresholds. Flame temperatures have been measured by a Pt-6%Rh/Pt-30%Rh thermocouple. A new mechanism involving 206 species and 1368 reactions has been proposed whose predictions are in reasonable agreement with measured species profiles for the three investigated flames. Rate-of-production and sensitivity analyses have been performed to track the key reaction paths governing furan consumption for different equivalence ratios. Both experimental and modeling results indicate that few aromatics could be formed in these flames. Furthermore, the current model has been validated against previous pyrolysis results of the literature obtained behind shock waves and the agreement is reasonable as well.

Mechanical catalysis on the centimetre scale

PubMed Central

Miyashita, Shuhei; Audretsch, Christof; Nagy, Zoltán; Füchslin, Rudolf M.; Pfeifer, Rolf

2015-01-01

Enzymes play important roles in catalysing biochemical transaction paths, acting as logical machines through the morphology of the processes. A key challenge in elucidating the nature of these systems, and for engineering manufacturing methods inspired by biochemical reactions, is to attain a comprehensive understanding of the stereochemical ground rules of enzymatic reactions. Here, we present a model of catalysis that can be performed magnetically by centimetre-sized passive floating units. The designed system, which is equipped with permanent magnets only, passively obeys the local causalities imposed by magnetic interactions, albeit it shows a spatial behaviour and an energy profile analogous to those of biochemical enzymes. In this process, the enzyme units trigger physical conformation changes of the target by levelling out the magnetic potential barrier (activation potential) to a funnel type and, thus, induce cascading conformation changes of the targeted substrate units reacting in parallel. The inhibitor units, conversely, suppress such changes by increasing the potential. Because the model is purely mechanical and established on a physics basis in the absence of turbulence, each performance can be explained by the morphology of the unit, extending the definition of catalysis to systems of alternative scales. PMID:25652461

Mechanical catalysis on the centimetre scale.

PubMed

Miyashita, Shuhei; Audretsch, Christof; Nagy, Zoltán; Füchslin, Rudolf M; Pfeifer, Rolf

2015-03-06

Enzymes play important roles in catalysing biochemical transaction paths, acting as logical machines through the morphology of the processes. A key challenge in elucidating the nature of these systems, and for engineering manufacturing methods inspired by biochemical reactions, is to attain a comprehensive understanding of the stereochemical ground rules of enzymatic reactions. Here, we present a model of catalysis that can be performed magnetically by centimetre-sized passive floating units. The designed system, which is equipped with permanent magnets only, passively obeys the local causalities imposed by magnetic interactions, albeit it shows a spatial behaviour and an energy profile analogous to those of biochemical enzymes. In this process, the enzyme units trigger physical conformation changes of the target by levelling out the magnetic potential barrier (activation potential) to a funnel type and, thus, induce cascading conformation changes of the targeted substrate units reacting in parallel. The inhibitor units, conversely, suppress such changes by increasing the potential. Because the model is purely mechanical and established on a physics basis in the absence of turbulence, each performance can be explained by the morphology of the unit, extending the definition of catalysis to systems of alternative scales.

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

Analysis of water flow paths: methodology and example calculations for a potential geological repository in Sweden.

PubMed

Werner, Kent; Bosson, Emma; Berglund, Sten

2006-12-01

Safety assessment related to the siting of a geological repository for spent nuclear fuel deep in the bedrock requires identification of potential flow paths and the associated travel times for radionuclides originating at repository depth. Using the Laxemar candidate site in Sweden as a case study, this paper describes modeling methodology, data integration, and the resulting water flow models, focusing on the Quaternary deposits and the upper 150 m of the bedrock. Example simulations identify flow paths to groundwater discharge areas and flow paths in the surface system. The majority of the simulated groundwater flow paths end up in the main surface waters and along the coastline, even though the particles used to trace the flow paths are introduced with a uniform spatial distribution at a relatively shallow depth. The calculated groundwater travel time, determining the time available for decay and retention of radionuclides, is on average longer to the coastal bays than to other biosphere objects at the site. Further, it is demonstrated how GIS-based modeling can be used to limit the number of surface flow paths that need to be characterized for safety assessment. Based on the results, the paper discusses an approach for coupling the present models to a model for groundwater flow in the deep bedrock.

Varying Paths for Learning to Revise.

ERIC Educational Resources Information Center

Zellermayer, Michal; Cohen, Judith

1996-01-01

Studied how preacademic students acquired revision strategies based upon their individual cognitive abilities. Revision Cuing Devices, teacher intervention and student reaction, peer support and collaboration, think-aloud protocols, and holistic assessments were used to develop individual strategies. Eventually revision support faded without signs…

Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods.

PubMed

Suleimanov, Yury V; Green, William H

2015-09-08

We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation double- and single-ended transition-state optimization algorithms--the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several single-molecule systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes.

Coming out during adolescence: Perceived parents' reactions and internalized sexual stigma.

PubMed

Baiocco, Roberto; Fontanesi, Lilybeth; Santamaria, Federica; Ioverno, Salvatore; Baumgartner, Emma; Laghi, Fiorenzo

2016-08-01

Disclosing sexual orientation to parents is a challenging developmental task for lesbian and gay adolescents. The aim of the study is to investigate parental negative reaction to coming out, which is associated with high levels of internalized sexual stigma and psychological problems. Participants' perceptions of their parents' reactions, age at coming out, gender, parental political orientation and religiosity, family functioning, and internalized sexual stigma were assessed in 150 Italian homosexual adolescents. Findings confirm that negative parental reactions are connected to poor family functioning and strong beliefs in traditional values. Path analysis results identified that negative reaction to coming out mediates the effect between a more rigid family functioning and internalized sexual stigma. Implications for clinical and social fields are discussed. © The Author(s) 2014.

Application of a pore-scale reactive transport model to a natural analog for reaction-induced pore alterations

DOE PAGES

Yoon, Hongkyu; Major, Jonathan; Dewers, Thomas; ...

2017-01-05

Dissolved CO 2 in the subsurface resulting from geological CO 2 storage may react with minerals in fractured rocks, confined aquifers, or faults, resulting in mineral precipitation and dissolution. The overall rate of reaction can be affected by coupled processes including hydrodynamics, transport, and reactions at the (sub) pore-scale. In this work pore-scale modeling of coupled fluid flow, reactive transport, and heterogeneous reactions at the mineral surface is applied to account for permeability alterations caused by precipitation-induced pore-blocking. This paper is motivated by observations of CO 2 seeps from a natural CO 2 sequestration analog, Crystal Geyser, Utah. Observations alongmore » the surface exposure of the Little Grand Wash fault indicate the lateral migration of CO 2 seep sites (i.e., alteration zones) of 10–50 m width with spacing on the order of ~100 m over time. Sandstone permeability in alteration zones is reduced by 3–4 orders of magnitude by carbonate cementation compared to unaltered zones. One granular porous medium and one fracture network systems are used to conceptually represent permeable porous media and locations of conduits controlled by fault-segment intersections and/or topography, respectively. Simulation cases accounted for a range of reaction regimes characterized by the Damköhler (Da) and Peclet (Pe) numbers. Pore-scale simulation results demonstrate that combinations of transport (Pe), geochemical conditions (Da), solution chemistry, and pore and fracture configurations contributed to match key patterns observed in the field of how calcite precipitation alters flow paths by pore plugging. This comparison of simulation results with field observations reveals mechanistic explanations of the lateral migration and enhances our understanding of subsurface processes associated with the CO 2 injection. In addition, permeability and porosity relations are constructed from pore-scale simulations which account for a range of reaction regimes characterized by the Da and Pe numbers. Finally, the functional relationships obtained from pore-scale simulations can be used in a continuum scale model that may account for large-scale phenomena mimicking lateral migration of surface CO 2 seeps.« less

Nitric Oxide Reduction to Ammonia by TiO 2 Electrons in Colloid Solution via Consecutive One-Electron Transfer Steps

DOE PAGES

Goldstein, Sara; Behar, David; Rajh, Tijana; ...

2015-03-02

The reaction mechanism of nitric oxide (NO) reduction by excess electrons on TiO 2 nanoparticles (e TiO2–) has been studied under anaerobic conditions. TiO 2 was loaded with 10–130 electrons per particle using γ-irradiation of acidic TiO 2 colloid solutions containing 2-propanol. The study is based on time-resolved kinetics and reactants and products analysis. The reduction of NO by e TiO2– is interpreted in terms of competition between a reaction path leading to formation of NH 3 and a path leading to N 2O and N 2. The proposed mechanism involves consecutive one-electron transfers of NO, and its reduction intermediatesmore » HNO, NH 2O•, and NH 2OH. The results show that e TiO2– does not reduce N 2O and N 2. Second-order rate constants of e TiO2– reactions with NO (740 ± 30 M –1 s –1) and NH 2OH (270 ± 30 M –1 s –1) have been determined employing the rapid-mixing stopped-flow technique and that with HNO (>1.3 × 10 6 M –1 s –1) was derived from fitting the kinetic traces to the suggested reaction mechanism, which is discussed in detail.« less

Engine Load Path Calculations - Project Neo

NASA Technical Reports Server (NTRS)

Fisher, Joseph

2014-01-01

A mathematical model of the engine and actuator geometry was developed and used to perform a static force analysis of the system with the engine at different pitch and yaw angles. This analysis yielded the direction and magnitude of the reaction forces at the mounting points of the engine and actuators. These data were used to validate the selection of the actuators installed in the system and to design a new spherical joint to mount the engine on the test fixture. To illustrate the motion of the system and to further interest in the project, a functional 3D printed version of the system was made, featuring the full mobility of the real system.

Experimental investigation of the auto-ignition characteristics of oxygenated reference fuel compounds

NASA Astrophysics Data System (ADS)

Walton, Stephen Michael

The increased use of biofuels presents an opportunity to improve combustion performance while simultaneously reducing greenhouse gases and pollutant emissions. This work focused on improving the fundamental understanding of the auto-ignition chemistry of oxygenated reference fuel compounds. A systematic study of the effects of ester structure on ignition chemistry was performed using the University of Michigan Rapid Compression Facility. The ignition properties of the ester compounds were investigated over a broad range of pressures (P=5-20 atm) and temperatures (T=850-1150 K) which are directly relevant to advanced combustion engine strategies. Ignition delay times for five esters were determined using the RCF. The esters were selected to systematically consider the chemical structure of the compounds. Three esters were saturated: methyl butanoate, butyl methanoate, and ethyl propanoate; and two were unsaturated: methyl crotonate and methyl trans-3-hexenoate. The unsaturated esters were more reactive than their saturated counterparts, with the largest unsaturated ester, methyl trans-3-hexenoate having the highest reactivity. Two isomers of the saturated esters, butyl methanoate and ethyl propanoate, were more reactive than the isomer methyl butanoate. The results are explained if we assume that butyl methanoate and ethyl propanoate form intermediate ring structures which decompose more rapidly than esters such as methyl butanoate, which do not form ring structures. Modeling studies of the reaction chemistry were conducted for methyl butanoate and ethyl propanoate, for which detailed mechanisms were available in the literature. The new experimental data indicated that literature rate coefficients for some of the methyl butanoate/HO2 reactions were too fast. Modifying these within the theoretical uncertainties for the reaction rates, led to excellent agreement between the model predictions and the experimental data. Comparison of the modeling results with the intermediates measured during methyl butanoate ignition indicated that pathways leading to the formation of small hydrocarbons are relatively well represented in the reaction mechanism. The results of this work provide archival benchmark data for improved understanding of the dominant reaction pathways and species controlling the auto-ignition of oxygenated reference fuel compounds. These data also provide a path for continued development of chemical kinetic models to optimize practical combustion systems.

Implications of path tolerance and path characteristics on critical vehicle manoeuvres

NASA Astrophysics Data System (ADS)

Lundahl, K.; Frisk, E.; Nielsen, L.

2017-12-01

Path planning and path following are core components in safe autonomous driving. Typically, a path planner provides a path with some tolerance on how tightly the path should be followed. Based on that, and other path characteristics, for example, sharpness of curves, a speed profile needs to be assigned so that the vehicle can stay within the given tolerance without going unnecessarily slow. Here, such trajectory planning is based on optimal control formulations where critical cases arise as on-the-limit solutions. The study focuses on heavy commercial vehicles, causing rollover to be of a major concern, due to the relatively high centre of gravity. Several results are obtained on required model complexity depending on path characteristics, for example, quantification of required path tolerance for a simple model to be sufficient, quantification of when yaw inertia needs to be considered in more detail, and how the curvature rate of change interplays with available friction. Overall, in situations where the vehicle is subject to a wide range of driving conditions, from good transport roads to more tricky avoidance manoeuvres, the requirements on the path following will vary. For this, the provided results form a basis for real-time path following.

Effects of social support and battle intensity on loneliness and breakdown during combat.

PubMed

Solomon, Z; Mikulincer, M; Hobfoll, S E

1986-12-01

A sample of 382 Israeli soldiers who developed combat stress reactions (CSR) during the 1982 Israel-Lebanon War were compared with groups of carefully matched controls who did not develop CSR. Lack of social support from officers was found to be related to greater feelings of loneliness and greater likelihood of CSR in soldiers. Lack of social support from buddies was found to be related to greater loneliness. Intensity of battle was also found to be related to greater feelings of loneliness and increased likelihood of CSR. A path model was tested and supported. The model suggests that battle intensity and officer support lead to CSR directly and indirectly by causing increased feelings of loneliness. Possible cognitive and psychodynamic explanations for the findings are offered. The limitations of making causal statements from retrospective perceptions is discussed.

Requirements Formulation and Dynamic Jitter Analysis for Fourier-Kelvin Stellar Interferometer

NASA Technical Reports Server (NTRS)

Liu, Kuo-Chia; Hyde, Tristram; Blaurock, Carl; Bolognese, Jeff; Howard, Joseph; Danchi, William

2004-01-01

The Fourier-Kelvin Stellar Interferometer (FKSI) has been proposed to detect and characterize extra solar giant planets. The baseline configuration for FKSI is a two- aperture, structurally connected nulling interferometer, capable of providing null depth less than lo4 in the infrared. The objective of this paper is to summarize the process for setting the top level requirements and the jitter analysis performed on FKSI to date. The first part of the paper discusses the derivation of dynamic stability requirements, necessary for meeting the FKSI nulling demands. An integrated model including structures, optics, and control systems has been developed to support dynamic jitter analysis and requirements verification. The second part of the paper describes how the integrated model is used to investigate the effects of reaction wheel disturbances on pointing and optical path difference stabilities.

Epidemic spreading by objective traveling

NASA Astrophysics Data System (ADS)

Tang, Ming; Liu, Zonghua; Li, Baowen

2009-07-01

A fundamental feature of agent traveling in social networks is that traveling is usually not a random walk but with a specific destination and goes through the shortest path from starting to destination. A serious consequence of the objective traveling is that it may result in a fast epidemic spreading, such as SARS etc. In this letter we present a reaction-traveling model to study how the objective traveling influences the epidemic spreading. We consider a random scale-free meta-population network with sub-population at each node. Through a SIS model we theoretically prove that near the threshold of epidemic outbreak, the objective traveling can significantly enhance the final infected population and the infected fraction at a node is proportional to its betweenness for the traveling agents and approximately proportional to its degree for the non-traveling agents. Numerical simulations have confirmed the theoretical predictions.

Personalized Modeling for Prediction with Decision-Path Models

PubMed Central

Visweswaran, Shyam; Ferreira, Antonio; Ribeiro, Guilherme A.; Oliveira, Alexandre C.; Cooper, Gregory F.

2015-01-01

Deriving predictive models in medicine typically relies on a population approach where a single model is developed from a dataset of individuals. In this paper we describe and evaluate a personalized approach in which we construct a new type of decision tree model called decision-path model that takes advantage of the particular features of a given person of interest. We introduce three personalized methods that derive personalized decision-path models. We compared the performance of these methods to that of Classification And Regression Tree (CART) that is a population decision tree to predict seven different outcomes in five medical datasets. Two of the three personalized methods performed statistically significantly better on area under the ROC curve (AUC) and Brier skill score compared to CART. The personalized approach of learning decision path models is a new approach for predictive modeling that can perform better than a population approach. PMID:26098570

Some new reaction pathways for the formation of cytosine in interstellar space - A quantum chemical study

NASA Astrophysics Data System (ADS)

Gupta, V. P.; Tandon, Poonam; Mishra, Priti

2013-03-01

The detection of nucleic acid bases in carbonaceous meteorites suggests that their formation and survival is possible outside of the Earth. Small N-heterocycles, including pyrimidine, purines and nucleobases, have been extensively sought in the interstellar medium. It has been suggested theoretically that reactions between some interstellar molecules may lead to the formation of cytosine, uracil and thymine though these processes involve significantly high potential barriers. We attempted therefore to use quantum chemical techniques to explore if cytosine can possibly form in the interstellar space by radical-radical and radical-molecule interaction schemes, both in the gas phase and in the grains, through barrier-less or low barrier pathways. Results of DFT calculations for the formation of cytosine starting from some of the simple molecules and radicals detected in the interstellar space are being reported. Global and local descriptors such as molecular hardness, softness and electrophilicity, and condensed Fukui functions and local philicity indices were used to understand the mechanistic aspects of chemical reaction. The presence and nature of weak bonds in the molecules and transition states formed during the reaction process have been ascertained using Bader's quantum theory of atoms in molecules (QTAIMs). Two exothermic reaction pathways starting from propynylidyne (CCCH) and cyanoacetylene (HCCCN), respectively, have been identified. While the first reaction path is found to be totally exothermic, it involves a barrier of 12.5 kcal/mol in the gas phase against the lowest value of about 32 kcal/mol reported in the literature. The second path is both exothermic and barrier-less. The later has, therefore, a greater probability of occurrence in the cold interstellar clouds (10-50 K).

NetpathXL - An Excel Interface to the Program NETPATH

USGS Publications Warehouse

Parkhurst, David L.; Charlton, Scott R.

2008-01-01

NetpathXL is a revised version of NETPATH that runs under Windows? operating systems. NETPATH is a computer program that uses inverse geochemical modeling techniques to calculate net geochemical reactions that can account for changes in water composition between initial and final evolutionary waters in hydrologic systems. The inverse models also can account for the isotopic composition of waters and can be used to estimate radiocarbon ages of dissolved carbon in ground water. NETPATH relies on an auxiliary, database program, DB, to enter the chemical analyses and to perform speciation calculations that define total concentrations of elements, charge balance, and redox state of aqueous solutions that are then used in inverse modeling. Instead of DB, NetpathXL relies on Microsoft Excel? to enter the chemical analyses. The speciation calculation formerly included in DB is implemented within the program NetpathXL. A program DBXL can be used to translate files from the old DB format (.lon files) to NetpathXL spreadsheets, or to create new NetpathXL spreadsheets. Once users have a NetpathXL spreadsheet with the proper format, new spreadsheets can be generated by copying or saving NetpathXL spreadsheets. In addition, DBXL can convert NetpathXL spreadsheets to PHREEQC input files. New capabilities in PHREEQC (version 2.15) allow solution compositions to be written to a .lon file, and inverse models developed in PHREEQC to be written as NetpathXL .pat and model files. NetpathXL can open NetpathXL spreadsheets, NETPATH-format path files (.pat files), and NetpathXL-format path files (.pat files). Once the speciation calculations have been performed on a spreadsheet file or a .pat file has been opened, the NetpathXL calculation engine is identical to the original NETPATH. Development of models and viewing results in NetpathXL rely on keyboard entry as in NETPATH.

Crack Path Selection in Thermally Loaded Borosilicate/Steel Bibeam Specimen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grutzik, Scott Joseph; Reedy, Jr., E. D.

Here, we have developed a novel specimen for studying crack paths in glass. Under certain conditions, the specimen reaches a state where the crack must select between multiple paths satisfying the K II = 0 condition. This path selection is a simple but challenging benchmark case for both analytical and numerical methods of predicting crack propagation. We document the development of the specimen, using an uncracked and instrumented test case to study the effect of adhesive choice and validate the accuracy of both a simple beam theory model and a finite element model. In addition, we present preliminary fracture testmore » results and provide a comparison to the path predicted by two numerical methods (mesh restructuring and XFEM). The directional stability of the crack path and differences in kink angle predicted by various crack kinking criteria is analyzed with a finite element model.« less

Crack Path Selection in Thermally Loaded Borosilicate/Steel Bibeam Specimen

DOE PAGES

Grutzik, Scott Joseph; Reedy, Jr., E. D.

2017-08-04

Here, we have developed a novel specimen for studying crack paths in glass. Under certain conditions, the specimen reaches a state where the crack must select between multiple paths satisfying the K II = 0 condition. This path selection is a simple but challenging benchmark case for both analytical and numerical methods of predicting crack propagation. We document the development of the specimen, using an uncracked and instrumented test case to study the effect of adhesive choice and validate the accuracy of both a simple beam theory model and a finite element model. In addition, we present preliminary fracture testmore » results and provide a comparison to the path predicted by two numerical methods (mesh restructuring and XFEM). The directional stability of the crack path and differences in kink angle predicted by various crack kinking criteria is analyzed with a finite element model.« less

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model.

PubMed

Plotnikov, Nikolay V

2014-08-12

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force.

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model

PubMed Central

2015-01-01

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force. PMID:25136268

The rate of the deoxygenation reaction limits myoglobin- and hemoglobin-facilitated O₂ diffusion in cells.

PubMed

Endeward, Volker

2012-05-01

A mathematical model describing facilitation of O(2) diffusion by the diffusion of myoglobin and hemoglobin is presented. The equations are solved numerically by a finite-difference method for the conditions as they prevail in cardiac and skeletal muscle and in red cells without major simplifications. It is demonstrated that, in the range of intracellular diffusion distances, the degree of facilitation is limited by the rate of the chemical reaction between myglobin or hemoglobin and O(2). The results are presented in the form of relationships between the degree of facilitation and the length of the diffusion path on the basis of the known kinetics of the oxygenation-deoxygenation reactions. It is concluded that the limitation by reaction kinetics reduces the maximally possible facilitated oxygen diffusion in cardiomyoctes by ∼50% and in skeletal muscle fibers by ∼ 20%. For human red blood cells, a reduction of facilitated O(2) diffusion by 36% is obtained in agreement with previous reports. This indicates that, especially in cardiomyocytes and red cells, chemical equilibrium between myoglobin or hemoglobin and O(2) is far from being established, an assumption that previously has often been made. Although the "O(2) transport function" of myoglobin in cardiac muscle cells thus is severely limited by the chemical reaction kinetics, and to a lesser extent also in skeletal muscle, it is noteworthy that the speed of release of O(2) from MbO(2), the "storage function," is not limited by the reaction kinetics under physiological conditions.

Long-term modeling of glass waste in portland cement- and clay-based matrices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stockman, H.W.; Nagy, K.L.; Morris, C.E.

A set of ``templates`` was developed for modeling waste glass interactions with cement-based and clay-based matrices. The templates consist of a modified thermodynamic database, and input files for the EQ3/6 reaction path code, containing embedded rate models and compositions for waste glass, cement, and several pozzolanic materials. Significant modifications were made in the thermodynamic data for Th, Pb, Ra, Ba, cement phases, and aqueous silica species. It was found that the cement-containing matrices could increase glass corrosion rates by several orders of magnitude (over matrixless or clay matrix systems), but they also offered the lowest overall solubility for Pb, Ra,more » Th and U. Addition of pozzolans to cement decreased calculated glass corrosion rates by up to a factor of 30. It is shown that with current modeling capabilities, the ``affinity effect`` cannot be trusted to passivate glass if nuclei are available for precipitation of secondary phases that reduce silica activity.« less

Rearfoot eversion has indirect effects on plantar fascia tension by changing the amount of arch collapse.

PubMed

Lee, Sae Yong; Hertel, Jay; Lee, Sung Cheol

2010-01-01

Rearfoot eversion motion and arch height are believed to contribute to increased tension on the plantar fascia and arch collapse during gait but the specifics of these relationships are not clear. To examine the relationships among static arch height, rearfoot eversion, dynamic arch height, and plantar fascia tension. 28 healthy males participated. After static arch height was measured, the subjects were asked to run at 4.5m/s while frontal plane rearfoot motion, dynamic arch height, and ground reaction forces were collected. The relationships among variables were examined with bivariate correlations and path analysis. The results indicated a high correlation between dynamic arch height and static arch height (r=0.642), plantar fascia tension (r=-0.797), and maximum rearfoot eversion motion during gait (r=-0.518). The path analysis model without the direct rearfoot eversion effect explained 81.2% of the variance in plantar fascia tension, while the model with the direct rearfoot eversion effect explained 82.1% of the variance in plantar fascia tension. Including the indirect effect of maximum rearfoot eversion motion on plantar fascia tension through control of dynamic arch height is the model that best explains the interrelationships of these foot characteristics. The amount of maximum rearfoot eversion motion itself is not a good predictor of plantar fascia tension, however, together with the arch height, maximum rearfoot eversion motion is a good predictor because it has a pronounced indirect effect on plantar fascia tension. Copyright 2010. Published by Elsevier Ltd.

Primary weathering rates, water transit times, and concentration-discharge relations: A theoretical analysis for the critical zone

NASA Astrophysics Data System (ADS)

Ameli, Ali A.; Beven, Keith; Erlandsson, Martin; Creed, Irena F.; McDonnell, Jeffrey J.; Bishop, Kevin

2017-01-01

The permeability architecture of the critical zone exerts a major influence on the hydrogeochemistry of the critical zone. Water flow path dynamics drive the spatiotemporal pattern of geochemical evolution and resulting streamflow concentration-discharge (C-Q) relation, but these flow paths are complex and difficult to map quantitatively. Here we couple a new integrated flow and particle tracking transport model with a general reversible Transition State Theory style dissolution rate law to explore theoretically how C-Q relations and concentration in the critical zone respond to decline in saturated hydraulic conductivity (Ks) with soil depth. We do this for a range of flow rates and mineral reaction kinetics. Our results show that for minerals with a high ratio of equilibrium concentration (Ceq) to intrinsic weathering rate (Rmax), vertical heterogeneity in Ks enhances the gradient of weathering-derived solute concentration in the critical zone and strengthens the inverse stream C-Q relation. As CeqRmax decreases, the spatial distribution of concentration in the critical zone becomes more uniform for a wide range of flow rates, and stream C-Q relation approaches chemostatic behavior, regardless of the degree of vertical heterogeneity in Ks. These findings suggest that the transport-controlled mechanisms in the hillslope can lead to chemostatic C-Q relations in the stream while the hillslope surface reaction-controlled mechanisms are associated with an inverse stream C-Q relation. In addition, as CeqRmax decreases, the concentration in the critical zone and stream become less dependent on groundwater age (or transit time).

Relationships between attitudes toward and achievement in science for rural middle school students: Patterns across gender

NASA Astrophysics Data System (ADS)

Mattern, Nancy Page Garland

Four causal models describing the relationships between attitudes and achievement have been proposed in the literature. The cross-effects, or reciprocal effects, model highlights the effects of prior attitudes on later achievement (over and above the effect of previous achievement) and of prior achievement on later attitudes (above the effect of previous attitudes). In the achievement predominant model, the effect of prior achievement on later attitudes is emphasized, controlling for the effect of previous attitudes. The effect of prior attitudes on later achievement, controlling for the effect of previous achievement, is emphasized in the attitudes predominant model. In the no cross-effects model there are no significant cross paths from prior attitudes to later achievement or from prior achievement to later attitudes. To determine the best-fitting model for rural seventh and eighth grade science girls and boys, the causal relationships over time between attitudes toward science and achievement in science were examined by gender using structural equation modeling. Data were collected in two waves, over one school year. A baseline measurement model was estimated in simultaneous two-group solutions and was a good fit to the data. Next, the four structural models were estimated and model fits compared. The three models nested within the structural cross-effects model showed significant decay of fit when compared to the fit of the cross-effects model. The cross-effects model was the best fit overall for middle school girls and boys. The cross-effects model was then tested for invariance across gender. There was significant decay of fit when model form, factor path loadings, and structural paths were constrained to be equal for girls and boys. Two structural paths, the path from prior achievement to later attitudes, and the path from prior attitudes to later attitudes, were the sources of gender non-invariance. Separate models were estimated for girls and boys, and the fits of nested models were compared. The no cross-effects model was the best-fitting model for rural middle school girls. The new no attitudes-path model was the best-fitting model for boys. Implications of these findings for teaching middle school students were discussed.

Carcinogenesis of urethane: simulation versus experiment.

PubMed

Lajovic, Andrej; Nagy, Leslie D; Guengerich, F Peter; Bren, Urban

2015-04-20

The carcinogenesis of urethane (ethyl carbamate), a byproduct of fermentation that is consistently found in various food products, was investigated with a combination of kinetic experiments and quantum chemical calculations. The main objective of the study was to find ΔG(⧧), the activation free energy for the rate-limiting step of the SN2 reaction among the ultimate carcinogen of urethane, vinyl carbamate epoxide (VCE), and different nucleobases of the DNA. In the experimental part, the second-order reaction rate constants for the formation of the main 7-(2-oxoethyl)guanine adduct in aqueous solutions of deoxyguanosine and in DNA were determined. A series of ab initio, density functional theory (DFT), and semiempirical molecular orbital (MO) calculations was then performed to determine the activation barriers for the reaction between VCE and nucleobases methylguanine, methyladenine, and methylcytosine. Effects of hydration were incorporated with the use of the solvent reaction field method of Tomasi and co-workers and the Langevine dipoles model of Florian and Warshel. The computational results for the main adduct were found to be in good agreement with the experiment, thus presenting strong evidence for the validity of the proposed SN2 mechanism. This allowed us to predict the activation barriers of reactions leading to side products for which kinetic experiments have not yet been performed. Our calculations have shown that the main 7-(2-oxoethyl)deoxyguanosine adduct indeed forms preferentially because the emergence of other adducts either proceeds across a significantly higher activation barrier or the geometry of the reaction requires the Watson-Crick pairs of the DNA to be broken. The computational study also considered the questions of stereoselectivity, the ease of the elimination of the leaving group, and the relative contributions of the two possible reaction paths for the formation of the 1,N(2)-ethenodeoxyguanosine adduct.

Using heat as a tracer to estimate spatially distributed mean residence times in the hyporheic zone of a riffle-pool sequence

USGS Publications Warehouse

Naranjo, Ramon C.

2013-01-01

Biochemical reactions that occur in the hyporheic zone are highly dependent on the time solutes that are in contact with sediments of the riverbed. In this investigation, we developed a 2-D longitudinal flow and solute-transport model to estimate the spatial distribution of mean residence time in the hyporheic zone. The flow model was calibrated using observations of temperature and pressure, and the mean residence times were simulated using the age-mass approach for steady-state flow conditions. The approach used in this investigation includes the mixing of different ages and flow paths of water through advection and dispersion. Uncertainty of flow and transport parameters was evaluated using standard Monte Carlo and the generalized likelihood uncertainty estimation method. Results of parameter estimation support the presence of a low-permeable zone in the riffle area that induced horizontal flow at a shallow depth within the riffle area. This establishes shallow and localized flow paths and limits deep vertical exchange. For the optimal model, mean residence times were found to be relatively long (9–40.0 days). The uncertainty of hydraulic conductivity resulted in a mean interquartile range (IQR) of 13 days across all piezometers and was reduced by 24% with the inclusion of temperature and pressure observations. To a lesser extent, uncertainty in streambed porosity and dispersivity resulted in a mean IQR of 2.2 and 4.7 days, respectively. Alternative conceptual models demonstrate the importance of accounting for the spatial distribution of hydraulic conductivity in simulating mean residence times in a riffle-pool sequence.

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

PubMed Central

2016-01-01

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition. PMID:27004858

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Wenjin; Ma, Ao, E-mail: aoma@uic.edu

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C{sub 7eq} → C{sub 7ax} transition of themore » alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.« less

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization.

PubMed

Li, Chun-Biu; Matsunaga, Yasuhiro; Toda, Mikito; Komatsuzaki, Tamiki

2005-11-08

By using the HCN/CNH isomerization reaction as an illustrative vehicle of chemical reactions on multisaddle energy landscapes, we give explicit visualizations of molecular motions associated with a straight-through reaction tube in the phase space inside which all reactive trajectories pass from one basin to another, with eliminating recrossing trajectories in the configuration space. This visualization provides us with a chemical intuition of how chemical species "walk along" the reaction-rate slope in the multidimensional phase space compared with the intrinsic reaction path in the configuration space. The distinct nonergodic features in the two different HCN and CNH wells can be easily demonstrated by a section of Poincare surface of section in those potential minima, which predicts in a priori the pattern of trajectories residing in the potential well. We elucidate the global phase-space structure which gives rise to the non-Markovian dynamics or the dynamical correlation of sequential multisaddle chemical reactions. The phase-space structure relevant to the controllability of the product state in chemical reactions is also discussed.

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Catalytic reactor

DOEpatents

Aaron, Timothy Mark [East Amherst, NY; Shah, Minish Mahendra [East Amherst, NY; Jibb, Richard John [Amherst, NY

2009-03-10

A catalytic reactor is provided with one or more reaction zones each formed of set(s) of reaction tubes containing a catalyst to promote chemical reaction within a feed stream. The reaction tubes are of helical configuration and are arranged in a substantially coaxial relationship to form a coil-like structure. Heat exchangers and steam generators can be formed by similar tube arrangements. In such manner, the reaction zone(s) and hence, the reactor is compact and the pressure drop through components is minimized. The resultant compact form has improved heat transfer characteristics and is far easier to thermally insulate than prior art compact reactor designs. Various chemical reactions are contemplated within such coil-like structures such that as steam methane reforming followed by water-gas shift. The coil-like structures can be housed within annular chambers of a cylindrical housing that also provide flow paths for various heat exchange fluids to heat and cool components.

Ab initio chemical kinetics for the HCCO + OH reaction

NASA Astrophysics Data System (ADS)

Mai, Tam V.-T.; Raghunath, P.; Le, Xuan T.; Huynh, Lam K.; Nam, Pham-Cam; Lin, M. C.

2014-01-01

The mechanism for the reaction of HCCO and OH has been investigated at different high-levels of theory. The reaction was found to occur on singlet and triplet potential energy surfaces with multiple accessible paths. Rate constants predicted by variational RRKM/ME calculations show that the reaction on both surfaces occurs primarily by barrierless OH attack at both C atoms producing excited intermediates which fragment to produce predominantly CO and 1,3HCOH with kS = 3.12 × 10-8T-0.59exp[-73.0/T] and kT = 6.29 × 10-11T0.13exp[108/T] cm3 molecule-1 s-1 at T = 300-2000 K, independent of pressure at P < 76 000 Torr.

Train repathing in emergencies based on fuzzy linear programming.

PubMed

Meng, Xuelei; Cui, Bingmou

2014-01-01

Train pathing is a typical problem which is to assign the train trips on the sets of rail segments, such as rail tracks and links. This paper focuses on the train pathing problem, determining the paths of the train trips in emergencies. We analyze the influencing factors of train pathing, such as transferring cost, running cost, and social adverse effect cost. With the overall consideration of the segment and station capability constraints, we build the fuzzy linear programming model to solve the train pathing problem. We design the fuzzy membership function to describe the fuzzy coefficients. Furthermore, the contraction-expansion factors are introduced to contract or expand the value ranges of the fuzzy coefficients, coping with the uncertainty of the value range of the fuzzy coefficients. We propose a method based on triangular fuzzy coefficient and transfer the train pathing (fuzzy linear programming model) to a determinate linear model to solve the fuzzy linear programming problem. An emergency is supposed based on the real data of the Beijing-Shanghai Railway. The model in this paper was solved and the computation results prove the availability of the model and efficiency of the algorithm.

Generation of RGB-D data for SLAM using robotic framework V-REP

NASA Astrophysics Data System (ADS)

Gritsenko, Pavel S.; Gritsenko, Igor S.; Seidakhmet, Askar Zh.; Abduraimov, Azizbek E.

2017-09-01

In this article, we will present a methodology to debug RGB-D SLAM systems as well as to generate testing data. We have created a model of a laboratory with an area of 250 m2 (25 × 10) with set of objects of different type. V-REP Microsoft Kinect sensor simulation model was used as a basis for robot vision system. Motion path of the sensor model has multiple loops. We have written a program in V-Rep native language Lua to record data array from the Microsoft Kinect sensor model. The array includes both RGB and Depth streams with full resolution (640 × 480) for every 10 cm of the path. The simulated path has absolute accuracy, since it is a simulation, and is represented by an array of transformation matrices (4 × 4). The length of the data array is 1000 steps or 100 m. The path simulates frequently occurring cases in SLAM, including loops. It is worth noting that the path was modeled for a mobile robot and it is represented by a 2D path parallel to the floor at a height of 40 cm.

A Path Model of School Violence Perpetration: Introducing Online Game Addiction as a New Risk Factor.

PubMed

Kim, Jae Yop; Lee, Jeen Suk; Oh, Sehun

2015-08-10

Drawing on the cognitive information-processing model of aggression and the general aggression model, we explored why adolescents become addicted to online games and how their immersion in online games affects school violence perpetration (SVP). For this purpose, we conducted statistical analyses on 1,775 elementary and middle school students who resided in northern districts of Seoul, South Korea. The results validated the proposed structural equation model and confirmed the statistical significance of the structural paths from the variables; that is, the paths from child abuse and self-esteem to SVP were significant. The levels of self-esteem and child abuse victimization affected SVP, and this effect was mediated by online game addiction (OGA). Furthermore, a multigroup path analysis showed significant gender differences in the path coefficients of the proposed model, indicating that gender exerted differential effects on adolescents' OGA and SVP. Based on these results, prevention and intervention methods to curb violence in schools have been proposed. © The Author(s) 2015.

Effect of shoe inserts on kinematics, center of pressure, and leg joint moments during running.

PubMed

Nigg, Benno M; Stergiou, Pro; Cole, Gerald; Stefanyshyn, Darren; Mündermann, Anne; Humble, Neil

2003-02-01

The purposes of this project were to assess the effect of four different shoe inserts on the path of the center of pressure (COP), to quantify the effect of these inserts on selected knee joint moments during running, and to assess the potential of COP data to predict the effects of inserts/orthotics on knee joint moments. Kinematics for the lower extremities, resultant ankle and knee joint moments, and the path of the COP were collected from the right foot of 15 male subjects while running heel-toe with five different shoe inserts (full or half with 4.5-mm postings). Individual movement changes with respect to the neutral insert condition were typically small and not systematic. Significant changes for the path of the COP were registered only for the full lateral insert condition with an average shift toward the lateral side. The mediolateral shift of the COP was not consistent for the full medial and the two half-shoe inserts. The subject-specific reactions to the inserts' intervention in the corresponding knee joint moments were typically not consistent. Compared with the neutral insert condition, subjects showed increases or decreases of the knee joint moments. The correlation between the individual COP shifts and the resultant knee joint moment was generally small. The results of this study showed that subject-specific reactions to the tested inserts were often not as expected. Additionally, reactions were not consistent between the subjects. This result suggests that the prescription of inserts and/or orthotics is a difficult task and that methods must be developed to test and assess these effects. Such methods, however, are not currently available.

Theoretical analysis of the time-resolved binary (e, 2e) binding energy spectra on three-body photodissociation of acetone at 195 nm

NASA Astrophysics Data System (ADS)

Yamazaki, M.; Nakayama, S.; Zhu, C. Y.; Takahashi, M.

2017-11-01

We report on theoretical progress in time-resolved (e, 2e) electron momentum spectroscopy of photodissociation dynamics of the deuterated acetone molecule at 195 nm. We have examined the predicted minimum energy reaction path to investigate whether associated (e, 2e) calculations meet the experimental results. A noticeable difference between the experiment and calculations has been found at around binding energy of 10 eV, suggesting that the observed difference may originate, at least partly, in ever-unconsidered non-minimum energy paths.

The Reactions of Polycyclic Aromatic Hydrocarbons with OH

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

2000-01-01

The OH radical adds to naphthalene and naphthalene cation without a barrier. For the neutrals, the most favorable path for this intermediate is the loss of the OH, and the next most favorable option is the loss of an H atom to form the alcohol. For the cation, the most favorable path appears to be a hydrogen migration followed by the loss of a hydrogen to form the alcohol. The OH at carbon atom 1 is energetically most favorable for both the initial complex and final product. This is true for both the neutrals and cations.

Protein-pigments and the photosystem II reaction center: a glimpse into the history of research and reminiscences.

PubMed

Satoh, Kimiyuki

2008-01-01

This article provides a glimpse into the dawning of research on chlorophyll-protein complexes and a brief recollection of the path that led us to the identification of the photosystem II reaction center, i.e., the polypeptides that carry the site of primary charge separation in oxygenic photosynthesis. A preliminary version of the personal review on the latter topic has already appeared in this journal (Satoh Photosynth Res 76:233-240, 2003).

Noncovalent Organocatalysis Based on Hydrogen Bonding: Elucidation of Reaction Paths by Computational Methods

NASA Astrophysics Data System (ADS)

Etzenbach-Effers, Kerstin; Berkessel, Albrecht

In this article, the functions of hydrogen bonds in organocatalytic reactions are discussed on atomic level by presenting DFT studies of selected examples. Theoretical investigation provides a detailed insight in the mechanism of substrate activation and orientation, and the stabilization of transition states and intermediates by hydrogen bonding (e.g. oxyanion hole). The examples selected comprise stereoselective catalysis by bifunctional thioureas, solvent catalysis by fluorinated alcohols in epoxidation by hydrogen peroxide, and intramolecular cooperative hydrogen bonding in TADDOL-type catalysts.

Multi-level quantum mechanics theories and molecular mechanics study of the double-inversion mechanism of the F- + CH3I reaction in aqueous solution.

PubMed

Liu, Peng; Zhang, Jingxue; Wang, Dunyou

2017-06-07

A double-inversion mechanism of the F - + CH 3 I reaction was discovered in aqueous solution using combined multi-level quantum mechanics theories and molecular mechanics. The stationary points along the reaction path show very different structures to the ones in the gas phase due to the interactions between the solvent and solute, especially strong hydrogen bonds. An intermediate complex, a minimum on the potential of mean force, was found to serve as a connecting-link between the abstraction-induced inversion transition state and the Walden-inversion transition state. The potentials of mean force were calculated with both the DFT/MM and CCSD(T)/MM levels of theory. Our calculated free energy barrier of the abstraction-induced inversion is 69.5 kcal mol -1 at the CCSD(T)/MM level of theory, which agrees with the one at 72.9 kcal mol -1 calculated using the Born solvation model and gas-phase data; and our calculated free energy barrier of the Walden inversion is 24.2 kcal mol -1 , which agrees very well with the experimental value at 25.2 kcal mol -1 in aqueous solution. The calculations show that the aqueous solution makes significant contributions to the potentials of mean force and exerts a big impact on the molecular-level evolution along the reaction pathway.

Analytical transmissibility based transfer path analysis for multi-energy-domain systems using four-pole parameter theory

NASA Astrophysics Data System (ADS)

Mashayekhi, Mohammad Jalali; Behdinan, Kamran

2017-10-01

The increasing demand to minimize undesired vibration and noise levels in several high-tech industries has generated a renewed interest in vibration transfer path analysis. Analyzing vibration transfer paths within a system is of crucial importance in designing an effective vibration isolation strategy. Most of the existing vibration transfer path analysis techniques are empirical which are suitable for diagnosis and troubleshooting purpose. The lack of an analytical transfer path analysis to be used in the design stage is the main motivation behind this research. In this paper an analytical transfer path analysis based on the four-pole theory is proposed for multi-energy-domain systems. Bond graph modeling technique which is an effective approach to model multi-energy-domain systems is used to develop the system model. In this paper an electro-mechanical system is used as a benchmark example to elucidate the effectiveness of the proposed technique. An algorithm to obtain the equivalent four-pole representation of a dynamical systems based on the corresponding bond graph model is also presented in this paper.

SensiPath: computer-aided design of sensing-enabling metabolic pathways.

PubMed

Delépine, Baudoin; Libis, Vincent; Carbonell, Pablo; Faulon, Jean-Loup

2016-07-08

Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying intracellular amounts of a compound of interest are central to whole-cell biosensors design for medical and environmental applications, and they also constitute essential parts for the selection and regulation of high-producer strains in metabolic engineering. However, the number of compounds that can be detected through natural mechanisms, like allosteric transcription factors, is limited; expanding the set of detectable compounds is therefore highly desirable. Here, we present the SensiPath web server, accessible at http://sensipath.micalis.fr SensiPath implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. The SensiPath approach is based on the encoding of reactions through signature descriptors to explore sensing-enabling metabolic pathways, which are putative biochemical transformations of the target compound leading to known effectors of transcription factors. In that way, SensiPath enlarges the design space by broadening the potential use of biosensors in synthetic biology applications. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Tunable catalytic properties of bi-functional mixed oxides in ethanol conversion to high value compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramasamy, Karthikeyan K.; Gray, Michel J.; Job, Heather M.

2016-04-10

tA highly versatile ethanol conversion process to selectively generate high value compounds is pre-sented here. By changing the reaction temperature, ethanol can be selectively converted to >C2alcohols/oxygenates or phenolic compounds over hydrotalcite derived bi-functional MgO–Al2O3cata-lyst via complex cascade mechanism. Reaction temperature plays a role in whether aldol condensationor the acetone formation is the path taken in changing the product composition. This article containsthe catalytic activity comparison between the mono-functional and physical mixture counterpart to thehydrotalcite derived mixed oxides and the detailed discussion on the reaction mechanisms.

Tunable catalytic properties of bi-functional mixed oxides in ethanol conversion to high value compounds

DOE PAGES

Ramasamy, Karthikeyan K.; Gray, Michel; Job, Heather; ...

2016-02-03

Here, a highly versatile ethanol conversion process to selectively generate high value compounds is presented here. By changing the reaction temperature, ethanol can be selectively converted to >C 2 alcohols/oxygenates or phenolic compounds over hydrotalcite derived bi-functional MgO–Al 2O 3 catalyst via complex cascade mechanism. Reaction temperature plays a role in whether aldol condensation or the acetone formation is the path taken in changing the product composition. This article contains the catalytic activity comparison between the mono-functional and physical mixture counterpart to the hydrotalcite derived mixed oxides and the detailed discussion on the reaction mechanisms.

Tracking trade transactions in water resource systems: A node-arc optimization formulation

NASA Astrophysics Data System (ADS)

Erfani, Tohid; Huskova, Ivana; Harou, Julien J.

2013-05-01

We formulate and apply a multicommodity network flow node-arc optimization model capable of tracking trade transactions in complex water resource systems. The model uses a simple node to node network connectivity matrix and does not require preprocessing of all possible flow paths in the network. We compare the proposed node-arc formulation with an existing arc-path (flow path) formulation and explain the advantages and difficulties of both approaches. We verify the proposed formulation model on a hypothetical water distribution network. Results indicate the arc-path model solves the problem with fewer constraints, but the proposed formulation allows using a simple network connectivity matrix which simplifies modeling large or complex networks. The proposed algorithm allows converting existing node-arc hydroeconomic models that broadly represent water trading to ones that also track individual supplier-receiver relationships (trade transactions).

Generating Performance Models for Irregular Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friese, Ryan D.; Tallent, Nathan R.; Vishnu, Abhinav

2017-05-30

Many applications have irregular behavior --- non-uniform input data, input-dependent solvers, irregular memory accesses, unbiased branches --- that cannot be captured using today's automated performance modeling techniques. We describe new hierarchical critical path analyses for the \\Palm model generation tool. To create a model's structure, we capture tasks along representative MPI critical paths. We create a histogram of critical tasks with parameterized task arguments and instance counts. To model each task, we identify hot instruction-level sub-paths and model each sub-path based on data flow, instruction scheduling, and data locality. We describe application models that generate accurate predictions for strong scalingmore » when varying CPU speed, cache speed, memory speed, and architecture. We present results for the Sweep3D neutron transport benchmark; Page Rank on multiple graphs; Support Vector Machine with pruning; and PFLOTRAN's reactive flow/transport solver with domain-induced load imbalance.« less

A horse’s locomotor signature: COP path determined by the individual limb

PubMed Central

Hobbs, Sarah Jane; Back, Willem

2017-01-01

Introduction Ground reaction forces in sound horses with asymmetric hooves show systematic differences in the horizontal braking force and relative timing of break-over. The Center Of Pressure (COP) path quantifies the dynamic load distribution under the hoof in a moving horse. The objective was to test whether anatomical asymmetry, quantified by the difference in dorsal wall angle between the left and right forelimbs, correlates with asymmetry in the COP path between these limbs. In addition, repeatability of the COP path was investigated. Methods A larger group (n = 31) visually sound horses with various degree of dorsal hoof wall asymmetry trotted three times over a pressure mat. COP path was determined in a hoof-bound coordinate system. A relationship between correlations between left and right COP paths and degree of asymmetry was investigated. Results Using a hoof-bound coordinate system made the COP path highly repeatable and unique for each limb. The craniocaudal patterns are usually highly correlated between left and right, but the mediolateral patterns are not. Some patterns were found between COP path and dorsal wall angle but asymmetry in dorsal wall angle did not necessarily result in asymmetry in COP path and the same could be stated for symmetry. Conclusion This method is a highly sensitive method to quantify the net result of the interaction between all of the forces and torques that occur in the limb and its inertial properties. We argue that changes in motor control, muscle force, inertial properties, kinematics and kinetics can potentially be picked up at an early stage using this method and could therefore be used as an early detection method for changes in the musculoskeletal apparatus. PMID:28196073

The role of grain boundaries and transient porosity increase as fluid pathways for reaction front propagation

NASA Astrophysics Data System (ADS)

Jonas, Laura; John, Timm; Geisler, Thorsten; Putnis, Andrew

2013-04-01

The pseudomorphic replacement of Carrara marble by calcium phosphates was studied as a model system to examine the influence of different fluid pathways for reaction front propagation induced by fluid-rock interaction. In this model system, the grain boundaries present in the rock and the transient porosity structures developing throughout the replacement reaction enable the reaction front to progress further into the rock as well as to the center of each single grain until complete transformation. Hydrothermal treatment of the marble using phosphate bearing solutions at temperature levels of 150° C and 200° C for different durations lead to the formation of two product phases which were identified as hydroxyapatite [Ca5(PO4)3OH] as well as β-tricalcium phosphate [β-Ca3(PO4)2] (β-TCP). The formation of β-TCP was probably favored by the presence of ~0.6wt.% of Mg in the parent phase. Completely transformed single grains show a distinctive zoning, both in composition and texture. Whereas areas next to the grain boundary consist of nearly pure hydroxyapatite and show a coarse porosity, areas close to the center of the single grains show a high amount of β-TCP and a very fine porous microstructure. If F was added as an additional solution component, the formation of β-TCP was avoided and up to 3wt.% of F were incorporated into the product apatite. The use of the isotope 18O as a chronometer for the replacement reaction makes it possible to reconstruct the chronological development of the calcium phosphate reaction front. Raman analysis revealed that the incorporation of 18O in the PO4 tetrahedron of hydroxyapatite results in the development of distinct profiles in the calcium phosphate reaction front perpendicular to the grain boundaries of the marble. Through the use of the 18O chronometer, it is possible to estimate and compare the time effectiveness of the different fluid pathways in this model system. The results show that the grain boundaries serve as a very effective pathway that enable the fluid to penetrate the rock more than one order of magnitude faster compared to the newly developing channel-like porosity structures which act as pathways towards the center of single mineral grains. Thus, it may be possible for the fluid to progress relatively large distances along the grain boundaries after only short reaction durations without producing broad reaction fronts along the path.

path integral approach to closed form pricing formulas in the Heston framework.

NASA Astrophysics Data System (ADS)

Lemmens, Damiaan; Wouters, Michiel; Tempere, Jacques; Foulon, Sven

2008-03-01

We present a path integral approach for finding closed form formulas for option prices in the framework of the Heston model. The first model for determining option prices was the Black-Scholes model, which assumed that the logreturn followed a Wiener process with a given drift and constant volatility. To provide a realistic description of the market, the Black-Scholes results must be extended to include stochastic volatility. This is achieved by the Heston model, which assumes that the volatility follows a mean reverting square root process. Current applications of the Heston model are hampered by the unavailability of fast numerical methods, due to a lack of closed-form formulae. Therefore the search for closed form solutions is an essential step before the qualitatively better stochastic volatility models will be used in practice. To attain this goal we outline a simplified path integral approach yielding straightforward results for vanilla Heston options with correlation. Extensions to barrier options and other path-dependent option are discussed, and the new derivation is compared to existing results obtained from alternative path-integral approaches (Dragulescu, Kleinert).

Notes on Experiments.

ERIC Educational Resources Information Center

Physics Education, 1984

1984-01-01

Describes (1) oil slick interference rings in the laboratory; (2) cracking of glass by impact; (3) multipurpose prism for refractometry and light path demonstrations; and (4) determination of liquid densities and volumes of solid bodies by the reaction force on a vessel. Procedures used and equipment needed are discussed. (JN)

Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces.

PubMed

Plotnikov, Nikolay V; Prasad, B Ram; Chakrabarty, Suman; Chu, Zhen T; Warshel, Arieh

2013-10-24

Understanding the nature of the free-energy surfaces for phosphate hydrolysis is a prerequisite for understanding the corresponding key chemical reactions in biology. Here, the challenge has been to move to careful ab initio QM/MM (QM(ai)/MM) free-energy calculations, where obtaining converging results is very demanding and computationally expensive. This work describes such calculations, focusing on the free-energy surface for the hydrolysis of phosphate monoesters, paying special attention to the comparison between the one water (1W) and two water (2W) paths for the proton-transfer (PT) step. This issue has been explored before by energy minimization with implicit solvent models and by nonsystematic QM/MM energy minimization, as well as by nonsystematic free-energy mapping. However, no study has provided the needed reliable 2D (3D) surfaces that are necessary for reaching concrete conclusions. Here we report a systematic evaluation of the 2D (3D) free-energy maps for several relevant systems, comparing the results of QM(ai)/MM and QM(ai)/implicit solvent surfaces, and provide an advanced description of the relevant energetics. It is found that the 1W path for the hydrolysis of the methyl diphosphate (MDP) trianion is 6-9 kcal/mol higher than that the 2W path. This difference becomes slightly larger in the presence of the Mg(2+) ion because this ion reduces the pKa of the conjugated acid form of the phosphate oxygen that accepts the proton. Interestingly, the BLYP approach (which has been used extensively in some studies) gives a much smaller difference between the 1W and 2W activation barriers. At any rate, it is worth pointing out that the 2W transition state for the PT is not much higher that the common plateau that serves as the starting point of both the 1W and 2W PT paths. Thus, the calculated catalytic effects of proteins based on the 2W PT mechanistic model are not expected to be different from the catalytic effects predicted using the 1W PT mechanistic model, which was calibrated on the observed barrier in solution and in which the TS charge distribution was similar to the that of the plateau (as was done in all of our previous EVB studies).

Kinetics of nitric oxide and oxygen gases on porous Y-stabilized ZrO2-based sensors.

PubMed

Killa, Sajin; Cui, Ling; Murray, Erica P; Mainardi, Daniela S

2013-08-16

Using impedance spectroscopy the electrical response of sensors with various porous Y-stabilized ZrO2 (YSZ) microstructures was measured for gas concentrations containing 0-100 ppm NO with 10.5%O2 at temperatures ranging from 600-700 °C. The impedance response increased substantially as the sensor porosity increased from 46%-50%. Activation energies calculated based on data from the impedance measurements increased in magnitude (97.4-104.9 kJ/mol for 100 ppm NO) with respect to increasing YSZ porosity. Analysis of the oxygen partial pressure dependence of the sensors suggested that dissociative adsorption was the dominant rate limiting. The PWC/DNP theory level was used to investigate the gas-phase energy barrier of the 2NO+O2 → 2NO2 reaction on a 56-atom YSZ/Au model cluster using Density Functional Theory and Linear Synchronous Transit/Quadratic Synchronous Transit calculations. The reaction path shows oxygen surface reactions that begin with NO association with adsorbed O2 on a Zr surface site, followed by O2 dissociative adsorption, atomic oxygen diffusion, and further NO2 formation. The free energy barrier was calculated to be 181.7 kJ/mol at PWC/DNP. A qualitative comparison with the extrapolated data at 62% ± 2% porosity representing the YSZ model cluster indicates that the calculated barriers are in reasonable agreement with experiments, especially when the RPBE functional is used.

Path Loss Prediction Over the Lunar Surface Utilizing a Modified Longley-Rice Irregular Terrain Model

NASA Technical Reports Server (NTRS)

Foore, Larry; Ida, Nathan

2007-01-01

This study introduces the use of a modified Longley-Rice irregular terrain model and digital elevation data representative of an analogue lunar site for the prediction of RF path loss over the lunar surface. The results are validated by theoretical models and past Apollo studies. The model is used to approximate the path loss deviation from theoretical attenuation over a reflecting sphere. Analysis of the simulation results provides statistics on the fade depths for frequencies of interest, and correspondingly a method for determining the maximum range of communications for various coverage confidence intervals. Communication system engineers and mission planners are provided a link margin and path loss policy for communication frequencies of interest.

Elucidating reactivity regimes in cyclopentane oxidation: Jet stirred reactor experiments, computational chemistry, and kinetic modeling

DOE PAGES

Al Rashidi, Mariam J.; Thion, Sebastien; Togbe, Casimir; ...

2016-06-22

This study is concerned with the identification and quantification of species generated during the combustion of cyclopentane in a jet stirred reactor (JSR). Experiments were carried out for temperatures between 740 and 1250 K, equivalence ratios from 0.5 to 3.0, and at an operating pressure of 10 atm. The fuel concentration was kept at 0.1% and the residence time of the fuel/O 2/N 2 mixture was maintained at 0.7 s. The reactant, product, and intermediate species concentration profiles were measured using gas chromatography and Fourier transform infrared spectroscopy. The concentration profiles of cyclopentane indicate inhibition of reactivity between 850-1000 Kmore » for φ=2.0 and φ=3.0. This behavior is interesting, as it has not been observed previously for other fuel molecules, cyclic or non-cyclic. A kinetic model including both low- and high-temperature reaction pathways was developed and used to simulate the JSR experiments. The pressure-dependent rate coefficients of all relevant reactions lying on the PES of cyclopentyl + O 2, as well as the C-C and C-H scission reactions of the cyclopentyl radical were calculated at the UCCSD(T)-F12b/cc-pVTZ-F12//M06-2X/6-311++G(d,p) level of theory. The simulations reproduced the unique reactivity trend of cyclopentane and the measured concentration profiles of intermediate and product species. Furthermore, sensitivity and reaction path analyses indicate that this reactivity trend may be attributed to differences in the reactivity of allyl radical at different conditions, and it is highly sensitive to the C-C/C-H scission branching ratio of the cyclopentyl radical decomposition.« less

Evaluating the risk of industrial espionage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bott, T.F.

1998-12-31

A methodology for estimating the relative probabilities of different compromise paths for protected information by insider and visitor intelligence collectors has been developed based on an event-tree analysis of the intelligence collection operation. The analyst identifies target information and ultimate users who might attempt to gain that information. The analyst then uses an event tree to develop a set of compromise paths. Probability models are developed for each of the compromise paths that user parameters based on expert judgment or historical data on security violations. The resulting probability estimates indicate the relative likelihood of different compromise paths and provide anmore » input for security resource allocation. Application of the methodology is demonstrated using a national security example. A set of compromise paths and probability models specifically addressing this example espionage problem are developed. The probability models for hard-copy information compromise paths are quantified as an illustration of the results using parametric values representative of historical data available in secure facilities, supplemented where necessary by expert judgment.« less

Congestion patterns of electric vehicles with limited battery capacity.

PubMed

Jing, Wentao; Ramezani, Mohsen; An, Kun; Kim, Inhi

2018-01-01

The path choice behavior of battery electric vehicle (BEV) drivers is influenced by the lack of public charging stations, limited battery capacity, range anxiety and long battery charging time. This paper investigates the congestion/flow pattern captured by stochastic user equilibrium (SUE) traffic assignment problem in transportation networks with BEVs, where the BEV paths are restricted by their battery capacities. The BEV energy consumption is assumed to be a linear function of path length and path travel time, which addresses both path distance limit problem and road congestion effect. A mathematical programming model is proposed for the path-based SUE traffic assignment where the path cost is the sum of the corresponding link costs and a path specific out-of-energy penalty. We then apply the convergent Lagrangian dual method to transform the original problem into a concave maximization problem and develop a customized gradient projection algorithm to solve it. A column generation procedure is incorporated to generate the path set. Finally, two numerical examples are presented to demonstrate the applicability of the proposed model and the solution algorithm.

Congestion patterns of electric vehicles with limited battery capacity

PubMed Central

2018-01-01

The path choice behavior of battery electric vehicle (BEV) drivers is influenced by the lack of public charging stations, limited battery capacity, range anxiety and long battery charging time. This paper investigates the congestion/flow pattern captured by stochastic user equilibrium (SUE) traffic assignment problem in transportation networks with BEVs, where the BEV paths are restricted by their battery capacities. The BEV energy consumption is assumed to be a linear function of path length and path travel time, which addresses both path distance limit problem and road congestion effect. A mathematical programming model is proposed for the path-based SUE traffic assignment where the path cost is the sum of the corresponding link costs and a path specific out-of-energy penalty. We then apply the convergent Lagrangian dual method to transform the original problem into a concave maximization problem and develop a customized gradient projection algorithm to solve it. A column generation procedure is incorporated to generate the path set. Finally, two numerical examples are presented to demonstrate the applicability of the proposed model and the solution algorithm. PMID:29543875

Changes in White Matter Microstructure Impact Cognition by Disrupting the Ability of Neural Assemblies to Synchronize.

PubMed

Bells, Sonya; Lefebvre, Jérémie; Prescott, Steven A; Dockstader, Colleen; Bouffet, Eric; Skocic, Jovanka; Laughlin, Suzanne; Mabbott, Donald J

2017-08-23

Cognition is compromised by white matter (WM) injury but the neurophysiological alterations linking them remain unclear. We hypothesized that reduced neural synchronization caused by disruption of neural signal propagation is involved. To test this, we evaluated group differences in: diffusion tensor WM microstructure measures within the optic radiations, primary visual area (V1), and cuneus; neural phase synchrony to a visual attention cue during visual-motor task; and reaction time to a response cue during the same task between 26 pediatric patients (17/9: male/female) treated with cranial radiation treatment for a brain tumor (12.67 ± 2.76 years), and 26 healthy children (16/10: male/female; 12.01 ± 3.9 years). We corroborated our findings using a corticocortical computational model representing perturbed signal conduction from myelin. Patients show delayed reaction time, WM compromise, and reduced phase synchrony during visual attention compared with healthy children. Notably, using partial least-squares-path modeling we found that WM insult within the optic radiations, V1, and cuneus is a strong predictor of the slower reaction times via disruption of neural synchrony in visual cortex. Observed changes in synchronization were reproduced in a computational model of WM injury. These findings provide new evidence linking cognition with WM via the reliance of neural synchronization on propagation of neural signals. SIGNIFICANCE STATEMENT By comparing brain tumor patients to healthy children, we establish that changes in the microstructure of the optic radiations and neural synchrony during visual attention predict reaction time. Furthermore, by testing the directionality of these links through statistical modeling and verifying our findings with computational modeling, we infer a causal relationship, namely that changes in white matter microstructure impact cognition in part by disturbing the ability of neural assemblies to synchronize. Together, our human imaging data and computer simulations show a fundamental connection between WM microstructure and neural synchronization that is critical for cognitive processing. Copyright © 2017 the authors 0270-6474/17/378227-12$15.00/0.

Modeling of Ureolytic Calcite Precipitation for the Remediation of Sr-90 Using a Variable Velocity Streamtube Ensemble

NASA Astrophysics Data System (ADS)

Weathers, T. S.; Ginn, T. R.; Spycher, N.; Barkouki, T. H.; Fujita, Y.; Smith, R. W.

2009-12-01

Subsurface contamination is often mitigated with an injection/extraction well system. An understanding of heterogeneities within this radial flowfield is critical for modeling, prediction, and remediation of the subsurface. We address this using a Lagrangian approach: instead of depicting spatial extents of solutes in the subsurface we focus on their arrival distribution at the control well(s). A well-to-well treatment system that incorporates in situ microbially-mediated ureolysis to induce calcite precipitation for the immobilization of strontium-90 has been explored at the Vadose Zone Research Park (VZRP) near Idaho Falls, Idaho. PHREEQC2 is utilized to model the kinetically-controlled ureolysis and consequent calcite precipitation. PHREEQC2 provides a one-dimensional advective-dispersive transport option that can be and has been used in streamtube ensemble models. Traditionally, each streamtube maintains uniform velocity; however in radial flow in homogeneous media, the velocity within any given streamtube is variable in space, being highest at the input and output wells and approaching a minimum at the midpoint between the wells. This idealized velocity variability is of significance if kinetic reactions are present with multiple components, if kinetic reaction rates vary in space, if the reactions involve multiple phases (e.g. heterogeneous reactions), and/or if they impact physical characteristics (porosity/permeability), as does ureolytically driven calcite precipitation. Streamtube velocity patterns for any particular configuration of injection and withdrawal wells are available as explicit calculations from potential theory, and also from particle tracking programs. To approximate the actual spatial distribution of velocity along streamtubes, we assume idealized non-uniform velocity associated with homogeneous media. This is implemented in PHREEQC2 via a non-uniform spatial discretization within each streamtube that honors both the streamtube’s travel time and the idealized “fast-slow-fast” nonuniform velocity along the streamline. Breakthrough curves produced by each simulation are weighted by the path-respective flux fractions (obtained by deconvolution of tracer tests conducted at the VZRP) to obtain the flux-average of flow contributions to the observation well. Breakthrough data from urea injection experiments performed at the VZRP are compared to the model results from the PHREEQC2 variable velocity ensemble.