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)

Increasing Flexibility in Energy Code Compliance: Performance Packages

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

Hart, Philip R.; Rosenberg, Michael I.

Energy codes and standards have provided significant increases in building efficiency over the last 38 years, since the first national energy code was published in late 1975. The most commonly used path in energy codes, the prescriptive path, appears to be reaching a point of diminishing returns. As the code matures, the prescriptive path becomes more complicated, and also more restrictive. It is likely that an approach that considers the building as an integrated system will be necessary to achieve the next real gains in building efficiency. Performance code paths are increasing in popularity; however, there remains a significant designmore » team overhead in following the performance path, especially for smaller buildings. This paper focuses on development of one alternative format, prescriptive packages. A method to develop building-specific prescriptive packages is reviewed based on a multiple runs of prototypical building models that are used to develop parametric decision analysis to determines a set of packages with equivalent energy performance. The approach is designed to be cost-effective and flexible for the design team while achieving a desired level of energy efficiency performance. A demonstration of the approach based on mid-sized office buildings with two HVAC system types is shown along with a discussion of potential applicability in the energy code process.« less

An improved reaction path optimization method using a chain of conformations

NASA Astrophysics Data System (ADS)

Asada, Toshio; Sawada, Nozomi; Nishikawa, Takuya; Koseki, Shiro

2018-05-01

The efficient fast path optimization (FPO) method is proposed to optimize the reaction paths on energy surfaces by using chains of conformations. No artificial spring force is used in the FPO method to ensure the equal spacing of adjacent conformations. The FPO method is applied to optimize the reaction path on two model potential surfaces. The use of this method enabled the optimization of the reaction paths with a drastically reduced number of optimization cycles for both potentials. It was also successfully utilized to define the MEP of the isomerization of the glycine molecule in water by FPO method.

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.

The Marriage of Residential Energy Codes and Rating Systems: Conflict Resolution or Just Conflict?

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

Taylor, Zachary T.; Mendon, Vrushali V.

2014-08-21

After three decades of coexistence at a distance, model residential energy codes and residential energy rating systems have come together in the 2015 International Energy Conservation Code. At the October, 2013, International Code Council’s Public Comment Hearing, a new compliance path based on an Energy Rating Index was added to the IECC. Although not specifically named in the code, RESNET’s HERS rating system is the likely candidate Index for most jurisdictions. While HERS has been a mainstay in various beyond-code programs for many years, its direct incorporation into the most popular model energy code raises questions about the equivalence ofmore » a HERS-based compliance path and the traditional IECC performance compliance path, especially because the two approaches use different efficiency metrics, are governed by different simulation rules, and have different scopes with regard to energy impacting house features. A detailed simulation analysis of more than 15,000 house configurations reveals a very large range of HERS Index values that achieve equivalence with the IECC’s performance path. This paper summarizes the results of that analysis and evaluates those results against the specific Energy Rating Index values required by the 2015 IECC. Based on the home characteristics most likely to result in disparities between HERS-based compliance and performance path compliance, potential impacts on the compliance process, state and local adoption of the new code, energy efficiency in the next generation of homes subject to this new code, and future evolution of model code formats are discussed.« less

Identification of limit cycles in multi-nonlinearity, multiple path systems

NASA Technical Reports Server (NTRS)

Mitchell, J. R.; Barron, O. L.

1979-01-01

A method of analysis which identifies limit cycles in autonomous systems with multiple nonlinearities and multiple forward paths is presented. The FORTRAN code for implementing the Harmonic Balance Algorithm is reported. The FORTRAN code is used to identify limit cycles in multiple path and nonlinearity systems while retaining the effects of several harmonic components.

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 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

Dynamic wavefront creation for processing units using a hybrid compactor

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

Puthoor, Sooraj; Beckmann, Bradford M.; Yudanov, Dmitri

A method, a non-transitory computer readable medium, and a processor for repacking dynamic wavefronts during program code execution on a processing unit, each dynamic wavefront including multiple threads are presented. If a branch instruction is detected, a determination is made whether all wavefronts following a same control path in the program code have reached a compaction point, which is the branch instruction. If no branch instruction is detected in executing the program code, a determination is made whether all wavefronts following the same control path have reached a reconvergence point, which is a beginning of a program code segment tomore » be executed by both a taken branch and a not taken branch from a previous branch instruction. The dynamic wavefronts are repacked with all threads that follow the same control path, if all wavefronts following the same control path have reached the branch instruction or the reconvergence point.« less

Electronic excited state paths of Stone-Wales rearrangement in pyrene: roles of conical intersections.

PubMed

Yamazaki, Kaoru; Niitsu, Naoyuki; Nakamura, Kosuke; Kanno, Manabu; Kono, Hirohiko

2012-11-26

We investigated the reaction paths of Stone-Wales rearrangement (SWR), i.e., π/2 rotation of two carbon atoms with respect to the midpoint of the bond, in graphene and carbon nanotube quantum chemically. Our particular attention is focused on the roles of electronic excitations and conical intersections (CIs) in the reaction mechanism. We used pyrene as a model system. The reaction paths were determined by constructing potential energy surfaces at the MS-CASPT2//SA-CASSCF level of theory. We found that there are no CIs involved in SWR when both of C-C bond cleavage and formation occur simultaneously (concerted mechanism). In contrast, for the reaction path with stepwise cleavage and formation of C-C bonds, C-C bond breaking and making processes proceed through two CIs. When SWR starts from the ground (S(0)) state, the concerted and stepwise paths have an equivalent reaction barrier ΔE(‡) (9.5-9.6 eV). For the reaction path starting from excited states, only the stepwise mechanism is energetically preferable. This path contains a nonadabatic transition between the S(1) and S(0) states via a CI associated with the first stage of C-C bond cleavage and has ΔE(‡) as large as in the S(0) paths. We confirmed that the main active molecular orbitals and electron configurations for the low-lying electronic states of larger nanocarbons are the same as those in pyrene. This result suggests the importance of the nonadiabatic transitions through CIs in the photochemical reactions in large nanocarbons.

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.

VLF Trimpi modelling on the path NWC-Dunedin using both finite element and 3D Born modelling

NASA Astrophysics Data System (ADS)

Nunn, D.; Hayakawa, K. B. M.

1998-10-01

This paper investigates the numerical modelling of VLF Trimpis, produced by a D region inhomogeneity on the great circle path. Two different codes are used to model Trimpis on the path NWC-Dunedin. The first is a 2D Finite Element Method Code (FEM), whose solutions are rigorous and valid in the strong scattering or non-Born limit. The second code is a 3D model that invokes the Born approximation. The predicted Trimpis from these codes compare very closely, thus confirming the validity of both models. The modal scattering matrices for both codes are analysed in some detail and are found to have a comparable structure. They indicate strong scattering between the dominant TM modes. Analysis of the scattering matrix from the FEM code shows that departure from linear Born behaviour occurs when the inhomogeneity has a horizontal scale size of about 100 km and a maximum electron density enhancement at 75 km altitude of about 6 electrons.

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.

A taxonomy of integral reaction path analysis

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

Grcar, Joseph F.; Day, Marcus S.; Bell, John B.

2004-12-23

W. C. Gardiner observed that achieving understanding through combustion modeling is limited by the ability to recognize the implications of what has been computed and to draw conclusions about the elementary steps underlying the reaction mechanism. This difficulty can be overcome in part by making better use of reaction path analysis in the context of multidimensional flame simulations. Following a survey of current practice, an integral reaction flux is formulated in terms of conserved scalars that can be calculated in a fully automated way. Conditional analyses are then introduced, and a taxonomy for bidirectional path analysis is explored. Many examplesmore » illustrate the resulting path analysis and uncover some new results about nonpremixed methane-air laminar jets.« less

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.

MapMaker and PathTracer for tracking carbon in genome-scale metabolic models

PubMed Central

Tervo, Christopher J.; Reed, Jennifer L.

2016-01-01

Constraint-based reconstruction and analysis (COBRA) modeling results can be difficult to interpret given the large numbers of reactions in genome-scale models. While paths in metabolic networks can be found, existing methods are not easily combined with constraint-based approaches. To address this limitation, two tools (MapMaker and PathTracer) were developed to find paths (including cycles) between metabolites, where each step transfers carbon from reactant to product. MapMaker predicts carbon transfer maps (CTMs) between metabolites using only information on molecular formulae and reaction stoichiometry, effectively determining which reactants and products share carbon atoms. MapMaker correctly assigned CTMs for over 97% of the 2,251 reactions in an Escherichia coli metabolic model (iJO1366). Using CTMs as inputs, PathTracer finds paths between two metabolites. PathTracer was applied to iJO1366 to investigate the importance of using CTMs and COBRA constraints when enumerating paths, to find active and high flux paths in flux balance analysis (FBA) solutions, to identify paths for putrescine utilization, and to elucidate a potential CO2 fixation pathway in E. coli. These results illustrate how MapMaker and PathTracer can be used in combination with constraint-based models to identify feasible, active, and high flux paths between metabolites. PMID:26771089

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.

Recovery Act: An Integrated Experimental and Numerical Study: Developing a Reaction Transport Model that Couples Chemical Reactions of Mineral Dissolution/Precipitation with Spatial and Temporal Flow Variations.

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

Saar, Martin O.; Seyfried, Jr., William E.; Longmire, Ellen K.

2016-06-24

A total of 12 publications and 23 abstracts were produced as a result of this study. In particular, the compilation of a thermodynamic database utilizing consistent, current thermodynamic data is a major step toward accurately modeling multi-phase fluid interactions with solids. Existing databases designed for aqueous fluids did not mesh well with existing solid phase databases. Addition of a second liquid phase (CO2) magnifies the inconsistencies between aqueous and solid thermodynamic databases. Overall, the combination of high temperature and pressure lab studies (task 1), using a purpose built apparatus, and solid characterization (task 2), using XRCT and more developed technologies,more » allowed observation of dissolution and precipitation processes under CO2 reservoir conditions. These observations were combined with results from PIV experiments on multi-phase fluids (task 3) in typical flow path geometries. The results of the tasks 1, 2, and 3 were compiled and integrated into numerical models utilizing Lattice-Boltzmann simulations (task 4) to realistically model the physical processes and were ultimately folded into TOUGH2 code for reservoir scale modeling (task 5). Compilation of the thermodynamic database assisted comparisons to PIV experiments (Task 3) and greatly improved Lattice Boltzmann (Task 4) and TOUGH2 simulations (Task 5). PIV (Task 3) and experimental apparatus (Task 1) have identified problem areas in TOUGHREACT code. Additional lab experiments and coding work has been integrated into an improved numerical modeling code.« less

The Modeling of Advanced BWR Fuel Designs with the NRC Fuel Depletion Codes PARCS/PATHS

DOE PAGES

Ward, Andrew; Downar, Thomas J.; Xu, Y.; ...

2015-04-22

The PATHS (PARCS Advanced Thermal Hydraulic Solver) code was developed at the University of Michigan in support of U.S. Nuclear Regulatory Commission research to solve the steady-state, two-phase, thermal-hydraulic equations for a boiling water reactor (BWR) and to provide thermal-hydraulic feedback for BWR depletion calculations with the neutronics code PARCS (Purdue Advanced Reactor Core Simulator). The simplified solution methodology, including a three-equation drift flux formulation and an optimized iteration scheme, yields very fast run times in comparison to conventional thermal-hydraulic systems codes used in the industry, while still retaining sufficient accuracy for applications such as BWR depletion calculations. Lastly, themore » capability to model advanced BWR fuel designs with part-length fuel rods and heterogeneous axial channel flow geometry has been implemented in PATHS, and the code has been validated against previously benchmarked advanced core simulators as well as BWR plant and experimental data. We describe the modifications to the codes and the results of the validation in this paper.« less

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

(U) Ristra Next Generation Code Report

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

Hungerford, Aimee L.; Daniel, David John

LANL’s Weapons Physics management (ADX) and ASC program office have defined a strategy for exascale-class application codes that follows two supportive, and mutually risk-mitigating paths: evolution for established codes (with a strong pedigree within the user community) based upon existing programming paradigms (MPI+X); and Ristra (formerly known as NGC), a high-risk/high-reward push for a next-generation multi-physics, multi-scale simulation toolkit based on emerging advanced programming systems (with an initial focus on data-flow task-based models exemplified by Legion [5]). Development along these paths is supported by the ATDM, IC, and CSSE elements of the ASC program, with the resulting codes forming amore » common ecosystem, and with algorithm and code exchange between them anticipated. Furthermore, solution of some of the more challenging problems of the future will require a federation of codes working together, using established-pedigree codes in partnership with new capabilities as they come on line. The role of Ristra as the high-risk/high-reward path for LANL’s codes is fully consistent with its role in the Advanced Technology Development and Mitigation (ATDM) sub-program of ASC (see Appendix C), in particular its emphasis on evolving ASC capabilities through novel programming models and data management technologies.« less

Software Security Knowledge: CWE. Knowing What Could Make Software Vulnerable to Attack

DTIC Science & Technology

2011-05-01

shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1...Buffer • CWE-642: External Control of Critical State Data • CWE-73: External Control of File Name or Path • CWE-426: Untrusted Search Path • CWE...94: Failure to Control Generation of Code (aka ’Code Injection’) • CWE-494: Download of Code Without Integrity Check • CWE-404: Improper Resource

Table-driven software architecture for a stitching system

NASA Technical Reports Server (NTRS)

Thrash, Patrick J. (Inventor); Miller, Jeffrey L. (Inventor); Pallas, Ken (Inventor); Trank, Robert C. (Inventor); Fox, Rhoda (Inventor); Korte, Mike (Inventor); Codos, Richard (Inventor); Korolev, Alexandre (Inventor); Collan, William (Inventor)

2001-01-01

Native code for a CNC stitching machine is generated by generating a geometry model of a preform; generating tool paths from the geometry model, the tool paths including stitching instructions for making stitches; and generating additional instructions indicating thickness values. The thickness values are obtained from a lookup table. When the stitching machine runs the native code, it accesses a lookup table to determine a thread tension value corresponding to the thickness value. The stitching machine accesses another lookup table to determine a thread path geometry value corresponding to the thickness value.

Improved multidimensional semiclassical tunneling theory.

PubMed

Wagner, Albert F

2013-12-12

We show that the analytic multidimensional semiclassical tunneling formula of Miller et al. [Miller, W. H.; Hernandez, R.; Handy, N. C.; Jayatilaka, D.; Willets, A. Chem. Phys. Lett. 1990, 172, 62] is qualitatively incorrect for deep tunneling at energies well below the top of the barrier. The origin of this deficiency is that the formula uses an effective barrier weakly related to the true energetics but correctly adjusted to reproduce the harmonic description and anharmonic corrections of the reaction path at the saddle point as determined by second order vibrational perturbation theory. We present an analytic improved semiclassical formula that correctly includes energetic information and allows a qualitatively correct representation of deep tunneling. This is done by constructing a three segment composite Eckart potential that is continuous everywhere in both value and derivative. This composite potential has an analytic barrier penetration integral from which the semiclassical action can be derived and then used to define the semiclassical tunneling probability. The middle segment of the composite potential by itself is superior to the original formula of Miller et al. because it incorporates the asymmetry of the reaction barrier produced by the known reaction exoergicity. Comparison of the semiclassical and exact quantum tunneling probability for the pure Eckart potential suggests a simple threshold multiplicative factor to the improved formula to account for quantum effects very near threshold not represented by semiclassical theory. The deep tunneling limitations of the original formula are echoed in semiclassical high-energy descriptions of bound vibrational states perpendicular to the reaction path at the saddle point. However, typically ab initio energetic information is not available to correct it. The Supporting Information contains a Fortran code, test input, and test output that implements the improved semiclassical tunneling formula.

The mineralogic evolution of the Martian surface through time: Implications from chemical reaction path modeling studies

NASA Technical Reports Server (NTRS)

Plumlee, G. S.; Ridley, W. I.; Debraal, J. D.; Reed, M. H.

1993-01-01

Chemical reaction path calculations were used to model the minerals that might have formed at or near the Martian surface as a result of volcano or meteorite impact driven hydrothermal systems; weathering at the Martian surface during an early warm, wet climate; and near-zero or sub-zero C brine-regolith reactions in the current cold climate. Although the chemical reaction path calculations carried out do not define the exact mineralogical evolution of the Martian surface over time, they do place valuable geochemical constraints on the types of minerals that formed from an aqueous phase under various surficial and geochemically complex conditions.

A Hybrid Path-Oriented Code Assignment CDMA-Based MAC Protocol for Underwater Acoustic Sensor Networks

PubMed Central

Chen, Huifang; Fan, Guangyu; Xie, Lei; Cui, Jun-Hong

2013-01-01

Due to the characteristics of underwater acoustic channel, media access control (MAC) protocols designed for underwater acoustic sensor networks (UWASNs) are quite different from those for terrestrial wireless sensor networks. Moreover, in a sink-oriented network with event information generation in a sensor field and message forwarding to the sink hop-by-hop, the sensors near the sink have to transmit more packets than those far from the sink, and then a funneling effect occurs, which leads to packet congestion, collisions and losses, especially in UWASNs with long propagation delays. An improved CDMA-based MAC protocol, named path-oriented code assignment (POCA) CDMA MAC (POCA-CDMA-MAC), is proposed for UWASNs in this paper. In the proposed MAC protocol, both the round-robin method and CDMA technology are adopted to make the sink receive packets from multiple paths simultaneously. Since the number of paths for information gathering is much less than that of nodes, the length of the spreading code used in the POCA-CDMA-MAC protocol is shorter greatly than that used in the CDMA-based protocols with transmitter-oriented code assignment (TOCA) or receiver-oriented code assignment (ROCA). Simulation results show that the proposed POCA-CDMA-MAC protocol achieves a higher network throughput and a lower end-to-end delay compared to other CDMA-based MAC protocols. PMID:24193100

A hybrid path-oriented code assignment CDMA-based MAC protocol for underwater acoustic sensor networks.

PubMed

Chen, Huifang; Fan, Guangyu; Xie, Lei; Cui, Jun-Hong

2013-11-04

Due to the characteristics of underwater acoustic channel, media access control (MAC) protocols designed for underwater acoustic sensor networks (UWASNs) are quite different from those for terrestrial wireless sensor networks. Moreover, in a sink-oriented network with event information generation in a sensor field and message forwarding to the sink hop-by-hop, the sensors near the sink have to transmit more packets than those far from the sink, and then a funneling effect occurs, which leads to packet congestion, collisions and losses, especially in UWASNs with long propagation delays. An improved CDMA-based MAC protocol, named path-oriented code assignment (POCA) CDMA MAC (POCA-CDMA-MAC), is proposed for UWASNs in this paper. In the proposed MAC protocol, both the round-robin method and CDMA technology are adopted to make the sink receive packets from multiple paths simultaneously. Since the number of paths for information gathering is much less than that of nodes, the length of the spreading code used in the POCA-CDMA-MAC protocol is shorter greatly than that used in the CDMA-based protocols with transmitter-oriented code assignment (TOCA) or receiver-oriented code assignment (ROCA). Simulation results show that the proposed POCA-CDMA-MAC protocol achieves a higher network throughput and a lower end-to-end delay compared to other CDMA-based MAC protocols.

Fast exploration of an optimal path on the multidimensional free energy surface

PubMed Central

Chen, Changjun

2017-01-01

In a reaction, determination of an optimal path with a high reaction rate (or a low free energy barrier) is important for the study of the reaction mechanism. This is a complicated problem that involves lots of degrees of freedom. For simple models, one can build an initial path in the collective variable space by the interpolation method first and then update the whole path constantly in the optimization. However, such interpolation method could be risky in the high dimensional space for large molecules. On the path, steric clashes between neighboring atoms could cause extremely high energy barriers and thus fail the optimization. Moreover, performing simulations for all the snapshots on the path is also time-consuming. In this paper, we build and optimize the path by a growing method on the free energy surface. The method grows a path from the reactant and extends its length in the collective variable space step by step. The growing direction is determined by both the free energy gradient at the end of the path and the direction vector pointing at the product. With fewer snapshots on the path, this strategy can let the path avoid the high energy states in the growing process and save the precious simulation time at each iteration step. Applications show that the presented method is efficient enough to produce optimal paths on either the two-dimensional or the twelve-dimensional free energy surfaces of different small molecules. PMID:28542475

Nitrogen oxides in the arctic stratosphere: Implications for ozone abundances. Ph.D. Thesis

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

Slusser, J.R.

1994-01-01

In the high latitude winter stratosphere, NO2 sequesters chlorine compounds which are extremely efficient at destroying ozone. During the nighttime, NO2 reacts with ozone to form N2O5 which acts as a reservoir of NO2. Under heavy aerosol loading, N2O5 may react with water on aerosol surfaces to form HNO3, a reservoir more resistant to photolysis. This heterogeneous reaction results in reduced NO2 concentration when the sun returns at the end of the winter. A spectrograph system has been developed to measure scattered zenith skylight and thereby determine stratospheric NO2 slant column abundance. Conversion of the measured slant column abundance tomore » vertical column abundance requires dividing by the air mass. The air mass is the enhancement in the optical path for the scattered twilight as compared to a vertical path. Air mass values determined using a multiple scattering radiative transfer code have been compared to those derived using a Monte Carlo code and were found to agree to within 6% at a 90 deg solar zenith angle for a stratospheric absorber. Six months of NO2 vertical column abundance measured over Fairbanks during the winter 1992-93 exhibited the daylight diminished and increased as the sunlight hours lengthened. The overall seasonal behavior was similar to high-latitude measurements made in the Southern Hemisphere. The ratios of morning to evening column abundance were consistent with predictions based on gas-phase chemistry. The possible heterogeneous reaction of N2O5 on sulfate aerosols was investigated using FTIR Spectrometer measurements of HNO3 column abundance and lidar determinations of the aerosol profile. Using an estimated N2O5 column abundance and aerosol profile as input to a simple model, significant HNO3 production was expected. No increase in HNO3 column abundance was measured. From this set of data, it was not possible to determine whether significant amounts of N2O5 were converted to HNO3 by this heterogeneous reaction.« less

Two Upper Bounds for the Weighted Path Length of Binary Trees. Report No. UIUCDCS-R-73-565.

ERIC Educational Resources Information Center

Pradels, Jean Louis

Rooted binary trees with weighted nodes are structures encountered in many areas, such as coding theory, searching and sorting, information storage and retrieval. The path length is a meaningful quantity which gives indications about the expected time of a search or the length of a code, for example. In this paper, two sharp bounds for the total…

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.

Seamount Hydrothermal Systems as Analogies for Ocean Worlds: Reaction Paths Throughout the Lo'ihi Seamount (Hawaii Archipelago)

NASA Astrophysics Data System (ADS)

Milesi, V.; Shock, E.

2018-05-01

Thermodynamic modeling is performed to investigate the possible reaction paths of sea water throughout the Lo'ihi seamount and the associated geochemical supplies of energy that can support autotrophic microbial communities.

Review of computer simulations of isotope effects on biochemical reactions: From the Bigeleisen equation to Feynman's path integral.

PubMed

Wong, Kin-Yiu; Xu, Yuqing; Xu, Liang

2015-11-01

Enzymatic reactions are integral components in many biological functions and malfunctions. The iconic structure of each reaction path for elucidating the reaction mechanism in details is the molecular structure of the rate-limiting transition state (RLTS). But RLTS is very hard to get caught or to get visualized by experimentalists. In spite of the lack of explicit molecular structure of the RLTS in experiment, we still can trace out the RLTS unique "fingerprints" by measuring the isotope effects on the reaction rate. This set of "fingerprints" is considered as a most direct probe of RLTS. By contrast, for computer simulations, oftentimes molecular structures of a number of TS can be precisely visualized on computer screen, however, theoreticians are not sure which TS is the actual rate-limiting one. As a result, this is an excellent stage setting for a perfect "marriage" between experiment and theory for determining the structure of RLTS, along with the reaction mechanism, i.e., experimentalists are responsible for "fingerprinting", whereas theoreticians are responsible for providing candidates that match the "fingerprints". In this Review, the origin of isotope effects on a chemical reaction is discussed from the perspectives of classical and quantum worlds, respectively (e.g., the origins of the inverse kinetic isotope effects and all the equilibrium isotope effects are purely from quantum). The conventional Bigeleisen equation for isotope effect calculations, as well as its refined version in the framework of Feynman's path integral and Kleinert's variational perturbation (KP) theory for systematically incorporating anharmonicity and (non-parabolic) quantum tunneling, are also presented. In addition, the outstanding interplay between theory and experiment for successfully deducing the RLTS structures and the reaction mechanisms is demonstrated by applications on biochemical reactions, namely models of bacterial squalene-to-hopene polycyclization and RNA 2'-O-transphosphorylation. For all these applications, we used our recently-developed path-integral method based on the KP theory, called automated integration-free path-integral (AIF-PI) method, to perform ab initio path-integral calculations of isotope effects. As opposed to the conventional path-integral molecular dynamics (PIMD) and Monte Carlo (PIMC) simulations, values calculated from our AIF-PI path-integral method can be as precise as (not as accurate as) the numerical precision of the computing machine. Lastly, comments are made on the general challenges in theoretical modeling of candidates matching the experimental "fingerprints" of RLTS. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Variance-reduced simulation of lattice discrete-time Markov chains with applications in reaction networks

NASA Astrophysics Data System (ADS)

Maginnis, P. A.; West, M.; Dullerud, G. E.

2016-10-01

We propose an algorithm to accelerate Monte Carlo simulation for a broad class of stochastic processes. Specifically, the class of countable-state, discrete-time Markov chains driven by additive Poisson noise, or lattice discrete-time Markov chains. In particular, this class includes simulation of reaction networks via the tau-leaping algorithm. To produce the speedup, we simulate pairs of fair-draw trajectories that are negatively correlated. Thus, when averaged, these paths produce an unbiased Monte Carlo estimator that has reduced variance and, therefore, reduced error. Numerical results for three example systems included in this work demonstrate two to four orders of magnitude reduction of mean-square error. The numerical examples were chosen to illustrate different application areas and levels of system complexity. The areas are: gene expression (affine state-dependent rates), aerosol particle coagulation with emission and human immunodeficiency virus infection (both with nonlinear state-dependent rates). Our algorithm views the system dynamics as a ;black-box;, i.e., we only require control of pseudorandom number generator inputs. As a result, typical codes can be retrofitted with our algorithm using only minor changes. We prove several analytical results. Among these, we characterize the relationship of covariances between paths in the general nonlinear state-dependent intensity rates case, and we prove variance reduction of mean estimators in the special case of affine intensity rates.

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.

Understanding large SEP events with the PATH code: Modeling of the 13 December 2006 SEP event

NASA Astrophysics Data System (ADS)

Verkhoglyadova, O. P.; Li, G.; Zank, G. P.; Hu, Q.; Cohen, C. M. S.; Mewaldt, R. A.; Mason, G. M.; Haggerty, D. K.; von Rosenvinge, T. T.; Looper, M. D.

2010-12-01

The Particle Acceleration and Transport in the Heliosphere (PATH) numerical code was developed to understand solar energetic particle (SEP) events in the near-Earth environment. We discuss simulation results for the 13 December 2006 SEP event. The PATH code includes modeling a background solar wind through which a CME-driven oblique shock propagates. The code incorporates a mixed population of both flare and shock-accelerated solar wind suprathermal particles. The shock parameters derived from ACE measurements at 1 AU and observational flare characteristics are used as input into the numerical model. We assume that the diffusive shock acceleration mechanism is responsible for particle energization. We model the subsequent transport of particles originated at the flare site and particles escaping from the shock and propagating in the equatorial plane through the interplanetary medium. We derive spectra for protons, oxygen, and iron ions, together with their time-intensity profiles at 1 AU. Our modeling results show reasonable agreement with in situ measurements by ACE, STEREO, GOES, and SAMPEX for this event. We numerically estimate the Fe/O abundance ratio and discuss the physics underlying a mixed SEP event. We point out that the flare population is as important as shock geometry changes during shock propagation for modeling time-intensity profiles and spectra at 1 AU. The combined effects of seed population and shock geometry will be examined in the framework of an extended PATH code in future modeling efforts.

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.

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

The CCONE Code System and its Application to Nuclear Data Evaluation for Fission and Other Reactions

NASA Astrophysics Data System (ADS)

Iwamoto, O.; Iwamoto, N.; Kunieda, S.; Minato, F.; Shibata, K.

2016-01-01

A computer code system, CCONE, was developed for nuclear data evaluation within the JENDL project. The CCONE code system integrates various nuclear reaction models needed to describe nucleon, light charged nuclei up to alpha-particle and photon induced reactions. The code is written in the C++ programming language using an object-oriented technology. At first, it was applied to neutron-induced reaction data on actinides, which were compiled into JENDL Actinide File 2008 and JENDL-4.0. It has been extensively used in various nuclear data evaluations for both actinide and non-actinide nuclei. The CCONE code has been upgraded to nuclear data evaluation at higher incident energies for neutron-, proton-, and photon-induced reactions. It was also used for estimating β-delayed neutron emission. This paper describes the CCONE code system indicating the concept and design of coding and inputs. Details of the formulation for modelings of the direct, pre-equilibrium and compound reactions are presented. Applications to the nuclear data evaluations such as neutron-induced reactions on actinides and medium-heavy nuclei, high-energy nucleon-induced reactions, photonuclear reaction and β-delayed neutron emission are mentioned.

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).

A Transmissible Plasmid Controlling Camphor Oxidation in Pseudomonas putida

PubMed Central

Rheinwald, J. G.; Chakrabarty, A. M.; Gunsalus, I. C.

1973-01-01

Earlier papers demonstrated an extensive genetic exchange among fluorescent Pseudomonads; this one documents for genes specifying enzymes of peripheral dissimilation an extrachromosomal array, segregation, and frequent interstrain transfer. An hypothesis is presented of a general mechanism for the formation and maintenance of metabolic diversity. The example used, the path of oxidative cleavage of the carbocyclic rings of the bicyclic monoterpene D- and L-camphor, terminates in acetate release and isobutyrate chain debranching. By transduction, two gene linkage groups are shown for the reactions before and after isobutyrate. The group for reactions before isobutyrate is plasmid borne, contransferable by conjugation, mitomycin curable, and shows a higher segregation rate from cells that are multiplasmid rather than carrying a single plasmid. The genes that code for isobutyrate and essential anaplerotic and amphibolic metabolism are chromosomal. By conjugation plasmid-borne genes are transferred at a higher frequency than are chromosomal, and are transferred in homologous crosses more frequently than between heterologous species. Most isobutyrate-positive fluorescent pseudomonad strains will accept and express the camphor plasmid. PMID:4351810

Path-Following Solutions Of Nonlinear Equations

NASA Technical Reports Server (NTRS)

Barger, Raymond L.; Walters, Robert W.

1989-01-01

Report describes some path-following techniques for solution of nonlinear equations and compares with other methods. Use of multipurpose techniques applicable at more than one stage of path-following computation results in system relatively simple to understand, program, and use. Comparison of techniques with method of parametric differentiation (MPD) reveals definite advantages for path-following methods. Emphasis in investigation on multiuse techniques being applied at more than one stage of path-following computation. Incorporation of multipurpose techniques results in concise computer code relatively simple to use.

Three-tier multi-granularity switching system based on PCE

NASA Astrophysics Data System (ADS)

Wang, Yubao; Sun, Hao; Liu, Yanfei

2017-10-01

With the growing demand for business communications, electrical signal processing optical path switching can't meet the demand. The multi-granularity switch system that can improve node routing and switching capabilities came into being. In the traditional network, each node is responsible for calculating the path; synchronize the whole network state, which will increase the burden on the network, so the concept of path calculation element (PCE) is proposed. The PCE is responsible for routing and allocating resources in the network1. In the traditional band-switched optical network, the wavelength is used as the basic routing unit, resulting in relatively low wavelength utilization. Due to the limitation of wavelength continuity, the routing design of the band technology becomes complicated, which directly affects the utilization of the system. In this paper, optical code granularity is adopted. There is no continuity of the optical code, and the number of optical codes is more flexible than the wavelength. For the introduction of optical code switching, we propose a Code Group Routing Entity (CGRE) algorithm. In short, the combination of three-tier multi-granularity optical switching system and PCE can simplify the network structure, reduce the node load, and enhance the network scalability and survivability. Realize the intelligentization of optical network.

High-Content Optical Codes for Protecting Rapid Diagnostic Tests from Counterfeiting.

PubMed

Gökçe, Onur; Mercandetti, Cristina; Delamarche, Emmanuel

2018-06-19

Warnings and reports on counterfeit diagnostic devices are released several times a year by regulators and public health agencies. Unfortunately, mishandling, altering, and counterfeiting point-of-care diagnostics (POCDs) and rapid diagnostic tests (RDTs) is lucrative, relatively simple and can lead to devastating consequences. Here, we demonstrate how to implement optical security codes in silicon- and nitrocellulose-based flow paths for device authentication using a smartphone. The codes are created by inkjet spotting inks directly on nitrocellulose or on micropillars. Codes containing up to 32 elements per mm 2 and 8 colors can encode as many as 10 45 combinations. Codes on silicon micropillars can be erased by setting a continuous flow path across the entire array of code elements or for nitrocellulose by simply wicking a liquid across the code. Static or labile code elements can further be formed on nitrocellulose to create a hidden code using poly(ethylene glycol) (PEG) or glycerol additives to the inks. More advanced codes having a specific deletion sequence can also be created in silicon microfluidic devices using an array of passive routing nodes, which activate in a particular, programmable sequence. Such codes are simple to fabricate, easy to view, and efficient in coding information; they can be ideally used in combination with information on a package to protect diagnostic devices from counterfeiting.

MO-F-CAMPUS-T-05: SQL Database Queries to Determine Treatment Planning Resource Usage

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

Fox, C; Gladstone, D

2015-06-15

Purpose: A radiation oncology clinic’s treatment capacity is traditionally thought to be limited by the number of machines in the clinic. As the number of fractions per course decrease and the number of adaptive plans increase, the question of how many treatment plans a clinic can plan becomes increasingly important. This work seeks to lay the ground work for assessing treatment planning resource usage. Methods: Care path templates were created using the Aria 11 care path interface. Care path tasks included key steps in the treatment planning process from the completion of CT simulation through the first radiation treatment. SQLmore » Server Management Studio was used to run SQL queries to extract task completion time stamps along with care path template information and diagnosis codes from the Aria database. 6 months of planning cycles were evaluated. Elapsed time was evaluated in terms of work hours within Monday – Friday, 7am to 5pm. Results: For the 195 validated treatment planning cycles, the average time for planning and MD review was 22.8 hours. Of those cases 33 were categorized as urgent. The average planning time for urgent plans was 5 hours. A strong correlation between diagnosis code and range of elapsed planning time was as well as between elapsed time and select diagnosis codes was observed. It was also observed that tasks were more likely to be completed on the date due than the time that they were due. Follow-up confirmed that most users did not look at the due time. Conclusion: Evaluation of elapsed planning time and other tasks suggest that care paths should be adjusted to allow for different contouring and planning times for certain diagnosis codes and urgent cases. Additional clinic training around task due times vs dates or a structuring of care paths around due dates is also needed.« less

Unified path integral approach to theories of diffusion-influenced reactions

NASA Astrophysics Data System (ADS)

Prüstel, Thorsten; Meier-Schellersheim, Martin

2017-08-01

Building on mathematical similarities between quantum mechanics and theories of diffusion-influenced reactions, we develop a general approach for computational modeling of diffusion-influenced reactions that is capable of capturing not only the classical Smoluchowski picture but also alternative theories, as is here exemplified by a volume reactivity model. In particular, we prove the path decomposition expansion of various Green's functions describing the irreversible and reversible reaction of an isolated pair of molecules. To this end, we exploit a connection between boundary value and interaction potential problems with δ - and δ'-function perturbation. We employ a known path-integral-based summation of a perturbation series to derive a number of exact identities relating propagators and survival probabilities satisfying different boundary conditions in a unified and systematic manner. Furthermore, we show how the path decomposition expansion represents the propagator as a product of three factors in the Laplace domain that correspond to quantities figuring prominently in stochastic spatially resolved simulation algorithms. This analysis will thus be useful for the interpretation of current and the design of future algorithms. Finally, we discuss the relation between the general approach and the theory of Brownian functionals and calculate the mean residence time for the case of irreversible and reversible reactions.

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.

CTViz: A tool for the visualization of transport in nanocomposites.

PubMed

Beach, Benjamin; Brown, Joshua; Tarlton, Taylor; Derosa, Pedro A

2016-05-01

A visualization tool (CTViz) for charge transport processes in 3-D hybrid materials (nanocomposites) was developed, inspired by the need for a graphical application to assist in code debugging and data presentation of an existing in-house code. As the simulation code grew, troubleshooting problems grew increasingly difficult without an effective way to visualize 3-D samples and charge transport in those samples. CTViz is able to produce publication and presentation quality visuals of the simulation box, as well as static and animated visuals of the paths of individual carriers through the sample. CTViz was designed to provide a high degree of flexibility in the visualization of the data. A feature that characterizes this tool is the use of shade and transparency levels to highlight important details in the morphology or in the transport paths by hiding or dimming elements of little relevance to the current view. This is fundamental for the visualization of 3-D systems with complex structures. The code presented here provides these required capabilities, but has gone beyond the original design and could be used as is or easily adapted for the visualization of other particulate transport where transport occurs on discrete paths. Copyright © 2016 Elsevier Inc. All rights reserved.

Method for Veterbi decoding of large constraint length convolutional codes

NASA Technical Reports Server (NTRS)

Hsu, In-Shek (Inventor); Truong, Trieu-Kie (Inventor); Reed, Irving S. (Inventor); Jing, Sun (Inventor)

1988-01-01

A new method of Viterbi decoding of convolutional codes lends itself to a pipline VLSI architecture using a single sequential processor to compute the path metrics in the Viterbi trellis. An array method is used to store the path information for NK intervals where N is a number, and K is constraint length. The selected path at the end of each NK interval is then selected from the last entry in the array. A trace-back method is used for returning to the beginning of the selected path back, i.e., to the first time unit of the interval NK to read out the stored branch metrics of the selected path which correspond to the message bits. The decoding decision made in this way is no longer maximum likelihood, but can be almost as good, provided that constraint length K in not too small. The advantage is that for a long message, it is not necessary to provide a large memory to store the trellis derived information until the end of the message to select the path that is to be decoded; the selection is made at the end of every NK time unit, thus decoding a long message in successive blocks.

Mobile robot dynamic path planning based on improved genetic algorithm

NASA Astrophysics Data System (ADS)

Wang, Yong; Zhou, Heng; Wang, Ying

2017-08-01

In dynamic unknown environment, the dynamic path planning of mobile robots is a difficult problem. In this paper, a dynamic path planning method based on genetic algorithm is proposed, and a reward value model is designed to estimate the probability of dynamic obstacles on the path, and the reward value function is applied to the genetic algorithm. Unique coding techniques reduce the computational complexity of the algorithm. The fitness function of the genetic algorithm fully considers three factors: the security of the path, the shortest distance of the path and the reward value of the path. The simulation results show that the proposed genetic algorithm is efficient in all kinds of complex dynamic environments.

Impulse Response Measurements Over Space-Earth Paths Using the GPS Coarse/Acquisition Codes

NASA Technical Reports Server (NTRS)

Lemmon, J. J.; Papazian, P. B.

1995-01-01

The impulse responses of radio transmission channels over space-earth paths were measured using the course/acquisition code signals from the Global Positioning System of satellites. The data acquisition system and signal processing techniques used to develop the impulse responses are described. Examples of impulse response measurements are presented. The results indicate that this measurement approach enables detection of multipath signals that are 20 dB or more below the power of the direct arrival. Channel characteristics that could be investigated with additional measurements and analyses are discussed.

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.

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.

Moving from Batch to Field Using the RT3D Reactive Transport Modeling System

NASA Astrophysics Data System (ADS)

Clement, T. P.; Gautam, T. R.

2002-12-01

The public domain reactive transport code RT3D (Clement, 1997) is a general-purpose numerical code for solving coupled, multi-species reactive transport in saturated groundwater systems. The code uses MODFLOW to simulate flow and several modules of MT3DMS to simulate the advection and dispersion processes. RT3D employs the operator-split strategy which allows the code solve the coupled reactive transport problem in a modular fashion. The coupling between reaction and transport is defined through a separate module where the reaction equations are specified. The code supports a versatile user-defined reaction option that allows users to define their own reaction system through a Fortran-90 subroutine, known as the RT3D-reaction package. Further a utility code, known as BATCHRXN, allows the users to independently test and debug their reaction package. To analyze a new reaction system at a batch scale, users should first run BATCHRXN to test the ability of their reaction package to model the batch data. After testing, the reaction package can simply be ported to the RT3D environment to study the model response under 1-, 2-, or 3-dimensional transport conditions. This paper presents example problems that demonstrate the methods for moving from batch to field-scale simulations using BATCHRXN and RT3D codes. The first example describes a simple first-order reaction system for simulating the sequential degradation of Tetrachloroethene (PCE) and its daughter products. The second example uses a relatively complex reaction system for describing the multiple degradation pathways of Tetrachloroethane (PCA) and its daughter products. References 1) Clement, T.P, RT3D - A modular computer code for simulating reactive multi-species transport in 3-Dimensional groundwater aquifers, Battelle Pacific Northwest National Laboratory Research Report, PNNL-SA-28967, September, 1997. Available at: http://bioprocess.pnl.gov/rt3d.htm.

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.

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.).

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

Particle acceleration and transport at a 2D CME-driven shock using the HAFv3 and PATH Code

NASA Astrophysics Data System (ADS)

Li, G.; Ao, X.; Fry, C. D.; Verkhoglyadova, O. P.; Zank, G. P.

2012-12-01

We study particle acceleration at a 2D CME-driven shock and the subsequent transport in the inner heliosphere (up to 2 AU) by coupling the kinematic Hakamada-Akasofu-Fry version 3 (HAFv3) solar wind model (Hakamada and Akasofu, 1982, Fry et al. 2003) with the Particle Acceleration and Transport in the Heliosphere (PATH) model (Zank et al., 2000, Li et al., 2003, 2005, Verkhoglyadova et al. 2009). The HAFv3 provides the evolution of a two-dimensional shock geometry and other plasma parameters, which are fed into the PATH model to investigate the effect of a varying shock geometry on particle acceleration and transport. The transport module of the PATH model is parallelized and utilizes the state-of-the-art GPU computation technique to achieve a rapid physics-based numerical description of the interplanetary energetic particles. Together with a fast execution of the HAFv3 model, the coupled code gives us a possibility to nowcast/forecast the interplanetary radiation environment.

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

Argo, P.E.; DeLapp, D.; Sutherland, C.D.

TRACKER is an extension of a three-dimensional Hamiltonian raytrace code developed some thirty years ago by R. Michael Jones. Subsequent modifications to this code, which is commonly called the {open_quotes}Jones Code,{close_quotes} were documented by Jones and Stephensen (1975). TRACKER incorporates an interactive user`s interface, modern differential equation integrators, graphical outputs, homing algorithms, and the Ionospheric Conductivity and Electron Density (ICED) ionosphere. TRACKER predicts the three-dimensional paths of radio waves through model ionospheres by numerically integrating Hamilton`s equations, which are a differential expression of Fermat`s principle of least time. By using continuous models, the Hamiltonian method avoids false caustics and discontinuousmore » raypath properties often encountered in other raytracing methods. In addition to computing the raypath, TRACKER also calculates the group path (or pulse travel time), the phase path, the geometrical (or {open_quotes}real{close_quotes}) pathlength, and the Doppler shift (if the time variation of the ionosphere is explicitly included). Computational speed can be traded for accuracy by specifying the maximum allowable integration error per step in the integration. Only geometrical optics are included in the main raytrace code; no partial reflections or diffraction effects are taken into account. In addition, TRACKER does not lend itself to statistical descriptions of propagation -- it requires a deterministic model of the ionosphere.« less

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).

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.

The potential role of magmatic gases in the genesis of Illinois- Kentucky fluorspar deposits: implications from chemical reaction path modeling

USGS Publications Warehouse

Plumlee, G.S.; Goldhaber, M.B.; Rowan, E.L.

1995-01-01

Presents results of reaction path calculations using the chemical speciation and reaction path program SOLVEQ and CHILLER to model possible fluorite deposition mechanisms in the Illinois-Kentucky fluorspar district. The results indicate that the fluids responsible for Illinois-Kentucky fluorspar mineralization were most likely quite acidic (pH < 4) and rich in fluorine in order to produce the fluorite-rich, dolomite-poor mineral assemblages and extensive dissolution of host limestones. A possible source for the acid and fluorine may have been HF-rich gases which were expelled from alkalic magmas and then incorporated by migrating basinal brines. An analysis of the geologic setting of other fluorite deposits and districts worldwide suggests that involvement of magmatic gases is probable for many of these districts as well. -from Authors

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

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.

Two way time transfer results at NRL and USNO

NASA Technical Reports Server (NTRS)

Galysh, Ivan J.; Landis, G. Paul

1993-01-01

The Naval Research Laboratory (NRL) has developed a two way time transfer modem system for the United States Naval Observatory (USNO). Two modems in conjunction with a pair of Very Small Aperture Terminal (VSAT) and a communication satellite can achieve sub nanosecond time transfer. This performance is demonstrated by the results of testing at and between NRL and USNO. The modems use Code Division Multiple Access (CDMA) methods to separate their signals through a single path in the satellite. Each modem transmitted a different Pseudo Random Noise (PRN) code and received the others PRN code. High precision time transfer is possible with two way methods because of reciprocity of many of the terms of the path and hardware delay between the two modems. The hardware description was given in a previous paper.

Design of supercritical cascades with high solidity

NASA Technical Reports Server (NTRS)

Sanz, J. M.

1982-01-01

The method of complex characteristics of Garabedian and Korn was successfully used to design shockless cascades with solidities of up to one. A code was developed using this method and a new hodograph transformation of the flow onto an ellipse. This code allows the design of cascades with solidities of up to two and larger turning angles. The equations of potential flow are solved in a complex hodograph like domain by setting a characteristic initial value problem and integrating along suitable paths. The topology that the new mapping introduces permits a simpler construction of these paths of integration.

Reactive transport modeling in fractured rock: A state-of-the-science review

NASA Astrophysics Data System (ADS)

MacQuarrie, Kerry T. B.; Mayer, K. Ulrich

2005-10-01

The field of reactive transport modeling has expanded significantly in the past two decades and has assisted in resolving many issues in Earth Sciences. Numerical models allow for detailed examination of coupled transport and reactions, or more general investigation of controlling processes over geologic time scales. Reactive transport models serve to provide guidance in field data collection and, in particular, enable researchers to link modeling and hydrogeochemical studies. In this state-of-science review, the key objectives were to examine the applicability of reactive transport codes for exploring issues of redox stability to depths of several hundreds of meters in sparsely fractured crystalline rock, with a focus on the Canadian Shield setting. A conceptual model of oxygen ingress and redox buffering, within a Shield environment at time and space scales relevant to nuclear waste repository performance, is developed through a review of previous research. This conceptual model describes geochemical and biological processes and mechanisms materially important to understanding redox buffering capacity and radionuclide mobility in the far-field. Consistent with this model, reactive transport codes should ideally be capable of simulating the effects of changing recharge water compositions as a result of long-term climate change, and fracture-matrix interactions that may govern water-rock interaction. Other aspects influencing the suitability of reactive transport codes include the treatment of various reaction and transport time scales, the ability to apply equilibrium or kinetic formulations simultaneously, the need to capture feedback between water-rock interactions and porosity-permeability changes, and the representation of fractured crystalline rock environments as discrete fracture or dual continuum media. A review of modern multicomponent reactive transport codes indicates a relatively high-level of maturity. Within the Yucca Mountain nuclear waste disposal program, reactive transport codes of varying complexity have been applied to investigate the migration of radionuclides and the geochemical evolution of host rock around the planned disposal facility. Through appropriate near- and far-field application of dual continuum codes, this example demonstrates how reactive transport models have been applied to assist in constraining historic water infiltration rates, interpreting the sealing of flow paths due to mineral precipitation, and investigating post-closure geochemical monitoring strategies. Natural analogue modeling studies, although few in number, are also of key importance as they allow the comparison of model results with hydrogeochemical and paleohydrogeological data over geologic time scales.

32. ISOMETRIC VIEW OF PIPING PLAN, SHOWING PATH OF CONDUIT ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

32. ISOMETRIC VIEW OF PIPING PLAN, SHOWING PATH OF CONDUIT FROM CONTROL BUNKER TO SHIELDING TANK. F.C. TORKELSON DRAWING NUMBER 842-ARVFS-701-P-1. INEL INDEX CODE NUMBER: 075 0701 60 851 151977. - Idaho National Engineering Laboratory, Advanced Reentry Vehicle Fusing System, Scoville, Butte County, ID

A systematic review of validated methods for identifying transfusion-related ABO incompatibility reactions using administrative and claims data.

PubMed

Carnahan, Ryan M; Kee, Vicki R

2012-01-01

This paper aimed to systematically review algorithms to identify transfusion-related ABO incompatibility reactions in administrative data, with a focus on studies that have examined the validity of the algorithms. A literature search was conducted using PubMed, Iowa Drug Information Service database, and Embase. A Google Scholar search was also conducted because of the difficulty identifying relevant studies. Reviews were conducted by two investigators to identify studies using data sources from the USA or Canada because these data sources were most likely to reflect the coding practices of Mini-Sentinel data sources. One study was found that validated International Classification of Diseases (ICD-9-CM) codes representing transfusion reactions. None of these cases were ABO incompatibility reactions. Several studies consistently used ICD-9-CM code 999.6, which represents ABO incompatibility reactions, and a technical report identified the ICD-10 code for these reactions. One study included the E-code E8760 for mismatched blood in transfusion in the algorithm. Another study reported finding no ABO incompatibility reaction codes in the Healthcare Cost and Utilization Project Nationwide Inpatient Sample database, which contains data of 2.23 million patients who received transfusions, raising questions about the sensitivity of administrative data for identifying such reactions. Two studies reported perfect specificity, with sensitivity ranging from 21% to 83%, for the code identifying allogeneic red blood cell transfusions in hospitalized patients. There is no information to assess the validity of algorithms to identify transfusion-related ABO incompatibility reactions. Further information on the validity of algorithms to identify transfusions would also be useful. Copyright © 2012 John Wiley & Sons, Ltd.

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/).

Real-time video streaming using H.264 scalable video coding (SVC) in multihomed mobile networks: a testbed approach

NASA Astrophysics Data System (ADS)

Nightingale, James; Wang, Qi; Grecos, Christos

2011-03-01

Users of the next generation wireless paradigm known as multihomed mobile networks expect satisfactory quality of service (QoS) when accessing streamed multimedia content. The recent H.264 Scalable Video Coding (SVC) extension to the Advanced Video Coding standard (AVC), offers the facility to adapt real-time video streams in response to the dynamic conditions of multiple network paths encountered in multihomed wireless mobile networks. Nevertheless, preexisting streaming algorithms were mainly proposed for AVC delivery over multipath wired networks and were evaluated by software simulation. This paper introduces a practical, hardware-based testbed upon which we implement and evaluate real-time H.264 SVC streaming algorithms in a realistic multihomed wireless mobile networks environment. We propose an optimised streaming algorithm with multi-fold technical contributions. Firstly, we extended the AVC packet prioritisation schemes to reflect the three-dimensional granularity of SVC. Secondly, we designed a mechanism for evaluating the effects of different streamer 'read ahead window' sizes on real-time performance. Thirdly, we took account of the previously unconsidered path switching and mobile networks tunnelling overheads encountered in real-world deployments. Finally, we implemented a path condition monitoring and reporting scheme to facilitate the intelligent path switching. The proposed system has been experimentally shown to offer a significant improvement in PSNR of the received stream compared with representative existing algorithms.

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.

Dexter - A one-dimensional code for calculating thermionic performance of long converters.

NASA Technical Reports Server (NTRS)

Sawyer, C. D.

1971-01-01

This paper describes a versatile code for computing the coupled thermionic electric-thermal performance of long thermionic converters in which the temperature and voltage variations cannot be neglected. The code is capable of accounting for a variety of external electrical connection schemes, coolant flow paths and converter failures by partial shorting. Example problem solutions are given.

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

NASA Technical Reports Server (NTRS)

Manchester, John I.; Shibata, Masayuki; Setlik, Robert F.; Ornstein, Rick L.; Rein, Robert

1993-01-01

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

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.

Epoch of Reionization : An Investigation of the Semi-Analytic 21CMMC Code

NASA Astrophysics Data System (ADS)

Miller, Michelle

2018-01-01

After the Big Bang the universe was filled with neutral hydrogen that began to cool and collapse into the first structures. These first stars and galaxies began to emit radiation that eventually ionized all of the neutral hydrogen in the universe. 21CMMC is a semi-numerical code that takes simulated boxes of this ionized universe from another code called 21cmFAST. Mock measurements are taken from the simulated boxes in 21cmFAST. Those measurements are thrown into 21CMMC and help us determine three major parameters of this simulated universe: virial temperature, mean free path, and ionization efficiency. My project tests the robustness of 21CMMC on universe simulations other than 21cmFAST to see whether 21CMMC can properly reconstruct early universe parameters given a mock “measurement” in the form of power spectra. We determine that while two of the three EoR parameters (Virial Temperature and Efficiency) have some reconstructability, the mean free path parameter in the code is the least robust. This requires development of the 21CMMC code.

CEM2k and LAQGSM Codes as Event-Generators for Space Radiation Shield and Cosmic Rays Propagation Applications

NASA Technical Reports Server (NTRS)

Mashnik, S. G.; Gudima, K. K.; Sierk, A. J.; Moskalenko, I. V.

2002-01-01

Space radiation shield applications and studies of cosmic ray propagation in the Galaxy require reliable cross sections to calculate spectra of secondary particles and yields of the isotopes produced in nuclear reactions induced both by particles and nuclei at energies from threshold to hundreds of GeV per nucleon. Since the data often exist in a very limited energy range or sometimes not at all, the only way to obtain an estimate of the production cross sections is to use theoretical models and codes. Recently, we have developed improved versions of the Cascade-Exciton Model (CEM) of nuclear reactions: the codes CEM97 and CEM2k for description of particle-nucleus reactions at energies up to about 5 GeV. In addition, we have developed a LANL version of the Quark-Gluon String Model (LAQGSM) to describe reactions induced both by particles and nuclei at energies up to hundreds of GeVhucleon. We have tested and benchmarked the CEM and LAQGSM codes against a large variety of experimental data and have compared their results with predictions by other currently available models and codes. Our benchmarks show that CEM and LAQGSM codes have predictive powers no worse than other currently used codes and describe many reactions better than other codes; therefore both our codes can be used as reliable event-generators for space radiation shield and cosmic ray propagation applications. The CEM2k code is being incorporated into the transport code MCNPX (and several other transport codes), and we plan to incorporate LAQGSM into MCNPX in the near future. Here, we present the current status of the CEM2k and LAQGSM codes, and show results and applications to studies of cosmic ray propagation in the Galaxy.

Sensory feedback in a bump attractor model of path integration.

PubMed

Poll, Daniel B; Nguyen, Khanh; Kilpatrick, Zachary P

2016-04-01

Mammalian spatial navigation systems utilize several different sensory information channels. This information is converted into a neural code that represents the animal's current position in space by engaging place cell, grid cell, and head direction cell networks. In particular, sensory landmark (allothetic) cues can be utilized in concert with an animal's knowledge of its own velocity (idiothetic) cues to generate a more accurate representation of position than path integration provides on its own (Battaglia et al. The Journal of Neuroscience 24(19):4541-4550 (2004)). We develop a computational model that merges path integration with feedback from external sensory cues that provide a reliable representation of spatial position along an annular track. Starting with a continuous bump attractor model, we explore the impact of synaptic spatial asymmetry and heterogeneity, which disrupt the position code of the path integration process. We use asymptotic analysis to reduce the bump attractor model to a single scalar equation whose potential represents the impact of asymmetry and heterogeneity. Such imperfections cause errors to build up when the network performs path integration, but these errors can be corrected by an external control signal representing the effects of sensory cues. We demonstrate that there is an optimal strength and decay rate of the control signal when cues appear either periodically or randomly. A similar analysis is performed when errors in path integration arise from dynamic noise fluctuations. Again, there is an optimal strength and decay of discrete control that minimizes the path integration error.

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.

Improved Geothermometry Through Multivariate Reaction-path Modeling and Evaluation of Geomicrobiological Influences on Geochemical Temperature Indicators: Final Report

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

Mattson, Earl; Smith, Robert; Fujita, Yoshiko

2015-03-01

The project was aimed at demonstrating that the geothermometric predictions can be improved through the application of multi-element reaction path modeling that accounts for lithologic and tectonic settings, while also accounting for biological influences on geochemical temperature indicators. The limited utilization of chemical signatures by individual traditional geothermometer in the development of reservoir temperature estimates may have been constraining their reliability for evaluation of potential geothermal resources. This project, however, was intended to build a geothermometry tool which can integrate multi-component reaction path modeling with process-optimization capability that can be applied to dilute, low-temperature water samples to consistently predict reservoirmore » temperature within ±30 °C. The project was also intended to evaluate the extent to which microbiological processes can modulate the geochemical signals in some thermal waters and influence the geothermometric predictions.« less

LSENS, a general chemical kinetics and sensitivity analysis code for gas-phase reactions: User's guide

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1993-01-01

A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS, are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include static system, steady, one-dimensional, inviscid flow, shock initiated reaction, and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method, which works efficiently for the extremes of very fast and very slow reaction, is used for solving the 'stiff' differential equation systems that arise in chemical kinetics. For static reactions, sensitivity coefficients of all dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters can be computed. This paper presents descriptions of the code and its usage, and includes several illustrative example problems.

LSENS, The NASA Lewis Kinetics and Sensitivity Analysis Code

NASA Technical Reports Server (NTRS)

Radhakrishnan, K.

2000-01-01

A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS (the NASA Lewis kinetics and sensitivity analysis code), are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include: static system; steady, one-dimensional, inviscid flow; incident-shock initiated reaction in a shock tube; and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method (LSODE, the Livermore Solver for Ordinary Differential Equations), which works efficiently for the extremes of very fast and very slow reactions, is used to solve the "stiff" ordinary differential equation systems that arise in chemical kinetics. For static reactions, the code uses the decoupled direct method to calculate sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters. Solution methods for the equilibrium and post-shock conditions and for perfectly stirred reactor problems are either adapted from or based on the procedures built into the NASA code CEA (Chemical Equilibrium and Applications).

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.

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.

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.

Simulation studies of chemical erosion on carbon based materials at elevated temperatures

NASA Astrophysics Data System (ADS)

Kenmotsu, T.; Kawamura, T.; Li, Zhijie; Ono, T.; Yamamura, Y.

1999-06-01

We simulated the fluence dependence of methane reaction yield in carbon with hydrogen bombardment using the ACAT-DIFFUSE code. The ACAT-DIFFUSE code is a simulation code based on a Monte Carlo method with a binary collision approximation and on solving diffusion equations. The chemical reaction model in carbon was studied by Roth or other researchers. Roth's model is suitable for the steady state methane reaction. But this model cannot estimate the fluence dependence of the methane reaction. Then, we derived an empirical formula based on Roth's model for methane reaction. In this empirical formula, we assumed the reaction region where chemical sputtering due to methane formation takes place. The reaction region corresponds to the peak range of incident hydrogen distribution in the target material. We adopted this empirical formula to the ACAT-DIFFUSE code. The simulation results indicate the similar fluence dependence compared with the experiment result. But, the fluence to achieve the steady state are different between experiment and simulation results.

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.

Global Coordinates and Exact Aberration Calculations Applied to Physical Optics Modeling of Complex Optical Systems

NASA Astrophysics Data System (ADS)

Lawrence, G.; Barnard, C.; Viswanathan, V.

1986-11-01

Historically, wave optics computer codes have been paraxial in nature. Folded systems could be modeled by "unfolding" the optical system. Calculation of optical aberrations is, in general, left for the analyst to do with off-line codes. While such paraxial codes were adequate for the simpler systems being studied 10 years ago, current problems such as phased arrays, ring resonators, coupled resonators, and grazing incidence optics require a major advance in analytical capability. This paper describes extension of the physical optics codes GLAD and GLAD V to include a global coordinate system and exact ray aberration calculations. The global coordinate system allows components to be positioned and rotated arbitrarily. Exact aberrations are calculated for components in aligned or misaligned configurations by using ray tracing to compute optical path differences and diffraction propagation. Optical path lengths between components and beam rotations in complex mirror systems are calculated accurately so that coherent interactions in phased arrays and coupled devices may be treated correctly.

Code-Time Diversity for Direct Sequence Spread Spectrum Systems

PubMed Central

Hassan, A. Y.

2014-01-01

Time diversity is achieved in direct sequence spread spectrum by receiving different faded delayed copies of the transmitted symbols from different uncorrelated channel paths when the transmission signal bandwidth is greater than the coherence bandwidth of the channel. In this paper, a new time diversity scheme is proposed for spread spectrum systems. It is called code-time diversity. In this new scheme, N spreading codes are used to transmit one data symbol over N successive symbols interval. The diversity order in the proposed scheme equals to the number of the used spreading codes N multiplied by the number of the uncorrelated paths of the channel L. The paper represents the transmitted signal model. Two demodulators structures will be proposed based on the received signal models from Rayleigh flat and frequency selective fading channels. Probability of error in the proposed diversity scheme is also calculated for the same two fading channels. Finally, simulation results are represented and compared with that of maximal ration combiner (MRC) and multiple-input and multiple-output (MIMO) systems. PMID:24982925

jFuzz: A Concolic Whitebox Fuzzer for Java

NASA Technical Reports Server (NTRS)

Jayaraman, Karthick; Harvison, David; Ganesh, Vijay; Kiezun, Adam

2009-01-01

We present jFuzz, a automatic testing tool for Java programs. jFuzz is a concolic whitebox fuzzer, built on the NASA Java PathFinder, an explicit-state Java model checker, and a framework for developing reliability and analysis tools for Java. Starting from a seed input, jFuzz automatically and systematically generates inputs that exercise new program paths. jFuzz uses a combination of concrete and symbolic execution, and constraint solving. Time spent on solving constraints can be significant. We implemented several well-known optimizations and name-independent caching, which aggressively normalizes the constraints to reduce the number of calls to the constraint solver. We present preliminary results due to the optimizations, and demonstrate the effectiveness of jFuzz in creating good test inputs. The source code of jFuzz is available as part of the NASA Java PathFinder. jFuzz is intended to be a research testbed for investigating new testing and analysis techniques based on concrete and symbolic execution. The source code of jFuzz is available as part of the NASA Java PathFinder.

JPL-ANTOPT antenna structure optimization program

NASA Technical Reports Server (NTRS)

Strain, D. M.

1994-01-01

New antenna path-length error and pointing-error structure optimization codes were recently added to the MSC/NASTRAN structural analysis computer program. Path-length and pointing errors are important measured of structure-related antenna performance. The path-length and pointing errors are treated as scalar displacements for statics loading cases. These scalar displacements can be subject to constraint during the optimization process. Path-length and pointing-error calculations supplement the other optimization and sensitivity capabilities of NASTRAN. The analysis and design functions were implemented as 'DMAP ALTERs' to the Design Optimization (SOL 200) Solution Sequence of MSC-NASTRAN, Version 67.5.

GCKP84-general chemical kinetics code for gas-phase flow and batch processes including heat transfer effects

NASA Technical Reports Server (NTRS)

Bittker, D. A.; Scullin, V. J.

1984-01-01

A general chemical kinetics code is described for complex, homogeneous ideal gas reactions in any chemical system. The main features of the GCKP84 code are flexibility, convenience, and speed of computation for many different reaction conditions. The code, which replaces the GCKP code published previously, solves numerically the differential equations for complex reaction in a batch system or one dimensional inviscid flow. It also solves numerically the nonlinear algebraic equations describing the well stirred reactor. A new state of the art numerical integration method is used for greatly increased speed in handling systems of stiff differential equations. The theory and the computer program, including details of input preparation and a guide to using the code are given.

Theoretical Proposal for the Whole Phosphate Diester Hydrolysis Mechanism Promoted by a Catalytic Promiscuous Dinuclear Copper(II) Complex.

PubMed

Esteves, Lucas F; Rey, Nicolás A; Dos Santos, Hélio F; Costa, Luiz Antônio S

2016-03-21

The catalytic mechanism that involves the cleavage of the phosphate diester model BDNPP (bis(2,4-dinitrophenyl) phosphate) catalyzed through a dinuclear copper complex is investigated in the current study. The metal complex was originally designed to catalyze catechol oxidation, and it showed an interesting catalytic promiscuity case in biomimetic systems. The current study investigates two different reaction mechanisms through quantum mechanics calculations in the gas phase, and it also includes the solvent effect through PCM (polarizable continuum model) single-point calculations using water as solvent. Two mechanisms are presented in order to fully describe the phosphate diester hydrolysis. Mechanism 1 is of the S(N)2 type, which involves the direct attack of the μ-OH bridge between the two copper(II) ions toward the phosphorus center, whereas mechanism 2 is the process in which hydrolysis takes place through proton transfer between the oxygen atom in the bridging hydroxo ligand and the other oxygen atom in the phosphate model. Actually, the present theoretical study shows two possible reaction paths in mechanism 1. Its first reaction path (p1) involves a proton transfer that occurs immediately after the hydrolytic cleavage, so that the proton transfer is the rate-determining step, which is followed by the entry of two water molecules. Its second reaction path (p2) consists of the entry of two water molecules right after the hydrolytic cleavage, but with no proton transfer; thus, hydrolytic cleavage is the rate-limiting step. The most likely catalytic path occurs in mechanism 1, following the second reaction path (p2), since it involves the lowest free energy activation barrier (ΔG(⧧) = 23.7 kcal mol(-1), in aqueous solution). A kinetic analysis showed that the experimental k(obs) value of 1.7 × 10(-5) s(-1) agrees with the calculated value k1 = 2.6 × 10(-5) s(-1); the concerted mechanism is kinetically favorable. The KIE (kinetic isotope effect) analysis applied to the second reaction path (p2) in mechanism 1 was also taken into account to assess the changes that take place in TS1-i (transition state of mechanism 1) and to perfectly characterize the mechanism described herein.

Computer code for predicting coolant flow and heat transfer in turbomachinery

NASA Technical Reports Server (NTRS)

Meitner, Peter L.

1990-01-01

A computer code was developed to analyze any turbomachinery coolant flow path geometry that consist of a single flow passage with a unique inlet and exit. Flow can be bled off for tip-cap impingement cooling, and a flow bypass can be specified in which coolant flow is taken off at one point in the flow channel and reintroduced at a point farther downstream in the same channel. The user may either choose the coolant flow rate or let the program determine the flow rate from specified inlet and exit conditions. The computer code integrates the 1-D momentum and energy equations along a defined flow path and calculates the coolant's flow rate, temperature, pressure, and velocity and the heat transfer coefficients along the passage. The equations account for area change, mass addition or subtraction, pumping, friction, and heat transfer.

Self-complementary circular codes in coding theory.

PubMed

Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

2018-04-01

Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

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.

Benefit of adaptive FEC in shared backup path protected elastic optical network.

PubMed

Guo, Hong; Dai, Hua; Wang, Chao; Li, Yongcheng; Bose, Sanjay K; Shen, Gangxiang

2015-07-27

We apply an adaptive forward error correction (FEC) allocation strategy to an Elastic Optical Network (EON) operated with shared backup path protection (SBPP). To maximize the protected network capacity that can be carried, an Integer Linear Programing (ILP) model and a spectrum window plane (SWP)-based heuristic algorithm are developed. Simulation results show that the FEC coding overhead required by the adaptive FEC scheme is significantly lower than that needed by a fixed FEC allocation strategy resulting in higher network capacity for the adaptive strategy. The adaptive FEC allocation strategy can also significantly outperform the fixed FEC allocation strategy both in terms of the spare capacity redundancy and the average FEC coding overhead needed per optical channel. The proposed heuristic algorithm is efficient and not only performs closer to the ILP model but also does much better than the shortest-path algorithm.

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

Patients' expectations of the role of the community pharmacist: Development and testing of a conceptual model.

PubMed

Sabater-Galindo, Marta; Ruiz de Maya, Salvador; Benrimoj, Shalom I; Gastelurrutia, Miguel Angel; Martínez-Martínez, Fernando; Sabater-Hernández, Daniel

The roles of community pharmacists are evolving to include provision of expanded professional pharmacy services, thus leading to an increased interest in pharmacist-patient interactions. Role theory can be used to explain the interaction between this pair of individuals, by focusing on the roles performed by each one. To develop and test a model that relates patients' image of the pharmacist to their expectations of pharmacist's role, and how this then influences patients' reactions toward the pharmacist's role. A qualitative study was undertaken, and a questionnaire was created for the development of the model, based on role theory. The content, dimensions, validity and reliability of the questionnaire were pre-tested qualitatively and in a pilot mail survey. The reliability and validity of the proposed model were tested using confirmatory factor analysis (CFA). Structural equation modelling (SEM) was used to explain relationships between dimensions of the final model. A final model was developed. CFA concluded that the model was valid and reliable (Goodness of Fit indices: χ 2 (109) = 227.662, P = 0.000, RMSEA = 0.05, SRMR = 0.05, GFI = 1.00, NNFI = 0.90, CFI = 0.92). SEM indicated that "perceived pharmacist image" was associated positively and significantly with both "professional expectations" (the standardized path coefficient of (H) = 0.719, P < 0.05), as well as "courtesy expectations" (the standardized path coefficient of (H) = 0.582, P < 0.05). At the same time, "professional expectations" were associated positively and significantly with "positive reactions" (the standardized path coefficient of (H) = 0.358, P < 0.05), but negatively with "Negative reactions" (the standardized path coefficient of (H) = -0.427, P < 0.05). "Courtesy expectations" were associated positively and significantly with "positive reactions" (the standardized path coefficient of (H) = 0.081, P < 0.05), as well as "negative reactions" (the standardized path coefficient of (H) = 0.450, P < 0.05). A valid and reliable model of patients' image of the pharmacist related to their expectations and reactions to the pharmacist's role was developed and tested. When the perceived image of the pharmacist is enhanced, patients' expectations of the pharmacist are heightened; in turn, these expectations were associated with reactions of patients. Copyright © 2016 Elsevier Inc. All rights reserved.

EMPIRE: A code for nuclear astrophysics

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

Palumbo, A.

The nuclear reaction code EMPIRE is presented as a useful tool for nuclear astrophysics. EMPIRE combines a variety of the reaction models with a comprehensive library of input parameters providing a diversity of options for the user. With exclusion of the directsemidirect capture all reaction mechanisms relevant to the nuclear astrophysics energy range of interest are implemented in the code. Comparison to experimental data show consistent agreement for all relevant channels.

CRUNCH_PARALLEL

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

Shumaker, Dana E.; Steefel, Carl I.

The code CRUNCH_PARALLEL is a parallel version of the CRUNCH code. CRUNCH code version 2.0 was previously released by LLNL, (UCRL-CODE-200063). Crunch is a general purpose reactive transport code developed by Carl Steefel and Yabusake (Steefel Yabsaki 1996). The code handles non-isothermal transport and reaction in one, two, and three dimensions. The reaction algorithm is generic in form, handling an arbitrary number of aqueous and surface complexation as well as mineral dissolution/precipitation. A standardized database is used containing thermodynamic and kinetic data. The code includes advective, dispersive, and diffusive transport.

Compliance Verification Paths for Residential and Commercial Energy Codes

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

Conover, David R.; Makela, Eric J.; Fannin, Jerica D.

2011-10-10

This report looks at different ways to verify energy code compliance and to ensure that the energy efficiency goals of an adopted document are achieved. Conformity assessment is the body of work that ensures compliance, including activities that can ensure residential and commercial buildings satisfy energy codes and standards. This report identifies and discusses conformity-assessment activities and provides guidance for conducting assessments.

DEXTER: A one-dimensional code for calculating thermionic performance of long converters

NASA Technical Reports Server (NTRS)

Sawyer, C. D.

1971-01-01

A versatile code is described for computing the coupled thermionic electric-thermal performance of long thermionic converters in which the temperature and voltage variations cannot be neglected. The code is capable of accounting for a variety of external electrical connection schemes, coolant flow paths and converter failures by partial shorting. Example problem solutions are included along with a user's manual.

Daytime tropical D region parameters from short path VLF phase and amplitude

NASA Astrophysics Data System (ADS)

Thomson, Neil R.

2010-09-01

Observed phases and amplitudes of VLF radio signals, propagating on a short (˜300-km) path, are used to find improved parameters for the lowest edge of the (D region of the) Earth's ionosphere. The phases, relative to GPS 1-s pulses, and the amplitudes were measured both near (˜100 km from) the transmitter, where the direct ground wave is very dominant, and at distances of ˜300 km near where the ionospherically reflected waves form a (modal) minimum with the (direct) ground wave. The signals came from the 19.8 kHz, 1 MW transmitter, NWC, on the North West Cape of Australia, propagating ˜300 km ENE, mainly over the sea, to the vicinity of Karratha/Dampier on the N.W. coast of Australia. The bottom edge of the mid-day tropical/equatorial ionosphere was thus found to be well-modeled by H‧ = 70.5 ± 0.5 km and β = 0.47 ± 0.03 km-1 where H‧ and β are the traditional height and sharpness parameters as used by Wait and by the U.S. Navy in their Earth-ionosphere VLF radio waveguide programs. U.S. Navy modal waveguide code calculations are also compared with those from the wave hop code of Berry and Herman (1971). At least for the vertical electric fields on the path studied here, the resulting phase and amplitude differences (between the ˜100-km and ˜300-km sites) agree very well after just a small adjustment of ˜0.2 km in H‧ between the two codes. Such short paths also allow more localization than the usual long paths; here this localization is to low latitudes.

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

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.

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.

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Effect of enhanced manganese oxidation in the hyporheic zone on basin-scale geochemical mass balance

USGS Publications Warehouse

Harvey, Judson W.; Fuller, Christopher C.

1998-01-01

We determined the role of the hyporheic zone (the subsurface zone where stream water and shallow groundwater mix) in enhancing microbially mediated oxidation of dissolved manganese (to form manganese precipitates) in a drainage basin contaminated by copper mining. The fate of manganese is of overall importance to water quality in Pinal Creek Basin, Arizona, because manganese reactions affect the transport of trace metals. The basin-scale role of the hyporheic zone is difficult to quantify because stream-tracer studies do not always reliably characterize the cumulative effects of the hyporheic zone. This study determined cumulative effects of hyporheic reactions in Pinal Creek basin by characterizing manganese uptake at several spatial scales (stream-reach scale, hyporheic-flow-path scale, and sediment-grain scale). At the stream-reach scale a one-dimensional stream-transport model (including storage zones to represent hyporheic flow paths) was used to determine a reach-averaged time constant for manganese uptake in hyporheic zones, 1/λs, of 1.3 hours, which was somewhat faster but still similar to manganese uptake time constants that were measured directly in centimeter-scale hyporheic flow paths (1/λh= 2.6 hours), and in laboratory batch experiments using streambed sediment (1/λ = 2.7 hours). The modeled depths of subsurface storage zones (ds = 4–17 cm) and modeled residence times of water in storage zones (ts = 3–12 min) were both consistent with direct measurements in hyporheic flow paths (dh = 0–15 cm, th = 1–25 min). There was also good agreement between reach-scale modeling and direct measurements of the percentage removal of dissolved manganese in hyporheic flow paths (fs = 8.9%, andfh = 9.3%rpar;. Manganese uptake experiments in the laboratory using sediment from Pinal Creek demonstrated (through comparison of poisoned and unpoisoned treatments) that the manganese removal process was enhanced by microbially mediated oxidation. The cumulative effect of hyporheic exchange in Pinal Creek basin was to remove approximately 20% of the dissolved manganese flowing out of the drainage basin. Our results illustrate that the cumulative significance of reactive uptake in the hyporheic zone depends on the balance between chemical reaction rates, hyporheic porewater residence time, and turnover of streamflow through hyporheic flow paths. The similarity between the hyporheic reaction timescale (1/λs ≈ 1.3 hours), and the hyporheic porewater residence timescale (ts ≈ 8 min) ensured that there was adequate time for the reaction to progress. Furthermore, it was the similarity between the turnover length for stream water flow through hyporheic flow paths (Ls = stream velocity/storage-zone exchange coefficient ≈ 1.3 km) and the length of Pinal Creek (L ≈ 7 km), which ensured that all stream water passed through hyporheic flow paths several times. As a means to generalize our findings to other sites where similar types of hydrologic and chemical information are available, we suggest a cumulative significance index for hyporheic reactions, Rs = λstsL/Ls (dimensionless); higher values indicate a greater potential for hyporheic reactions to influence geochemical mass balance. Our experience in Pinal Creek basin suggests that values of Rs > 0.2 characterize systems where hyporheic reactions are likely to influence geochemical mass balance at the drainage-basin scale.

Open-path FTIR data reduction algorithm with atmospheric absorption corrections: the NONLIN code

NASA Astrophysics Data System (ADS)

Phillips, William; Russwurm, George M.

1999-02-01

This paper describes the progress made to date in developing, testing, and refining a data reduction computer code, NONLIN, that alleviates many of the difficulties experienced in the analysis of open path FTIR data. Among the problems that currently effect FTIR open path data quality are: the inability to obtain a true I degree or background, spectral interferences of atmospheric gases such as water vapor and carbon dioxide, and matching the spectral resolution and shift of the reference spectra to a particular field instrument. This algorithm is based on a non-linear fitting scheme and is therefore not constrained by many of the assumptions required for the application of linear methods such as classical least squares (CLS). As a result, a more realistic mathematical model of the spectral absorption measurement process can be employed in the curve fitting process. Applications of the algorithm have proven successful in circumventing open path data reduction problems. However, recent studies, by one of the authors, of the temperature and pressure effects on atmospheric absorption indicate there exist temperature and water partial pressure effects that should be incorporated into the NONLIN algorithm for accurate quantification of gas concentrations. This paper investigates the sources of these phenomena. As a result of this study a partial pressure correction has been employed in NONLIN computer code. Two typical field spectra are examined to determine what effect the partial pressure correction has on gas quantification.

Hydrogen analysis depth calibration by CORTEO Monte-Carlo simulation

NASA Astrophysics Data System (ADS)

Moser, M.; Reichart, P.; Bergmaier, A.; Greubel, C.; Schiettekatte, F.; Dollinger, G.

2016-03-01

Hydrogen imaging with sub-μm lateral resolution and sub-ppm sensitivity has become possible with coincident proton-proton (pp) scattering analysis (Reichart et al., 2004). Depth information is evaluated from the energy sum signal with respect to energy loss of both protons on their path through the sample. In first order, there is no angular dependence due to elastic scattering. In second order, a path length effect due to different energy loss on the paths of the protons causes an angular dependence of the energy sum. Therefore, the energy sum signal has to be de-convoluted depending on the matrix composition, i.e. mainly the atomic number Z, in order to get a depth calibrated hydrogen profile. Although the path effect can be calculated analytically in first order, multiple scattering effects lead to significant deviations in the depth profile. Hence, in our new approach, we use the CORTEO Monte-Carlo code (Schiettekatte, 2008) in order to calculate the depth of a coincidence event depending on the scattering angle. The code takes individual detector geometry into account. In this paper we show, that the code correctly reproduces measured pp-scattering energy spectra with roughness effects considered. With more than 100 μm thick Mylar-sandwich targets (Si, Fe, Ge) we demonstrate the deconvolution of the energy spectra on our current multistrip detector at the microprobe SNAKE at the Munich tandem accelerator lab. As a result, hydrogen profiles can be evaluated with an accuracy in depth of about 1% of the sample thickness.

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.

Eye-Movements During Search for Coded and Uncoded Targets

DTIC Science & Technology

1974-06-28

effective a coding system as solor . Subjects did not exhibit a reliable, characteristic scan-path, except for two subjects in the uncoded condition...Psychophysics 8, 171- 172, 1970. 31. Clarke, S. E. Retrieval of color information from the pre-perceptu- al storage system . J Exp Psychol 82, 263

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.

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

Performance Analysis of IEEE 802.11g TCM Waveforms Transmitted over a Channel with Pulse-Noise Interference

DTIC Science & Technology

2007-06-01

17 Table 2. Best (maximum free distance) rate r=2/3 punctured convolutional code ...Hamming distance between all pairs of non-zero paths. Table 2 lists the best rate r=2/3, punctured convolutional code information weight structure dB...Table 2. Best (maximum free distance) rate r=2/3 punctured convolutional code information weight structure. (From: [12]). K freed freeB

Comparison of Damage Path Predictions for Composite Laminates by Explicit and Standard Finite Element Analysis Tools

NASA Technical Reports Server (NTRS)

Bogert, Philip B.; Satyanarayana, Arunkumar; Chunchu, Prasad B.

2006-01-01

Splitting, ultimate failure load and the damage path in center notched composite specimens subjected to in-plane tension loading are predicted using progressive failure analysis methodology. A 2-D Hashin-Rotem failure criterion is used in determining intra-laminar fiber and matrix failures. This progressive failure methodology has been implemented in the Abaqus/Explicit and Abaqus/Standard finite element codes through user written subroutines "VUMAT" and "USDFLD" respectively. A 2-D finite element model is used for predicting the intra-laminar damages. Analysis results obtained from the Abaqus/Explicit and Abaqus/Standard code show good agreement with experimental results. The importance of modeling delamination in progressive failure analysis methodology is recognized for future studies. The use of an explicit integration dynamics code for simple specimen geometry and static loading establishes a foundation for future analyses where complex loading and nonlinear dynamic interactions of damage and structure will necessitate it.

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

Development of the Off-line Analysis Code for GODDESS

NASA Astrophysics Data System (ADS)

Garland, Heather; Cizewski, Jolie; Lepailleur, Alex; Walters, David; Pain, Steve; Smith, Karl

2016-09-01

Determining (n, γ) cross sections on unstable nuclei is important for understanding the r-process that is theorized to occur in supernovae and neutron-star mergers. However, (n, γ) reactions are difficult to measure directly because of the short lifetime of the involved neutron rich nuclei. A possible surrogate for the (n, γ) reaction is the (d,p γ) reaction; the measurement of these reactions in inverse kinematics is part of the scope of GODDESS - Gammasphere ORRUBA (Oak Ridge Rutgers University Barrel Array): Dual Detectors for Experimental Structure Studies. The development of an accurate and efficient off-line analysis code for GODDESS experiments is not only essential, but also provides a unique opportunity to create an analysis code designed specifically for transfer reaction experiments. The off-line analysis code has been developed to produce histograms from the binary data file to determine how to best sort events. Recent developments in the off-line analysis code will be presented as well as details on the energy and position calibrations for the ORRUBA detectors. This work is supported in part by the U.S. Department of Energy and National Science Foundation.

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.

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.

A Deterministic Transport Code for Space Environment Electrons

NASA Technical Reports Server (NTRS)

Nealy, John E.; Chang, C. K.; Norman, Ryan B.; Blattnig, Steve R.; Badavi, Francis F.; Adamczyk, Anne M.

2010-01-01

A deterministic computational procedure has been developed to describe transport of space environment electrons in various shield media. This code is an upgrade and extension of an earlier electron code. Whereas the former code was formulated on the basis of parametric functions derived from limited laboratory data, the present code utilizes well established theoretical representations to describe the relevant interactions and transport processes. The shield material specification has been made more general, as have the pertinent cross sections. A combined mean free path and average trajectory approach has been used in the transport formalism. Comparisons with Monte Carlo calculations are presented.

RELAP-7 Theory Manual

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

Berry, Ray Alden; Zou, Ling; Zhao, Haihua

This document summarizes the physical models and mathematical formulations used in the RELAP-7 code. In summary, the MOOSE based RELAP-7 code development is an ongoing effort. The MOOSE framework enables rapid development of the RELAP-7 code. The developmental efforts and results demonstrate that the RELAP-7 project is on a path to success. This theory manual documents the main features implemented into the RELAP-7 code. Because the code is an ongoing development effort, this RELAP-7 Theory Manual will evolve with periodic updates to keep it current with the state of the development, implementation, and model additions/revisions.

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.

Displaying the results of three-dimensional analysis using GRAPE. Part one: vector graphics. [In FORTRAN for CDC 7600

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

Brown, B.E.

1979-10-01

GRAPE is a display program for three-dimensional polygon and polyhedral models. It can produce line-drawing and continuous-tone black and white or color images in still frame or movie mode. The code was written specifically to be a post-processor for finite element and finite difference analyses. It runs on the CDC 7600 computer, and is compiled with the LLL FTN system. The allocation of storage is dynamic. There are presently three data paths into the code. The first is the binary inerface from the analyses codes and this with the other databases is described. The second data path is the SAMPPmore » format, and the last is the MOVIE format. The code structure is described first; then the commands are discussed in general terms to try to give the user some feel for what they do. The next section deals with the exact format of the commands by overlay. Then examples are given and discussed. Next, the various output options are covered. 57 figures. (RWR)« less

Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase SN2 Reaction of Acetate Ion with 1,2-Dichloroethane

PubMed Central

Valero, Rosendo; Song, Lingchun; Gao, Jiali; Truhlar, Donald G.

2009-01-01

Diabatic models are widely employed for studying chemical reactivity in condensed phases and enzymes, but there has been little discussion of the pros and cons of various diabatic representations for this purpose. Here we discuss and contrast six different schemes for computing diabatic potentials for a charge rearrangement reaction. They include (i) the variational diabatic configurations (VDC) constructed by variationally optimizing individual valence bond structures and (ii) the consistent diabatic configurations (CDC) obtained by variationally optimizing the ground-state adiabatic energy, both in the nonorthogonal molecular orbital valence bond (MOVB) method, along with the orthogonalized (iii) VDC-MOVB and (iv) CDC-MOVB models. In addition, we consider (v) the fourfold way (based on diabatic molecular orbitals and configuration uniformity), and (vi) empirical valence bond (EVB) theory. To make the considerations concrete, we calculate diabatic electronic states and diabatic potential energies along the reaction path that connects the reactant and the product ion-molecule complexes of the gas-phase bimolecular nucleophilic substitution (SN2) reaction of 1,2-dichloethane (DCE) with acetate ion, which is a model reaction corresponding to the reaction catalyzed by haloalkane dehalogenase. We utilize ab initio block-localized molecular orbital theory to construct the MOVB diabatic states and ab initio multi-configuration quasidegenerate perturbation theory to construct the fourfold-way diabatic states; the latter are calculated at reaction path geometries obtained with the M06-2X density functional. The EVB diabatic states are computed with parameters taken from the literature. The MOVB and fourfold-way adiabatic and diabatic potential energy profiles along the reaction path are in qualitative but not quantitative agreement with each other. In order to validate that these wave-function-based diabatic states are qualitatively correct, we show that the reaction energy and barrier for the adiabatic ground state, obtained with these methods, agree reasonably well with the results of high-level calculations using the composite G3SX and G3SX(MP3) methods and the BMC-CCSD multi-coefficient correlation method. However, a comparison of the EVB gas-phase adiabatic ground-state reaction path with those obtained from MOVB and with the fourfold way reveals that the EVB reaction path geometries show a systematic shift towards the products region, and that the EVB lowest-energy path has a much lower barrier. The free energies of solvation and activation energy in water reported from dynamical calculations based on EVB also imply a low activation barrier in the gas phase. In addition, calculations of the free energy of solvation using the recently proposed SM8 continuum solvation model with CM4M partial atomic charges lead to an activation barrier in reasonable agreement with experiment only when the geometries and the gas-phase barrier are those obtained from electronic structure calculations, i.e., methods i–v. These comparisons show the danger of basing the diabatic states on molecular mechanics without the explicit calculation of electronic wave functions. Furthermore, comparison of schemes i–v with one another shows that significantly different quantitative results can be obtained by using different methods for extracting diabatic states from wave function calculations, and it is important for each user to justify the choice of diabatization method in the context of its intended use. PMID:20047005

Progress towards understanding and predicting convection heat transfer in the turbine gas path

NASA Technical Reports Server (NTRS)

Simoneau, Robert J.; Simon, Frederick F.

1992-01-01

A new era is drawing in the ability to predict convection heat transfer in the turbine gas path. We feel that the technical community now has the capability to mount a major assault on this problem, which has eluded significant progress for a long time. We hope to make a case for this bold statement by reviewing the state of the art in three major heat transfer, configuration-specific experiments, whose data have provided the big picture and guided both the fundamental modeling research and the code development. Following that, we review progress and directions in the development of computer codes to predict turbine gas path heat transfer. Finally, we cite examples and make observations on the more recent efforts to do all this work in a simultaneous, interactive, and more synergistic manner. We conclude with an assessment of progress, suggestions for how to use the current state of the art, and recommendations for the future.

FY16 ASME High Temperature Code Activities

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

Swindeman, M. J.; Jetter, R. I.; Sham, T. -L.

2016-09-01

One of the objectives of the ASME high temperature Code activities is to develop and validate both improvements and the basic features of Section III, Division 5, Subsection HB, Subpart B (HBB). The overall scope of this task is to develop a computer program to be used to assess whether or not a specific component under specified loading conditions will satisfy the elevated temperature design requirements for Class A components in Section III, Division 5, Subsection HB, Subpart B (HBB). There are many features and alternative paths of varying complexity in HBB. The initial focus of this task is amore » basic path through the various options for a single reference material, 316H stainless steel. However, the program will be structured for eventual incorporation all the features and permitted materials of HBB. Since this task has recently been initiated, this report focuses on the description of the initial path forward and an overall description of the approach to computer program development.« less

Assessing flow paths in a karst aquifer based on multiple dye tracing tests using stochastic simulation and the MODFLOW-CFP code

NASA Astrophysics Data System (ADS)

Assari, Amin; Mohammadi, Zargham

2017-09-01

Karst systems show high spatial variability of hydraulic parameters over small distances and this makes their modeling a difficult task with several uncertainties. Interconnections of fractures have a major role on the transport of groundwater, but many of the stochastic methods in use do not have the capability to reproduce these complex structures. A methodology is presented for the quantification of tortuosity using the single normal equation simulation (SNESIM) algorithm and a groundwater flow model. A training image was produced based on the statistical parameters of fractures and then used in the simulation process. The SNESIM algorithm was used to generate 75 realizations of the four classes of fractures in a karst aquifer in Iran. The results from six dye tracing tests were used to assign hydraulic conductivity values to each class of fractures. In the next step, the MODFLOW-CFP and MODPATH codes were consecutively implemented to compute the groundwater flow paths. The 9,000 flow paths obtained from the MODPATH code were further analyzed to calculate the tortuosity factor. Finally, the hydraulic conductivity values calculated from the dye tracing experiments were refined using the actual flow paths of groundwater. The key outcomes of this research are: (1) a methodology for the quantification of tortuosity; (2) hydraulic conductivities, that are incorrectly estimated (biased low) with empirical equations that assume Darcian (laminar) flow with parallel rather than tortuous streamlines; and (3) an understanding of the scale-dependence and non-normal distributions of tortuosity.

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.

EMPIRE: A Reaction Model Code for Nuclear Astrophysics

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

Palumbo, A., E-mail: apalumbo@bnl.gov; Herman, M.; Capote, R.

The correct modeling of abundances requires knowledge of nuclear cross sections for a variety of neutron, charged particle and γ induced reactions. These involve targets far from stability and are therefore difficult (or currently impossible) to measure. Nuclear reaction theory provides the only way to estimate values of such cross sections. In this paper we present application of the EMPIRE reaction code to nuclear astrophysics. Recent measurements are compared to the calculated cross sections showing consistent agreement for n-, p- and α-induced reactions of strophysical relevance.

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...

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

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.

Users manual for updated computer code for axial-flow compressor conceptual design

NASA Technical Reports Server (NTRS)

Glassman, Arthur J.

1992-01-01

An existing computer code that determines the flow path for an axial-flow compressor either for a given number of stages or for a given overall pressure ratio was modified for use in air-breathing engine conceptual design studies. This code uses a rapid approximate design methodology that is based on isentropic simple radial equilibrium. Calculations are performed at constant-span-fraction locations from tip to hub. Energy addition per stage is controlled by specifying the maximum allowable values for several aerodynamic design parameters. New modeling was introduced to the code to overcome perceived limitations. Specific changes included variable rather than constant tip radius, flow path inclination added to the continuity equation, input of mass flow rate directly rather than indirectly as inlet axial velocity, solution for the exact value of overall pressure ratio rather than for any value that met or exceeded it, and internal computation of efficiency rather than the use of input values. The modified code was shown to be capable of computing efficiencies that are compatible with those of five multistage compressors and one fan that were tested experimentally. This report serves as a users manual for the revised code, Compressor Spanline Analysis (CSPAN). The modeling modifications, including two internal loss correlations, are presented. Program input and output are described. A sample case for a multistage compressor is included.

133. ARAII SL1 burial ground. Shows gravel path from ARAII ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

133. ARA-II SL-1 burial ground. Shows gravel path from ARA-II compound to the burial ground, detail of security fence and entry gate, and sign "Danger radiation hazard." F. C. Torkelson Company 842-area-101-1. Date: October 1961. Ineel index code no. 059-0101-00-851-150723. - Idaho National Engineering Laboratory, Army Reactors Experimental Area, Scoville, Butte County, ID

Minimal-memory realization of pearl-necklace encoders of general quantum convolutional codes

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

Houshmand, Monireh; Hosseini-Khayat, Saied

2011-02-15

Quantum convolutional codes, like their classical counterparts, promise to offer higher error correction performance than block codes of equivalent encoding complexity, and are expected to find important applications in reliable quantum communication where a continuous stream of qubits is transmitted. Grassl and Roetteler devised an algorithm to encode a quantum convolutional code with a ''pearl-necklace'' encoder. Despite their algorithm's theoretical significance as a neat way of representing quantum convolutional codes, it is not well suited to practical realization. In fact, there is no straightforward way to implement any given pearl-necklace structure. This paper closes the gap between theoretical representation andmore » practical implementation. In our previous work, we presented an efficient algorithm to find a minimal-memory realization of a pearl-necklace encoder for Calderbank-Shor-Steane (CSS) convolutional codes. This work is an extension of our previous work and presents an algorithm for turning a pearl-necklace encoder for a general (non-CSS) quantum convolutional code into a realizable quantum convolutional encoder. We show that a minimal-memory realization depends on the commutativity relations between the gate strings in the pearl-necklace encoder. We find a realization by means of a weighted graph which details the noncommutative paths through the pearl necklace. The weight of the longest path in this graph is equal to the minimal amount of memory needed to implement the encoder. The algorithm has a polynomial-time complexity in the number of gate strings in the pearl-necklace encoder.« less

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.

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.

Coding/decoding and reversibility of droplet trains in microfluidic networks.

PubMed

Fuerstman, Michael J; Garstecki, Piotr; Whitesides, George M

2007-02-09

Droplets of one liquid suspended in a second, immiscible liquid move through a microfluidic device in which a channel splits into two branches that reconnect downstream. The droplets choose a path based on the number of droplets that occupy each branch. The interaction among droplets in the channels results in complex sequences of path selection. The linearity of the flow through the microchannels, however, ensures that the behavior of the system can be reversed. This reversibility makes it possible to encrypt and decrypt signals coded in the intervals between droplets. The encoding/decoding device is a functional microfluidic system that requires droplets to navigate a network in a precise manner without the use of valves, switches, or other means of external control.

(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 .

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

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.

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

Characterization of Aerodynamic Interactions with the Mars Science Laboratory Reaction Control System Using Computation and Experiment

NASA Technical Reports Server (NTRS)

Schoenenberger, Mark; VanNorman, John; Rhode, Matthew; Paulson, John

2013-01-01

On August 5 , 2012, the Mars Science Laboratory (MSL) entry capsule successfully entered Mars' atmosphere and landed the Curiosity rover in Gale Crater. The capsule used a reaction control system (RCS) consisting of four pairs of hydrazine thrusters to fly a guided entry. The RCS provided bank control to fly along a flight path commanded by an onboard computer and also damped unwanted rates due to atmospheric disturbances and any dynamic instabilities of the capsule. A preliminary assessment of the MSL's flight data from entry showed that the capsule flew much as predicted. This paper will describe how the MSL aerodynamics team used engineering analyses, computational codes and wind tunnel testing in concert to develop the RCS system and certify it for flight. Over the course of MSL's development, the RCS configuration underwent a number of design iterations to accommodate mechanical constraints, aeroheating concerns and excessive aero/RCS interactions. A brief overview of the MSL RCS configuration design evolution is provided. Then, a brief description is presented of how the computational predictions of RCS jet interactions were validated. The primary work to certify that the RCS interactions were acceptable for flight was centered on validating computational predictions at hypersonic speeds. A comparison of computational fluid dynamics (CFD) predictions to wind tunnel force and moment data gathered in the NASA Langley 31-Inch Mach 10 Tunnel was the lynch pin to validating the CFD codes used to predict aero/RCS interactions. Using the CFD predictions and experimental data, an interaction model was developed for Monte Carlo analyses using 6-degree-of-freedom trajectory simulation. The interaction model used in the flight simulation is presented.

Ice Accretion and Performance Degradation Calculations with LEWICE/NS

NASA Technical Reports Server (NTRS)

Potapczuk, Mark G.; Al-Khalil, Kamel M.; Velazquez, Matthew T.

1993-01-01

The LEWICE ice accretion computer code has been extended to include the solution of the two-dimensional Navier-Stokes equations. The code is modular and contains separate stand-alone program elements that create a grid, calculate the flow field parameters, calculate the droplet trajectory paths, determine the amount of ice growth, calculate aeroperformance changes, and plot results. The new elements of the code are described. Calculated results are compared to experiment for several cases, including both ice shape and drag rise.

Developing a Multi-Dimensional Hydrodynamics Code with Astrochemical Reactions

NASA Astrophysics Data System (ADS)

Kwak, Kyujin; Yang, Seungwon

2015-08-01

The Atacama Large Millimeter/submillimeter Array (ALMA) revealed high resolution molecular lines some of which are still unidentified yet. Because formation of these astrochemical molecules has been seldom studied in traditional chemistry, observations of new molecular lines drew a lot of attention from not only astronomers but also chemists both experimental and theoretical. Theoretical calculations for the formation of these astrochemical molecules have been carried out providing reaction rates for some important molecules, and some of theoretical predictions have been measured in laboratories. The reaction rates for the astronomically important molecules are now collected to form databases some of which are publically available. By utilizing these databases, we develop a multi-dimensional hydrodynamics code that includes the reaction rates of astrochemical molecules. Because this type of hydrodynamics code is able to trace the molecular formation in a non-equilibrium fashion, it is useful to study the formation history of these molecules that affects the spatial distribution of some specific molecules. We present the development procedure of this code and some test problems in order to verify and validate the developed code.

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.

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

A Radiation Chemistry Code Based on the Green's Function of the Diffusion Equation

NASA Technical Reports Server (NTRS)

Plante, Ianik; Wu, Honglu

2014-01-01

Stochastic radiation track structure codes are of great interest for space radiation studies and hadron therapy in medicine. These codes are used for a many purposes, notably for microdosimetry and DNA damage studies. In the last two decades, they were also used with the Independent Reaction Times (IRT) method in the simulation of chemical reactions, to calculate the yield of various radiolytic species produced during the radiolysis of water and in chemical dosimeters. Recently, we have developed a Green's function based code to simulate reversible chemical reactions with an intermediate state, which yielded results in excellent agreement with those obtained by using the IRT method. This code was also used to simulate and the interaction of particles with membrane receptors. We are in the process of including this program for use with the Monte-Carlo track structure code Relativistic Ion Tracks (RITRACKS). This recent addition should greatly expand the capabilities of RITRACKS, notably to simulate DNA damage by both the direct and indirect effect.

Drivers anticipate lead-vehicle conflicts during automated longitudinal control: Sensory cues capture driver attention and promote appropriate and timely responses.

PubMed

Morando, Alberto; Victor, Trent; Dozza, Marco

2016-12-01

Adaptive Cruise Control (ACC) has been shown to reduce the exposure to critical situations by maintaining a safe speed and headway. It has also been shown that drivers adapt their visual behavior in response to the driving task demand with ACC, anticipating an impending lead vehicle conflict by directing their eyes to the forward path before a situation becomes critical. The purpose of this paper is to identify the causes related to this anticipatory mechanism, by investigating drivers' visual behavior while driving with ACC when a potential critical situation is encountered, identified as a forward collision warning (FCW) onset (including false positive warnings). This paper discusses how sensory cues capture attention to the forward path in anticipation of the FCW onset. The analysis used the naturalistic database EuroFOT to examine visual behavior with respect to two manually-coded metrics, glance location and glance eccentricity, and then related the findings to vehicle data (such as speed, acceleration, and radar information). Three sensory cues (longitudinal deceleration, looming, and brake lights) were found to be relevant for capturing driver attention and increase glances to the forward path in anticipation of the threat; the deceleration cue seems to be dominant. The results also show that the FCW acts as an effective attention-orienting mechanism when no threat anticipation is present. These findings, relevant to the study of automation, provide additional information about drivers' response to potential lead-vehicle conflicts when longitudinal control is automated. Moreover, these results suggest that sensory cues are important for alerting drivers to an impending critical situation, allowing for a prompt reaction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modeling of temporal variation of very low frequency radio waves over long paths as observed from Indian Antarctic stations

NASA Astrophysics Data System (ADS)

Sasmal, Sudipta; Basak, Tamal; Chakraborty, Suman; Palit, Sourav; Chakrabarti, Sandip K.

2017-07-01

Characteristics of very low frequency (VLF) signal depends on solar illumination across the propagation path. For a long path, solar zenith angle varies widely over the path and this has a significant influence on the propagation characteristics. To study the effect, Indian Centre for Space Physics participated in the 27th and 35th Scientific Expedition to Antarctica. VLF signals transmitted from the transmitters, namely, VTX (18.2 kHz), Vijayanarayanam, India, and NWC (19.8 kHz), North West Cape, Australia, were recorded simultaneously at Indian permanent stations Maitri and Bharati having respective geographic coordinates 70.75°S, 11.67°E, and 69.4°S, 76.17°E. A very stable diurnal variation of the signal has been obtained from both the stations. We reproduced the signal variations of VLF signal using solar zenith angle model coupled with long wavelength propagation capability (LWPC) code. We divided the whole path into several segments and computed the solar zenith angle (χ) profile. We assumed a linear relationship between the Wait's exponential model parameters effective reflection height (h'), steepness parameter (β), and solar zenith angle. The h' and β values were later used in the LWPC code to obtain the VLF signal amplitude at a particular time. The same procedure was repeated to obtain the whole day signal. Nature of the whole day signal variation from the theoretical modeling is also found to match with our observation to some extent.

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.

Hermeneutic and Cultural Codes of S/Z: A Semiological Reading of James Joyce's "The Boarding House"

ERIC Educational Resources Information Center

Booryazadeh, Seyed Ali; Faghfori, Sohila; Shamsi, Habibe

2014-01-01

Roland Barthes as a fervent proponent of semiology believes that semiology is a branch of a comprehensive linguistics: it is the study of how language articulates the world. Semiotic codes, the paths of this articulation, accordingly underlie his attention. Barthes in a structural analysis of Balzac's "Sarrasine" in S/Z expounds five…

Z-path SAW RFID tag.

PubMed

Härmä, Sanna; Plessky, Victor P; Hartmann, Clinton S; Steichen, William

2008-01-01

Surface acoustic wave (SAW) radio-frequency identification (RFID) tags are soon expected to be produced in very high volumes. The size and cost of a SAW RFID tag will be key parameters for many applications. Therefore, it is of primary importance to reduce the chip size. In this work, we describe the design principles of a 2.4-GHz SAW RFID tag that is significantly smaller than earlier reported tags. We also present simulated and experimental results. The coded signal should arrive at the reader with a certain delay (typically about 1 micros), i.e., after the reception of environmental echoes. If the tag uses a bidirectional interdigital transducer (IDT), space for the initial delay is needed on both sides of the IDT. In this work, we replace the bidirectional IDT by a unidirectional one. This halves the space required by the initial delay because all the code reflectors must now be placed on the same side of the IDT. We reduce tag size even further by using a Z-path geometry in which the same space in x-direction is used for both the initial delay and the code reflectors. Chip length is thus determined only by the space required by the code reflectors.

Critical evaluation of Jet-A spray combustion using propane chemical kinetics in gas turbine combustion simulated by KIVA-2

NASA Technical Reports Server (NTRS)

Nguyen, H. L.; Ying, S.-J.

1990-01-01

Jet-A spray combustion has been evaluated in gas turbine combustion with the use of propane chemical kinetics as the first approximation for the chemical reactions. Here, the numerical solutions are obtained by using the KIVA-2 computer code. The KIVA-2 code is the most developed of the available multidimensional combustion computer programs for application of the in-cylinder combustion dynamics of internal combustion engines. The released version of KIVA-2 assumes that 12 chemical species are present; the code uses an Arrhenius kinetic-controlled combustion model governed by a four-step global chemical reaction and six equilibrium reactions. Researchers efforts involve the addition of Jet-A thermophysical properties and the implementation of detailed reaction mechanisms for propane oxidation. Three different detailed reaction mechanism models are considered. The first model consists of 131 reactions and 45 species. This is considered as the full mechanism which is developed through the study of chemical kinetics of propane combustion in an enclosed chamber. The full mechanism is evaluated by comparing calculated ignition delay times with available shock tube data. However, these detailed reactions occupy too much computer memory and CPU time for the computation. Therefore, it only serves as a benchmark case by which to evaluate other simplified models. Two possible simplified models were tested in the existing computer code KIVA-2 for the same conditions as used with the full mechanism. One model is obtained through a sensitivity analysis using LSENS, the general kinetics and sensitivity analysis program code of D. A. Bittker and K. Radhakrishnan. This model consists of 45 chemical reactions and 27 species. The other model is based on the work published by C. K. Westbrook and F. L. Dryer.

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.

Flow of GE90 Turbofan Engine Simulated

NASA Technical Reports Server (NTRS)

Veres, Joseph P.

1999-01-01

The objective of this task was to create and validate a three-dimensional model of the GE90 turbofan engine (General Electric) using the APNASA (average passage) flow code. This was a joint effort between GE Aircraft Engines and the NASA Lewis Research Center. The goal was to perform an aerodynamic analysis of the engine primary flow path, in under 24 hours of CPU time, on a parallel distributed workstation system. Enhancements were made to the APNASA Navier-Stokes code to make it faster and more robust and to allow for the analysis of more arbitrary geometry. The resulting simulation exploited the use of parallel computations by using two levels of parallelism, with extremely high efficiency.The primary flow path of the GE90 turbofan consists of a nacelle and inlet, 49 blade rows of turbomachinery, and an exhaust nozzle. Secondary flows entering and exiting the primary flow path-such as bleed, purge, and cooling flows-were modeled macroscopically as source terms to accurately simulate the engine. The information on these source terms came from detailed descriptions of the cooling flow and from thermodynamic cycle system simulations. These provided boundary condition data to the three-dimensional analysis. A simplified combustor was used to feed boundary conditions to the turbomachinery. Flow simulations of the fan, high-pressure compressor, and high- and low-pressure turbines were completed with the APNASA code.

Sir John Pople, Gaussian Code, and Complex Chemical Reactions

Science.gov Websites

tool that describes the dance of molecules in chemical reactions ... . Dr. Pople was among the first to colors of light they will absorb or emit, and the pace of chemical reactions. The work culminated in a dropdown arrow Site Map A-Z Index Menu Synopsis Sir John Pople, Gaussian Code, and Complex Chemical

Iterative retrieval of surface emissivity and temperature for a hyperspectral sensor

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

Borel, C.C.

1997-11-01

The central problem of temperature-emissivity separation is that we obtain N spectral measurements of radiance and need to find N + 1 unknowns (N emissivities and one temperature). To solve this problem in the presence of the atmosphere we need to find even more unknowns: N spectral transmissions {tau}{sub atmo}({lambda}) up-welling path radiances L{sub path}{up_arrow}({lambda}) and N down-welling path radiances L{sub path}{down_arrow}({lambda}). Fortunately there are radiative transfer codes such as MODTRAN 3 and FASCODE available to get good estimates of {tau}{sub atmo}({lambda}), L{sub path}{up_arrow}({lambda}) and L{sub path}{down_arrow}({lambda}) in the order of a few percent. With the growing use of hyperspectralmore » imagers, e.g. AVIRIS in the visible and short-wave infrared there is hope of using such instruments in the mid-wave and thermal IR (TIR) some day. We believe that this will enable us to get around using the present temperature - emissivity separation (TES) algorithms using methods which take advantage of the many channels available in hyperspectral imagers. The first idea we had is to take advantage of the simple fact that a typical surface emissivity spectrum is rather smooth compared to spectral features introduced by the atmosphere. Thus iterative solution techniques can be devised which retrieve emissivity spectra {epsilon} based on spectral smoothness. To make the emissivities realistic, atmospheric parameters are varied using approximations, look-up tables derived from a radiative transfer code and spectral libraries. By varying the surface temperature over a small range a series of emissivity spectra are calculated. The one with the smoothest characteristic is chosen. The algorithm was tested on synthetic data using MODTRAN and the Salisbury emissivity database.« less

Data-driven Modeling of the Solar Corona by a New Three-dimensional Path-conservative Osher-Solomon MHD Model

NASA Astrophysics Data System (ADS)

Feng, Xueshang; Li, Caixia; Xiang, Changqing; Zhang, Man; Li, HuiChao; Wei, Fengsi

2017-11-01

A second-order path-conservative scheme with a Godunov-type finite-volume method has been implemented to advance the equations of single-fluid solar wind plasma magnetohydrodynamics (MHD) in time. This code operates on the six-component composite grid system in three-dimensional spherical coordinates with hexahedral cells of quadrilateral frustum type. The generalized Osher-Solomon Riemann solver is employed based on a numerical integration of the path-dependent dissipation matrix. For simplicity, the straight line segment path is used, and the path integral is evaluated in a fully numerical way by a high-order numerical Gauss-Legendre quadrature. Besides its very close similarity to Godunov type, the resulting scheme retains the attractive features of the original solver: it is nonlinear, free of entropy-fix, differentiable, and complete, in that each characteristic field results in a different numerical viscosity, due to the full use of the MHD eigenstructure. By using a minmod limiter for spatial oscillation control, the path-conservative scheme is realized for the generalized Lagrange multiplier and the extended generalized Lagrange multiplier formulation of solar wind MHD systems. This new model that is second order in space and time is written in the FORTRAN language with Message Passing Interface parallelization and validated in modeling the time-dependent large-scale structure of the solar corona, driven continuously by Global Oscillation Network Group data. To demonstrate the suitability of our code for the simulation of solar wind, we present selected results from 2009 October 9 to 2009 December 29 show its capability of producing a structured solar corona in agreement with solar coronal observations.

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.

Calculation and plotting of retinal nerve fiber paths based on Jansonius et al. 2009/2012 with an R program.

PubMed

Bach, M; Hoffmann, M B

2018-06-01

The data presented in this article are related to the research article entitled "Retinal conduction speed analysis reveals different origins of the P50 and N95 components of the (multifocal) pattern electroretinogram" (Bach et al., 2018) [1]. That analysis required the individual length data of the retinal nerve fibers (from ganglion cell body to optic nerve head, depending on the position of the ganglion cell body). Jansonius et al. (2009, 2012) [2,3] mathematically modeled the path morphology of the human retinal nerve fibers. We here present a working implementation with source code (for the free and open-source programming environment "R") of the Jansonius' formulas, including all errata. One file defines Jansonius et al.'s "phi" function. This function allows quantitative modelling of paths (and any measures derived from them) of the retinal nerve fibers. As a working demonstration, a second file contains a graph which plots samples of nerve fibers. The included R code runs in base R without the need of any additional packages.

ICF target 2D modeling using Monte Carlo SNB electron thermal transport in DRACO

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Cao, Duc; Moses, Gregory

2016-10-01

The iSNB (implicit Schurtz Nicolai Busquet multigroup diffusion electron thermal transport method is adapted into a Monte Carlo (MC) transport method to better model angular and long mean free path non-local effects. The MC model was first implemented in the 1D LILAC code to verify consistency with the iSNB model. Implementation of the MC SNB model in the 2D DRACO code enables higher fidelity non-local thermal transport modeling in 2D implosions such as polar drive experiments on NIF. The final step is to optimize the MC model by hybridizing it with a MC version of the iSNB diffusion method. The hybrid method will combine the efficiency of a diffusion method in intermediate mean free path regions with the accuracy of a transport method in long mean free path regions allowing for improved computational efficiency while maintaining accuracy. Work to date on the method will be presented. This work was supported by Sandia National Laboratories and the Univ. of Rochester Laboratory for Laser Energetics.

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.

Energy spectrum of 208Pb(n,x) reactions

NASA Astrophysics Data System (ADS)

Tel, E.; Kavun, Y.; Özdoǧan, H.; Kaplan, A.

2018-02-01

Fission and fusion reactor technologies have been investigated since 1950's on the world. For reactor technology, fission and fusion reaction investigations are play important role for improve new generation technologies. Especially, neutron reaction studies have an important place in the development of nuclear materials. So neutron effects on materials should study as theoretically and experimentally for improve reactor design. For this reason, Nuclear reaction codes are very useful tools when experimental data are unavailable. For such circumstances scientists created many nuclear reaction codes such as ALICE/ASH, CEM95, PCROSS, TALYS, GEANT, FLUKA. In this study we used ALICE/ASH, PCROSS and CEM95 codes for energy spectrum calculation of outgoing particles from Pb bombardment by neutron. While Weisskopf-Ewing model has been used for the equilibrium process in the calculations, full exciton, hybrid and geometry dependent hybrid nuclear reaction models have been used for the pre-equilibrium process. The calculated results have been discussed and compared with the experimental data taken from EXFOR.

Evaluating progressive-rendering algorithms in appearance design tasks.

PubMed

Jiawei Ou; Karlik, Ondrej; Křivánek, Jaroslav; Pellacini, Fabio

2013-01-01

Progressive rendering is becoming a popular alternative to precomputational approaches to appearance design. However, progressive algorithms create images exhibiting visual artifacts at early stages. A user study investigated these artifacts' effects on user performance in appearance design tasks. Novice and expert subjects performed lighting and material editing tasks with four algorithms: random path tracing, quasirandom path tracing, progressive photon mapping, and virtual-point-light rendering. Both the novices and experts strongly preferred path tracing to progressive photon mapping and virtual-point-light rendering. None of the participants preferred random path tracing to quasirandom path tracing or vice versa; the same situation held between progressive photon mapping and virtual-point-light rendering. The user workflow didn’t differ significantly with the four algorithms. The Web Extras include a video showing how four progressive-rendering algorithms converged (at http://youtu.be/ck-Gevl1e9s), the source code used, and other supplementary materials.

Efficient computation paths for the systematic analysis of sensitivities

NASA Astrophysics Data System (ADS)

Greppi, Paolo; Arato, Elisabetta

2013-01-01

A systematic sensitivity analysis requires computing the model on all points of a multi-dimensional grid covering the domain of interest, defined by the ranges of variability of the inputs. The issues to efficiently perform such analyses on algebraic models are handling solution failures within and close to the feasible region and minimizing the total iteration count. Scanning the domain in the obvious order is sub-optimal in terms of total iterations and is likely to cause many solution failures. The problem of choosing a better order can be translated geometrically into finding Hamiltonian paths on certain grid graphs. This work proposes two paths, one based on a mixed-radix Gray code and the other, a quasi-spiral path, produced by a novel heuristic algorithm. Some simple, easy-to-visualize examples are presented, followed by performance results for the quasi-spiral algorithm and the practical application of the different paths in a process simulation tool.

Vision-based obstacle avoidance

DOEpatents

Galbraith, John [Los Alamos, NM

2006-07-18

A method for allowing a robot to avoid objects along a programmed path: first, a field of view for an electronic imager of the robot is established along a path where the electronic imager obtains the object location information within the field of view; second, a population coded control signal is then derived from the object location information and is transmitted to the robot; finally, the robot then responds to the control signal and avoids the detected object.

Study of the population of neutron-rich heavy nuclei in the A 200 mass region via multinucleon transfer reactions

NASA Astrophysics Data System (ADS)

Fioretto, E.; Corradi, L.; Galtarossa, F.; Szilner, S.; Montanari, D.; Mijatović, T.; Pollarolo, G.; Jia, H. M.; Ackermann, D.; Bourgin, D.; Colucci, G.; Courtin, S.; Fruet, G.; Goasduff, A.; Grebosz, J.; Haas, F.; Jelavić Malenica, D.; Jeong, S. C.; John, P. R.; Milin, M.; Montagnoli, G.; Skukan, N.; Scarlassara, F.; Soić, N.; Stefanini, A. M.; Strano, E.; Tokić, V.; Ur, C. A.; Valiente-Dobón, J. J.; Watanabe, Y. X.

2017-11-01

Multineutron and multiproton transfer channels, populated in the inverse kinematics reaction 197Au+130Te at Elab=1.07 GeV, were measured at Laboratori Nazionali di Legnaro using the presently heaviest ion beam delivered by the PIAVE-ALPI accelerator complex and detecting both projectile-like and targetlike ions. To this end the large solid angle magnetic spectrometer PRISMA was coupled to a second arm for the detection of the heavy fragments in kinematic coincidence with the light ones selected and identified with the spectrometer. The data analysis is still in progress and will allow to compare the yields of both light and heavy partner with theoretical predictions performed with the GRAZING code to get quantitative information on transfer channels and the effect of evaporation and fission on the production rate of primary fragments. The mass integrated Z distribution, extracted from the experimental data, evidenced the population of proton pickup channels that, in conjunction with the neutron stripping ones from the 130Te, open the path for the production of neutron-rich heavy nuclei. In the following, we will present some preliminary results as well as details on the experimental configuration and perspectives for future investigations in the neutron-rich heavy region.

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

Modeling chemical gradients in sediments under losing and gaining flow conditions: The GRADIENT code

NASA Astrophysics Data System (ADS)

Boano, Fulvio; De Falco, Natalie; Arnon, Shai

2018-02-01

Interfaces between sediments and water bodies often represent biochemical hotspots for nutrient reactions and are characterized by steep concentration gradients of different reactive solutes. Vertical profiles of these concentrations are routinely collected to obtain information on nutrient dynamics, and simple codes have been developed to analyze these profiles and determine the magnitude and distribution of reaction rates within sediments. However, existing publicly available codes do not consider the potential contribution of water flow in the sediments to nutrient transport, and their applications to field sites with significant water-borne nutrient fluxes may lead to large errors in the estimated reaction rates. To fill this gap, the present work presents GRADIENT, a novel algorithm to evaluate distributions of reaction rates from observed concentration profiles. GRADIENT is a Matlab code that extends a previously published framework to include the role of nutrient advection, and provides robust estimates of reaction rates in sediments with significant water flow. This work discusses the theoretical basis of the method and shows its performance by comparing the results to a series of synthetic data and to laboratory experiments. The results clearly show that in systems with losing or gaining fluxes, the inclusion of such fluxes is critical for estimating local and overall reaction rates in sediments.

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.

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.

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 kinetics database and scripts for PHREEQC

NASA Astrophysics Data System (ADS)

Hu, B.; Zhang, Y.; Teng, Y.; Zhu, C.

2017-12-01

Kinetics of geochemical reactions has been increasingly used in numerical models to simulate coupled flow, mass transport, and chemical reactions. However, the kinetic data are scattered in the literature. To assemble a kinetic dataset for a modeling project is an intimidating task for most. In order to facilitate the application of kinetics in geochemical modeling, we assembled kinetics parameters into a database for the geochemical simulation program, PHREEQC (version 3.0). Kinetics data were collected from the literature. Our database includes kinetic data for over 70 minerals. The rate equations are also programmed into scripts with the Basic language. Using the new kinetic database, we simulated reaction path during the albite dissolution process using various rate equations in the literature. The simulation results with three different rate equations gave difference reaction paths at different time scale. Another application involves a coupled reactive transport model simulating the advancement of an acid plume in an acid mine drainage site associated with Bear Creek Uranium tailings pond. Geochemical reactions including calcite, gypsum, and illite were simulated with PHREEQC using the new kinetic database. The simulation results successfully demonstrated the utility of new kinetic database.

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.

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.

Simulation of prompt gamma-ray emission during proton radiotherapy.

PubMed

Verburg, Joost M; Shih, Helen A; Seco, Joao

2012-09-07

The measurement of prompt gamma rays emitted from proton-induced nuclear reactions has been proposed as a method to verify in vivo the range of a clinical proton radiotherapy beam. A good understanding of the prompt gamma-ray emission during proton therapy is key to develop a clinically feasible technique, as it can facilitate accurate simulations and uncertainty analysis of gamma detector designs. Also, the gamma production cross-sections may be incorporated as prior knowledge in the reconstruction of the proton range from the measurements. In this work, we performed simulations of proton-induced nuclear reactions with the main elements of human tissue, carbon-12, oxygen-16 and nitrogen-14, using the nuclear reaction models of the GEANT4 and MCNP6 Monte Carlo codes and the dedicated nuclear reaction codes TALYS and EMPIRE. For each code, we made an effort to optimize the input parameters and model selection. The results of the models were compared to available experimental data of discrete gamma line cross-sections. Overall, the dedicated nuclear reaction codes reproduced the experimental data more consistently, while the Monte Carlo codes showed larger discrepancies for a number of gamma lines. The model differences lead to a variation of the total gamma production near the end of the proton range by a factor of about 2. These results indicate a need for additional theoretical and experimental study of proton-induced gamma emission in human tissue.

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.

Common Errors in the Calculation of Aircrew Doses from Cosmic Rays

NASA Astrophysics Data System (ADS)

O'Brien, Keran; Felsberger, Ernst; Kindl, Peter

2010-05-01

Radiation doses to air crew are calculated using flight codes. Flight codes integrate dose rates over the aircraft flight path, which were calculated by transport codes or obtained by measurements from take off at a specific airport to landing at another. The dose rates are stored in various ways, such as by latitude and longitude, or in terms of the geomagnetic vertical cutoff. The transport codes are generally quite satisfactory, but the treatment of the boundary conditions is frequently incorrect. Both the treatment of solar modulation and of the effect of the geomagnetic field are often defective, leading to the systematic overestimate of the crew doses.

Importance biasing scheme implemented in the PRIZMA code

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

Kandiev, I.Z.; Malyshkin, G.N.

1997-12-31

PRIZMA code is intended for Monte Carlo calculations of linear radiation transport problems. The code has wide capabilities to describe geometry, sources, material composition, and to obtain parameters specified by user. There is a capability to calculate path of particle cascade (including neutrons, photons, electrons, positrons and heavy charged particles) taking into account possible transmutations. Importance biasing scheme was implemented to solve the problems which require calculation of functionals related to small probabilities (for example, problems of protection against radiation, problems of detection, etc.). The scheme enables to adapt trajectory building algorithm to problem peculiarities.

NSEG, a segmented mission analysis program for low and high speed aircraft. Volume 1: Theoretical development

NASA Technical Reports Server (NTRS)

Hague, D. S.; Rozendaal, H. L.

1977-01-01

A rapid mission analysis code based on the use of approximate flight path equations of motion is presented. Equation form varies with the segment type, for example, accelerations, climbs, cruises, descents, and decelerations. Realistic and detailed characteristics were specified in tabular form. The code also contains extensive flight envelope performance mapping capabilities. Approximate take off and landing analyses were performed. At high speeds, centrifugal lift effects were accounted for. Extensive turbojet and ramjet engine scaling procedures were incorporated in the code.

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.

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.

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

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)

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.

NSRD-10: Leak Path Factor Guidance Using MELCOR

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

Louie, David; Humphries, Larry L.

Estimates of the source term from a U.S. Department of Energy (DOE) nuclear facility requires that the analysts know how to apply the simulation tools used, such as the MELCOR code, particularly for a complicated facility that may include an air ventilation system and other active systems that can influence the environmental pathway of the materials released. DOE has designated MELCOR 1.8.5, an unsupported version, as a DOE ToolBox code in its Central Registry, which includes a leak-path-factor guidance report written in 2004 that did not include experimental validation data. To continue to use this MELCOR version requires additional verificationmore » and validations, which may not be feasible from a project cost standpoint. Instead, the recent MELCOR should be used. Without any developer support and lack of experimental data validation, it is difficult to convince regulators that the calculated source term from the DOE facility is accurate and defensible. This research replaces the obsolete version in the 2004 DOE leak path factor guidance report by using MELCOR 2.1 (the latest version of MELCOR with continuing modeling development and user support) and by including applicable experimental data from the reactor safety arena and from applicable experimental data used in the DOE-HDBK-3010. This research provides best practice values used in MELCOR 2.1 specifically for the leak path determination. With these enhancements, the revised leak-path-guidance report should provide confidence to the DOE safety analyst who would be using MELCOR as a source-term determination tool for mitigated accident evaluations.« less

GLSENS: A Generalized Extension of LSENS Including Global Reactions and Added Sensitivity Analysis for the Perfectly Stirred Reactor

NASA Technical Reports Server (NTRS)

Bittker, David A.

1996-01-01

A generalized version of the NASA Lewis general kinetics code, LSENS, is described. The new code allows the use of global reactions as well as molecular processes in a chemical mechanism. The code also incorporates the capability of performing sensitivity analysis calculations for a perfectly stirred reactor rapidly and conveniently at the same time that the main kinetics calculations are being done. The GLSENS code has been extensively tested and has been found to be accurate and efficient. Nine example problems are presented and complete user instructions are given for the new capabilities. This report is to be used in conjunction with the documentation for the original LSENS code.

System Data Model (SDM) Source Code

DTIC Science & Technology

2012-08-23

CROSS_COMPILE=/opt/gumstix/build_arm_nofpu/staging_dir/bin/arm-linux-uclibcgnueabi- 8 : CC=$(CROSS_COMPILE)gcc 9: CXX=$(CROSS_COMPILE)g++ 10 : AR...and flags to pass to it 6: LEX=flex 7: LEXFLAGS=-B 8 : 9: ## The parser generator to invoke and flags to pass to it 10 : YACC=bison 11: YACCFLAGS...5: # Point to default PetaLinux root directory 6: ifndef ROOTDIR 7: ROOTDIR=$(PETALINUX)/software/petalinux-dist 8 : endif 9: 10 : PATH:=$(PATH

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.

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.

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.

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of {sup 64}Cu and {sup 67}Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

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

Nasrabadi, M. N., E-mail: mnnasrabadi@ast.ui.ac.ir; Sepiani, M.

2015-03-30

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE and LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of 64Cu and 67Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

NASA Astrophysics Data System (ADS)

Nasrabadi, M. N.; Sepiani, M.

2015-03-01

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE & LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

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.

Relativistic Klystron Amplifiers Driven by Modulated Intense Relativistic Electron Beams

DTIC Science & Technology

1990-04-11

electrical parameters of the cavity were calculated using the SUPERFISH computer code. We found: (1) that the gap voltage, V was half as high as the...SUPERFISH computer code and experimenting with various cavities we found the best cavity geometry that fulfilled the above conditions. For this cavity...paths. Experiments along this line are being planned (T. Godlove and F. Mako, private communciation ). A somewhat different concept which also

High rate concatenated coding systems using bandwidth efficient trellis inner codes

NASA Technical Reports Server (NTRS)

Deng, Robert H.; Costello, Daniel J., Jr.

1989-01-01

High-rate concatenated coding systems with bandwidth-efficient trellis inner codes and Reed-Solomon (RS) outer codes are investigated for application in high-speed satellite communication systems. Two concatenated coding schemes are proposed. In one the inner code is decoded with soft-decision Viterbi decoding, and the outer RS code performs error-correction-only decoding (decoding without side information). In the other, the inner code is decoded with a modified Viterbi algorithm, which produces reliability information along with the decoded output. In this algorithm, path metrics are used to estimate the entire information sequence, whereas branch metrics are used to provide reliability information on the decoded sequence. This information is used to erase unreliable bits in the decoded output. An errors-and-erasures RS decoder is then used for the outer code. The two schemes have been proposed for high-speed data communication on NASA satellite channels. The rates considered are at least double those used in current NASA systems, and the results indicate that high system reliability can still be achieved.

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.

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.

Moving Towards a State of the Art Charge-Exchange Reaction Code

NASA Astrophysics Data System (ADS)

Poxon-Pearson, Terri; Nunes, Filomena; Potel, Gregory

2017-09-01

Charge-exchange reactions have a wide range of applications, including late stellar evolution, constraining the matrix elements for neutrinoless double β-decay, and exploring symmetry energy and other aspects of exotic nuclear matter. Still, much of the reaction theory needed to describe these transitions is underdeveloped and relies on assumptions and simplifications that are often extended outside of their region of validity. In this work, we have begun to move towards a state of the art charge-exchange reaction code. As a first step, we focus on Fermi transitions using a Lane potential in a few body, Distorted Wave Born Approximation (DWBA) framework. We have focused on maintaining a modular structure for the code so we can later incorporate complications such as nonlocality, breakup, and microscopic inputs. Results using this new charge-exchange code will be shown compared to the analysis in for the case of 48Ca(p,n)48Sc. This work was supported in part by the National Nuclear Security Administration under the Stewardship Science Academic Alliances program through the U.S. DOE Cooperative Agreement No. DE- FG52-08NA2855.

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.

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.

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.

A Radiation Shielding Code for Spacecraft and Its Validation

NASA Technical Reports Server (NTRS)

Shinn, J. L.; Cucinotta, F. A.; Singleterry, R. C.; Wilson, J. W.; Badavi, F. F.; Badhwar, G. D.; Miller, J.; Zeitlin, C.; Heilbronn, L.; Tripathi, R. K.

2000-01-01

The HZETRN code, which uses a deterministic approach pioneered at NASA Langley Research Center, has been developed over the past decade to evaluate the local radiation fields within sensitive materials (electronic devices and human tissue) on spacecraft in the space environment. The code describes the interactions of shield materials with the incident galactic cosmic rays, trapped protons, or energetic protons from solar particle events in free space and low Earth orbit. The content of incident radiations is modified by atomic and nuclear reactions with the spacecraft and radiation shield materials. High-energy heavy ions are fragmented into less massive reaction products, and reaction products are produced by direct knockout of shield constituents or from de-excitation products. An overview of the computational procedures and database which describe these interactions is given. Validation of the code with recent Monte Carlo benchmarks, and laboratory and flight measurement is also included.

Multi-scale modeling of irradiation effects in spallation neutron source materials

NASA Astrophysics Data System (ADS)

Yoshiie, T.; Ito, T.; Iwase, H.; Kaneko, Y.; Kawai, M.; Kishida, I.; Kunieda, S.; Sato, K.; Shimakawa, S.; Shimizu, F.; Hashimoto, S.; Hashimoto, N.; Fukahori, T.; Watanabe, Y.; Xu, Q.; Ishino, S.

2011-07-01

Changes in mechanical property of Ni under irradiation by 3 GeV protons were estimated by multi-scale modeling. The code consisted of four parts. The first part was based on the Particle and Heavy-Ion Transport code System (PHITS) code for nuclear reactions, and modeled the interactions between high energy protons and nuclei in the target. The second part covered atomic collisions by particles without nuclear reactions. Because the energy of the particles was high, subcascade analysis was employed. The direct formation of clusters and the number of mobile defects were estimated using molecular dynamics (MD) and kinetic Monte-Carlo (kMC) methods in each subcascade. The third part considered damage structural evolutions estimated by reaction kinetic analysis. The fourth part involved the estimation of mechanical property change using three-dimensional discrete dislocation dynamics (DDD). Using the above four part code, stress-strain curves for high energy proton irradiated Ni were obtained.

Implementing a strand of a scalable fault-tolerant quantum computing fabric.

PubMed

Chow, Jerry M; Gambetta, Jay M; Magesan, Easwar; Abraham, David W; Cross, Andrew W; Johnson, B R; Masluk, Nicholas A; Ryan, Colm A; Smolin, John A; Srinivasan, Srikanth J; Steffen, M

2014-06-24

With favourable error thresholds and requiring only nearest-neighbour interactions on a lattice, the surface code is an error-correcting code that has garnered considerable attention. At the heart of this code is the ability to perform a low-weight parity measurement of local code qubits. Here we demonstrate high-fidelity parity detection of two code qubits via measurement of a third syndrome qubit. With high-fidelity gates, we generate entanglement distributed across three superconducting qubits in a lattice where each code qubit is coupled to two bus resonators. Via high-fidelity measurement of the syndrome qubit, we deterministically entangle the code qubits in either an even or odd parity Bell state, conditioned on the syndrome qubit state. Finally, to fully characterize this parity readout, we develop a measurement tomography protocol. The lattice presented naturally extends to larger networks of qubits, outlining a path towards fault-tolerant quantum computing.

Jet-A reaction mechanism study for combustion application

NASA Technical Reports Server (NTRS)

Lee, Chi-Ming; Kundu, Krishna; Acosta, Waldo

1991-01-01

Simplified chemical kinetic reaction mechanisms for the combustion of Jet A fuel was studied. Initially, 40 reacting species and 118 elementary chemical reactions were chosen based on a literature review. Through a sensitivity analysis with the use of LSENS General Kinetics and Sensitivity Analysis Code, 16 species and 21 elementary chemical reactions were determined from this study. This mechanism is first justified by comparison of calculated ignition delay time with the available shock tube data, then it is validated by comparison of calculated emissions from the plug flow reactor code with in-house flame tube data.

A Consistent System for Coding Laboratory Samples

NASA Astrophysics Data System (ADS)

Sih, John C.

1996-07-01

A formal laboratory coding system is presented to keep track of laboratory samples. Preliminary useful information regarding the sample (origin and history) is gained without consulting a research notebook. Since this system uses and retains the same research notebook page number for each new experiment (reaction), finding and distinguishing products (samples) of the same or different reactions becomes an easy task. Using this system multiple products generated from a single reaction can be identified and classified in a uniform fashion. Samples can be stored and filed according to stage and degree of purification, e.g. crude reaction mixtures, recrystallized samples, chromatographed or distilled products.

Equilibrium paths of an imperfect plate with respect to its aspect ratio

NASA Astrophysics Data System (ADS)

Psotny, Martin

2017-07-01

The stability analysis of a rectangular plate loaded in compression is presented, a specialized code based on FEM has been created. Special finite element with 48 degrees of freedom has been used for analysis. The nonlinear finite element method equations are derived from the variational principle of minimum of total potential energy. To trace the complete nonlinear equilibrium paths, the Newton-Raphson iteration algorithm is used, load versus displacement control was changed during the calculation process. The peculiarities of the effects of the initial imperfections on the load-deflection paths are investigated with respect to aspect ratio of the plate. Special attention is paid to the influence of imperfections on the post-critical buckling mode.

LANDSAT 4 band 6 data evaluation

NASA Technical Reports Server (NTRS)

1983-01-01

Computer modelled atmospheric transmittance and path radiance values were compared with empirical values derived from aircraft underflight data. Aircraft thermal infrared imagery and calibration data were available on two dates as were corresponding atmospheric radiosonde data. The radiosonde data were used as input to the LOWTRAN 5A code. The aircraft data were calibrated and utilized to generate analogous measurements. The results of the analysis indicate that there is a tendancy for the LOWTRAN model to underestimate atmospheric path radiance and overestimate atmospheric transmittance.

The Complexity of Parallel Algorithms,

DTIC Science & Technology

1985-11-01

programns have been written for se(luiential coiipn ters. Many p~eop~le want coimp ~ilers dihal. will c(nimpile t he, code for parallel machines, to avoid...between two vertices. We also rely on parallel algorithms for maintaining data structures and manipulating graphs. We do not go into the details of these...Jpatlis and maintain connected coimp ~onents. The routine is: - 35 .- ExtendPath(r, Q, V) begin P +-0; s 4- while there is a path in V - P from s to a vertex

Non-Normal Projectile Penetration in Soil and Rock: User’s Guide for Computer Code PENC02D.

DTIC Science & Technology

1982-09-01

the path traveled , with projec- tile orientation shown every FREQI projectile lengths. In this run, FREQI was input as 2.5. The horizontal lines...must be a closed surface in the direction of travel ; the bluntness of the nose requires a near 90-deg element for closure. Sheet 3 shows the beginning...plots for this problem. Sheets 1 and 2 automatically verify the projectile shape and path traveled . Sheets 3, 4, and 5 show the axial deceleration

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.

Foreign Object Damage Identification in Turbine Engines

NASA Technical Reports Server (NTRS)

Strack, William; Zhang, Desheng; Turso, James; Pavlik, William; Lopez, Isaac

2005-01-01

This report summarizes the collective work of a five-person team from different organizations examining the problem of detecting foreign object damage (FOD) events in turbofan engines from gas path thermodynamic and bearing accelerometer sensors, and determining the severity of damage to each component (diagnosis). Several detection and diagnostic approaches were investigated and a software tool (FODID) was developed to assist researchers detect/diagnose FOD events. These approaches include (1) fan efficiency deviation computed from upstream and downstream temperature/ pressure measurements, (2) gas path weighted least squares estimation of component health parameter deficiencies, (3) Kalman filter estimation of component health parameters, and (4) use of structural vibration signal processing to detect both large and small FOD events. The last three of these approaches require a significant amount of computation in conjunction with a physics-based analytic model of the underlying phenomenon the NPSS thermodynamic cycle code for approaches 1 to 3 and the DyRoBeS reduced-order rotor dynamics code for approach 4. A potential application of the FODID software tool, in addition to its detection/diagnosis role, is using its sensitivity results to help identify the best types of sensors and their optimum locations within the gas path, and similarly for bearing accelerometers.

Automatic Processing of Reactive Polymers

NASA Technical Reports Server (NTRS)

Roylance, D.

1985-01-01

A series of process modeling computer codes were examined. The codes use finite element techniques to determine the time-dependent process parameters operative during nonisothermal reactive flows such as can occur in reaction injection molding or composites fabrication. The use of these analytical codes to perform experimental control functions is examined; since the models can determine the state of all variables everywhere in the system, they can be used in a manner similar to currently available experimental probes. A small but well instrumented reaction vessel in which fiber-reinforced plaques are cured using computer control and data acquisition was used. The finite element codes were also extended to treat this particular process.

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.

Combustion chamber analysis code

NASA Technical Reports Server (NTRS)

Przekwas, A. J.; Lai, Y. G.; Krishnan, A.; Avva, R. K.; Giridharan, M. G.

1993-01-01

A three-dimensional, time dependent, Favre averaged, finite volume Navier-Stokes code has been developed to model compressible and incompressible flows (with and without chemical reactions) in liquid rocket engines. The code has a non-staggered formulation with generalized body-fitted-coordinates (BFC) capability. Higher order differencing methodologies such as MUSCL and Osher-Chakravarthy schemes are available. Turbulent flows can be modeled using any of the five turbulent models present in the code. A two-phase, two-liquid, Lagrangian spray model has been incorporated into the code. Chemical equilibrium and finite rate reaction models are available to model chemically reacting flows. The discrete ordinate method is used to model effects of thermal radiation. The code has been validated extensively against benchmark experimental data and has been applied to model flows in several propulsion system components of the SSME and the STME.

Fission Activities of the Nuclear Reactions Group in Uppsala

NASA Astrophysics Data System (ADS)

Al-Adili, A.; Alhassan, E.; Gustavsson, C.; Helgesson, P.; Jansson, K.; Koning, A.; Lantz, M.; Mattera, A.; Prokofiev, A. V.; Rakopoulos, V.; Sjöstrand, H.; Solders, A.; Tarrío, D.; Österlund, M.; Pomp, S.

This paper highlights some of the main activities related to fission of the nuclear reactions group at Uppsala University. The group is involved for instance in fission yield experiments at the IGISOL facility, cross-section measurements at the NFS facility, as well as fission dynamics studies at the IRMM JRC-EC. Moreover, work is ongoing on the Total Monte Carlo (TMC) methodology and on including the GEF fission code into the TALYS nuclear reaction code. Selected results from these projects are discussed.

Computer model of one-dimensional equilibrium controlled sorption processes

USGS Publications Warehouse

Grove, D.B.; Stollenwerk, K.G.

1984-01-01

A numerical solution to the one-dimensional solute-transport equation with equilibrium-controlled sorption and a first-order irreversible-rate reaction is presented. The computer code is written in FORTRAN language, with a variety of options for input and output for user ease. Sorption reactions include Langmuir, Freundlich, and ion-exchange, with or without equal valance. General equations describing transport and reaction processes are solved by finite-difference methods, with nonlinearities accounted for by iteration. Complete documentation of the code, with examples, is included. (USGS)

Wilson and Domainwall Kernels on Oakforest-PACS

NASA Astrophysics Data System (ADS)

Kanamori, Issaku; Matsufuru, Hideo

2018-03-01

We report the performance of Wilson and Domainwall Kernels on a new Intel Xeon Phi Knights Landing based machine named Oakforest-PACS, which is co-hosted by University of Tokyo and Tsukuba University and is currently fastest in Japan. This machine uses Intel Omni-Path for the internode network. We compare performance with several types of implementation including that makes use of the Grid library. The code is incorporated with the code set Bridge++.

Qualification of Simulation Software for Safety Assessment of Sodium Cooled Fast Reactors. Requirements and Recommendations

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

Brown, Nicholas R.; Pointer, William David; Sieger, Matt

2016-04-01

The goal of this review is to enable application of codes or software packages for safety assessment of advanced sodium-cooled fast reactor (SFR) designs. To address near-term programmatic needs, the authors have focused on two objectives. First, the authors have focused on identification of requirements for software QA that must be satisfied to enable the application of software to future safety analyses. Second, the authors have collected best practices applied by other code development teams to minimize cost and time of initial code qualification activities and to recommend a path to the stated goal.

NSEG: A segmented mission analysis program for low and high speed aircraft. Volume 2: Program users manual

NASA Technical Reports Server (NTRS)

Hague, D. S.; Rozendaal, H. L.

1977-01-01

A rapid mission analysis code based on the use of approximate flight path equations of motion is described. Equation form varies with the segment type, for example, accelerations, climbs, cruises, descents, and decelerations. Realistic and detailed vehicle characteristics are specified in tabular form. In addition to its mission performance calculation capabilities, the code also contains extensive flight envelop performance mapping capabilities. Approximate take off and landing analyses can be performed. At high speeds, centrifugal lift effects are taken into account. Extensive turbojet and ramjet engine scaling procedures are incorporated in the code.

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

SurfKin: an ab initio kinetic code for modeling surface reactions.

PubMed

Le, Thong Nguyen-Minh; Liu, Bin; Huynh, Lam K

2014-10-05

In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas-surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water-gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts. Copyright © 2014 Wiley Periodicals, Inc.

Subgroup A : nuclear model codes report to the Sixteenth Meeting of the WPEC

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

Talou, P.; Chadwick, M. B.; Dietrich, F. S.

2004-01-01

The Subgroup A activities focus on the development of nuclear reaction models and codes, used in evaluation work for nuclear reactions from the unresolved energy region up to the pion threshold production limit, and for target nuclides from the low teens and heavier. Much of the efforts are devoted by each participant to the continuing development of their own Institution codes. Progresses in this arena are reported in detail for each code in the present document. EMPIRE-II is of public access. The release of the TALYS code has been announced for the ND2004 Conference in Santa Fe, NM, October 2004.more » McGNASH is still under development and is not expected to be released in the very near future. In addition, Subgroup A members have demonstrated a growing interest in working on common modeling and codes capabilities, which would significantly reduce the amount of duplicate work, help manage efficiently the growing lines of existing codes, and render codes inter-comparison much easier. A recent and important activity of the Subgroup A has therefore been to develop the framework and the first bricks of the ModLib library, which is constituted of mostly independent pieces of codes written in Fortran 90 (and above) to be used in existing and future nuclear reaction codes. Significant progresses in the development of ModLib have been made during the past year. Several physics modules have been added to the library, and a few more have been planned in detail for the coming year.« less

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.

Adaptive decoding of convolutional codes

NASA Astrophysics Data System (ADS)

Hueske, K.; Geldmacher, J.; Götze, J.

2007-06-01

Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

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.

Characteristics code for shock initiation

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

Partom, Y.

1986-10-01

We developed SHIN, a characteristics code for shock initiation studies. We describe in detail the equations of state, reaction model, rate equations, and numerical difference equations that SHIN incorporates. SHIN uses the previously developed surface burning reaction model which better represents the shock initiation process in TATB, than do bulk reaction models. A large number of computed simulations prove the code is a reliable and efficient tool for shock initiation studies. A parametric study shows the effect on build-up and run distance to detonation of (1) type of boundary condtion, (2) burning velocity curve, (3) shock duration, (4) rise timemore » in ramp loading, (5) initial density (or porosity) of the explosive, (6) initial temperature, and (7) grain size. 29 refs., 65 figs.« less

Data-Driven Modeling of Solar Corona by a New 3d Path-Conservative Osher-Solomon MHD Odel

NASA Astrophysics Data System (ADS)

Feng, X. S.; Li, C.

2017-12-01

A second-order path-conservative scheme with Godunov-type finite volume method (FVM) has been implemented to advance the equations of single-fluid solar wind plasma magnetohydrodynamics (MHD) in time. This code operates on the six-component composite grid system in 3D spherical coordinates with hexahedral cells of quadrilateral frustum type. The generalized Osher-Solomon Riemann solver is employed based on a numerical integration of the path-dependentdissipation matrix. For simplicity, the straight line segment path is used and the path-integral is evaluated in a fully numerical way by high-order numerical Gauss-Legendre quadrature. Besides its closest similarity to Godunov, the resulting scheme retains the attractive features of the original solver: it is nonlinear, free of entropy-fix, differentiable and complete in that each characteristic field results in a different numerical viscosity, due to the full use of the MHD eigenstructure. By using a minmod limiter for spatial oscillation control, the pathconservative scheme is realized for the generalized Lagrange multiplier (GLM) and the extended generalized Lagrange multiplier (EGLM) formulation of solar wind MHD systems. This new model of second-order in space and time is written in FORTRAN language with Message Passing Interface (MPI) parallelization, and validated in modeling time-dependent large-scale structure of solar corona, driven continuously by the Global Oscillation Network Group (GONG) data. To demonstrate the suitability of our code for the simulation of solar wind, we present selected results from October 9th, 2009 to December 29th, 2009 , & Year 2008 to show its capability of producing structured solar wind in agreement with the observations.

Experimental Evaluation of Time Diversity Effect in Hybrid ARQ Considering Space and Path Diversity for Downlink OFDM-Based Broadband Radio Access

NASA Astrophysics Data System (ADS)

Miki, Nobuhiko; Atarashi, Hiroyuki; Higuchi, Kenichi; Sawahashi, Mamoru; Nakagawa, Masao

This paper presents experimental evaluations of the effect of time diversity obtained by hybrid automatic repeat request (HARQ) with soft combining in space and path diversity schemes on orthogonal frequency division multiplexing (OFDM)-based packet radio access in a downlink broadband multipath fading channel. The effect of HARQ is analyzed through laboratory experiments employing fading simulators and field experiments conducted in downtown Yokosuka near Tokyo. After confirming the validity of experimental results based on numerical analysis of the time diversity gain in HARQ, we show by the experimental results that, for a fixed modulation and channel coding scheme (MCS), time diversity obtained by HARQ is effective in reducing the required received signal-to-interference plus noise power ratio (SINR) according to an increase in the number of transmissions, K, up to 10, even when the diversity effects are obtained through two-branch antenna diversity reception and path diversity using a number of multipaths greater than 12 observed in a real fading channel. Meanwhile, in combined use with the adaptive modulation and channel coding (AMC) scheme associated with space and path diversity, we clarify that the gain obtained by time diversity is almost saturated at the maximum number of transmissions in HARQ, K' = 4 in Chase combining and K' = 2 in Incremental redundancy, since the improvement in the residual packet error rate (PER) obtained through time diversity becomes small owing to the low PER in the initial packet transmission arising from appropriately selecting the optimum MCS in AMC. However, the experimental results elucidate that the time diversity in HARQ with soft combining associated with antenna diversity reception is effective in improving the throughput even in a broadband multipath channel with sufficient path diversity.

Multicast Routing of Hierarchical Data

NASA Technical Reports Server (NTRS)

Shacham, Nachum

1992-01-01

The issue of multicast of broadband, real-time data in a heterogeneous environment, in which the data recipients differ in their reception abilities, is considered. Traditional multicast schemes, which are designed to deliver all the source data to all recipients, offer limited performance in such an environment, since they must either force the source to overcompress its signal or restrict the destination population to those who can receive the full signal. We present an approach for resolving this issue by combining hierarchical source coding techniques, which allow recipients to trade off reception bandwidth for signal quality, and sophisticated routing algorithms that deliver to each destination the maximum possible signal quality. The field of hierarchical coding is briefly surveyed and new multicast routing algorithms are presented. The algorithms are compared in terms of network utilization efficiency, lengths of paths, and the required mechanisms for forwarding packets on the resulting paths.

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.

On decoding of multi-level MPSK modulation codes

NASA Technical Reports Server (NTRS)

Lin, Shu; Gupta, Alok Kumar

1990-01-01

The decoding problem of multi-level block modulation codes is investigated. The hardware design of soft-decision Viterbi decoder for some short length 8-PSK block modulation codes is presented. An effective way to reduce the hardware complexity of the decoder by reducing the branch metric and path metric, using a non-uniform floating-point to integer mapping scheme, is proposed and discussed. The simulation results of the design are presented. The multi-stage decoding (MSD) of multi-level modulation codes is also investigated. The cases of soft-decision and hard-decision MSD are considered and their performance are evaluated for several codes of different lengths and different minimum squared Euclidean distances. It is shown that the soft-decision MSD reduces the decoding complexity drastically and it is suboptimum. The hard-decision MSD further simplifies the decoding while still maintaining a reasonable coding gain over the uncoded system, if the component codes are chosen properly. Finally, some basic 3-level 8-PSK modulation codes using BCH codes as component codes are constructed and their coding gains are found for hard decision multistage decoding.

A comparison of total reaction cross section models used in particle and heavy ion transport codes

NASA Astrophysics Data System (ADS)

Sihver, Lembit; Lantz, M.; Takechi, M.; Kohama, A.; Ferrari, A.; Cerutti, F.; Sato, T.

To be able to calculate the nucleon-nucleus and nucleus-nucleus total reaction cross sections with precision is very important for studies of basic nuclear properties, e.g. nuclear structure. This is also of importance for particle and heavy ion transport calculations because, in all particle and heavy ion transport codes, the probability function that a projectile particle will collide within a certain distance x in the matter depends on the total reaction cross sections. Furthermore, the total reaction cross sections will also scale the calculated partial fragmentation cross sections. It is therefore crucial that accurate total reaction cross section models are used in the transport calculations. In this paper, different models for calculating nucleon-nucleus and nucleus-nucleus total reaction cross sections are compared and discussed.

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

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.

The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis - modeled and analyzed using a Petri net-based approach.

PubMed

Formanowicz, Dorota; Radom, Marcin; Rybarczyk, Agnieszka; Formanowicz, Piotr

2018-03-01

The superoxide-driven Fenton reaction plays an important role in the transformation of poorly reactive radicals into highly reactive ones. These highly reactive species (ROS), especially hydroxyl radicals can lead to many disturbances contributing to the endothelial dysfunction being a starting point for atherosclerosis. Although, iron has been identified as a possible culprit influencing formation of ROS, its significance in this process is still debatable. To better understand this phenomenon, the influence of blockade of Fenton reaction in a proposed Petri net-based model of the selected aspects of the iron ROS-induced toxicity in atherosclerosis has been evaluated. As a result of the blockade of iron ions formation in the model, even up to 70% of the paths leading to the progression of atherosclerosis in this model has been blocked. In addition, after adding to the model, the blockade of the lipids peroxidation paths, progression of atherosclerotic plaque has been not observed. This allowed to conclude that the superoxide-driven Fenton reaction plays a significant role in the atherosclerosis. Copyright © 2018 Elsevier B.V. All rights reserved.

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

Mobility aid for the blind

NASA Technical Reports Server (NTRS)

1982-01-01

A project to develop an effective mobility aid for blind pedestrians which acquires consecutive images of the scenes before a moving pedestrian, which locates and identifies the pedestrian's path and potential obstacles in the path, which presents path and obstacle information to the pedestrian, and which operates in real-time is discussed. The mobility aid has three principal components: an image acquisition system, an image interpretation system, and an information presentation system. The image acquisition system consists of a miniature, solid-state TV camera which transforms the scene before the blind pedestrian into an image which can be received by the image interpretation system. The image interpretation system is implemented on a microprocessor which has been programmed to execute real-time feature extraction and scene analysis algorithms for locating and identifying the pedestrian's path and potential obstacles. Identity and location information is presented to the pedestrian by means of tactile coding and machine-generated speech.

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

Uchibori, Akihiro; Kurihara, Akikazu; Ohshima, Hiroyuki

A multiphysics analysis system for sodium-water reaction phenomena in a steam generator of sodium-cooled fast reactors was newly developed. The analysis system consists of the mechanistic numerical analysis codes, SERAPHIM, TACT, and RELAP5. The SERAPHIM code calculates the multicomponent multiphase flow and sodium-water chemical reaction caused by discharging of pressurized water vapor. Applicability of the SERAPHIM code was confirmed through the analyses of the experiment on water vapor discharging in liquid sodium. The TACT code was developed to calculate heat transfer from the reacting jet to the adjacent tube and to predict the tube failure occurrence. The numerical models integratedmore » into the TACT code were verified through some related experiments. The RELAP5 code evaluates thermal hydraulic behavior of water inside the tube. The original heat transfer correlations were corrected for the tube rapidly heated by the reacting jet. The developed system enables evaluation of the wastage environment and the possibility of the failure propagation.« less

Maximum-likelihood soft-decision decoding of block codes using the A* algorithm

NASA Technical Reports Server (NTRS)

Ekroot, L.; Dolinar, S.

1994-01-01

The A* algorithm finds the path in a finite depth binary tree that optimizes a function. Here, it is applied to maximum-likelihood soft-decision decoding of block codes where the function optimized over the codewords is the likelihood function of the received sequence given each codeword. The algorithm considers codewords one bit at a time, making use of the most reliable received symbols first and pursuing only the partially expanded codewords that might be maximally likely. A version of the A* algorithm for maximum-likelihood decoding of block codes has been implemented for block codes up to 64 bits in length. The efficiency of this algorithm makes simulations of codes up to length 64 feasible. This article details the implementation currently in use, compares the decoding complexity with that of exhaustive search and Viterbi decoding algorithms, and presents performance curves obtained with this implementation of the A* algorithm for several codes.

Vulnerabilities in Bytecode Removed by Analysis, Nuanced Confinement and Diversification (VIBRANCE)

DTIC Science & Technology

2015-06-01

VIBRANCE tool starts with a vulnerable Java application and automatically hardens it against SQL injection, OS command injection, file path traversal...7 2.2 Java Front End...7 2.2.2 Java Byte Code Parser

A reaction-diffusion-based coding rate control mechanism for camera sensor networks.

PubMed

Yamamoto, Hiroshi; Hyodo, Katsuya; Wakamiya, Naoki; Murata, Masayuki

2010-01-01

A wireless camera sensor network is useful for surveillance and monitoring for its visibility and easy deployment. However, it suffers from the limited capacity of wireless communication and a network is easily overflown with a considerable amount of video traffic. In this paper, we propose an autonomous video coding rate control mechanism where each camera sensor node can autonomously determine its coding rate in accordance with the location and velocity of target objects. For this purpose, we adopted a biological model, i.e., reaction-diffusion model, inspired by the similarity of biological spatial patterns and the spatial distribution of video coding rate. Through simulation and practical experiments, we verify the effectiveness of our proposal.

WESCOM. A Fortran Code for Evaluation of Nuclear Weapon Effects on Satellite Communications. Volume 2. Code Structure

DTIC Science & Technology

1981-01-31

quantities for h i ;.;h-:t It i 1 ndc hurst s 1BMI.I Determines t ime-independent fireball quantities for low-altitude bursts 10 Table 1...of reference Oval of Cassini (km) LAFBP - vortex longitudinal radius (km) LAFBP - vortex transverse radius (km) Power law exponent Inner scale...Maximum slant range of ionization from transmitter (km) Power law exponent Frequency (Hz) Striation velocity flag Propagation path index Radius

Kinetic modelling of the oxidation of large aliphatic hydrocarbons using an automatic mechanism generation.

PubMed

Muharam, Yuswan; Warnatz, Jürgen

2007-08-21

A mechanism generator code to automatically generate mechanisms for the oxidation of large hydrocarbons has been successfully modified and considerably expanded in this work. The modification was through (1) improvement of the existing rules such as cyclic-ether reactions and aldehyde reactions, (2) inclusion of some additional rules to the code, such as ketone reactions, hydroperoxy cyclic-ether formations and additional reactions of alkenes, (3) inclusion of small oxygenates, produced by the code but not included in the handwritten C(1)-C(4) sub-mechanism yet, to the handwritten C(1)-C(4) sub-mechanism. In order to evaluate mechanisms generated by the code, simulations of observed results in different experimental environments have been carried out. Experimentally derived and numerically predicted ignition delays of n-heptane-air and n-decane-air mixtures in high-pressure shock tubes in a wide range of temperatures, pressures and equivalence ratios agree very well. Concentration profiles of the main products and intermediates of n-heptane and n-decane oxidation in jet-stirred reactors at a wide range of temperatures and equivalence ratios are generally well reproduced. In addition, the ignition delay times of different normal alkanes was numerically studied.

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.

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

LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 3: Illustrative test problems

NASA Technical Reports Server (NTRS)

Bittker, David A.; Radhakrishnan, Krishnan

1994-01-01

LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 3 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 3 explains the kinetics and kinetics-plus-sensitivity analysis problems supplied with LSENS and presents sample results. These problems illustrate the various capabilities of, and reaction models that can be solved by, the code and may provide a convenient starting point for the user to construct the problem data file required to execute LSENS. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

PathVisio 3: an extendable pathway analysis toolbox.

PubMed

Kutmon, Martina; van Iersel, Martijn P; Bohler, Anwesha; Kelder, Thomas; Nunes, Nuno; Pico, Alexander R; Evelo, Chris T

2015-02-01

PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways. Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application. PathVisio can be downloaded from http://www.pathvisio.org and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license (http://www.apache.org/licenses/LICENSE-2.0). It is implemented in Java and thus runs on all major operating systems. The code repository is available at http://svn.bigcat.unimaas.nl/pathvisio. The support mailing list for users is available on https://groups.google.com/forum/#!forum/wikipathways-discuss and for developers on https://groups.google.com/forum/#!forum/wikipathways-devel.

Multiplexed Detection of Cytokines Based on Dual Bar-Code Strategy and Single-Molecule Counting.

PubMed

Li, Wei; Jiang, Wei; Dai, Shuang; Wang, Lei

2016-02-02

Cytokines play important roles in the immune system and have been regarded as biomarkers. While single cytokine is not specific and accurate enough to meet the strict diagnosis in practice, in this work, we constructed a multiplexed detection method for cytokines based on dual bar-code strategy and single-molecule counting. Taking interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α) as model analytes, first, the magnetic nanobead was functionalized with the second antibody and primary bar-code strands, forming a magnetic nanoprobe. Then, through the specific reaction of the second antibody and the antigen that fixed by the primary antibody, sandwich-type immunocomplex was formed on the substrate. Next, the primary bar-code strands as amplification units triggered multibranched hybridization chain reaction (mHCR), producing nicked double-stranded polymers with multiple branched arms, which were served as secondary bar-code strands. Finally, the secondary bar-code strands hybridized with the multimolecule labeled fluorescence probes, generating enhanced fluorescence signals. The numbers of fluorescence dots were counted one by one for quantification with epi-fluorescence microscope. By integrating the primary and secondary bar-code-based amplification strategy and the multimolecule labeled fluorescence probes, this method displayed an excellent sensitivity with the detection limits were both 5 fM. Unlike the typical bar-code assay that the bar-code strands should be released and identified on a microarray, this method is more direct. Moreover, because of the selective immune reaction and the dual bar-code mechanism, the resulting method could detect the two targets simultaneously. Multiple analysis in human serum was also performed, suggesting that our strategy was reliable and had a great potential application in early clinical diagnosis.

LSENS, a general chemical kinetics and sensitivity analysis code for homogeneous gas-phase reactions. 2: Code description and usage

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1994-01-01

LSENS, the Lewis General Chemical Kinetics Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 2 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 2 describes the code, how to modify it, and its usage, including preparation of the problem data file required to execute LSENS. Code usage is illustrated by several example problems, which further explain preparation of the problem data file and show how to obtain desired accuracy in the computed results. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions. Part 1 (NASA RP-1328) derives the governing equations describes the numerical solution procedures for the types of problems that can be solved by lSENS. Part 3 (NASA RP-1330) explains the kinetics and kinetics-plus-sensitivity-analysis problems supplied with LSENS and presents sample results.

EMPIRE: Nuclear Reaction Model Code System for Data Evaluation

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

Herman, M.; Capote, R.; Carlson, B.V.

EMPIRE is a modular system of nuclear reaction codes, comprising various nuclear models, and designed for calculations over a broad range of energies and incident particles. A projectile can be a neutron, proton, any ion (including heavy-ions) or a photon. The energy range extends from the beginning of the unresolved resonance region for neutron-induced reactions ({approx} keV) and goes up to several hundred MeV for heavy-ion induced reactions. The code accounts for the major nuclear reaction mechanisms, including direct, pre-equilibrium and compound nucleus ones. Direct reactions are described by a generalized optical model (ECIS03) or by the simplified coupled-channels approachmore » (CCFUS). The pre-equilibrium mechanism can be treated by a deformation dependent multi-step direct (ORION + TRISTAN) model, by a NVWY multi-step compound one or by either a pre-equilibrium exciton model with cluster emission (PCROSS) or by another with full angular momentum coupling (DEGAS). Finally, the compound nucleus decay is described by the full featured Hauser-Feshbach model with {gamma}-cascade and width-fluctuations. Advanced treatment of the fission channel takes into account transmission through a multiple-humped fission barrier with absorption in the wells. The fission probability is derived in the WKB approximation within the optical model of fission. Several options for nuclear level densities include the EMPIRE-specific approach, which accounts for the effects of the dynamic deformation of a fast rotating nucleus, the classical Gilbert-Cameron approach and pre-calculated tables obtained with a microscopic model based on HFB single-particle level schemes with collective enhancement. A comprehensive library of input parameters covers nuclear masses, optical model parameters, ground state deformations, discrete levels and decay schemes, level densities, fission barriers, moments of inertia and {gamma}-ray strength functions. The results can be converted into ENDF-6 formatted files using the accompanying code EMPEND and completed with neutron resonances extracted from the existing evaluations. The package contains the full EXFOR (CSISRS) library of experimental reaction data that are automatically retrieved during the calculations. Publication quality graphs can be obtained using the powerful and flexible plotting package ZVView. The graphic user interface, written in Tcl/Tk, provides for easy operation of the system. This paper describes the capabilities of the code, outlines physical models and indicates parameter libraries used by EMPIRE to predict reaction cross sections and spectra, mainly for nucleon-induced reactions. Selected applications of EMPIRE are discussed, the most important being an extensive use of the code in evaluations of neutron reactions for the new US library ENDF/B-VII.0. Future extensions of the system are outlined, including neutron resonance module as well as capabilities of generating covariances, using both KALMAN and Monte-Carlo methods, that are still being advanced and refined.« less

Clinical coding of prospectively identified paediatric adverse drug reactions--a retrospective review of patient records.

PubMed

Bellis, Jennifer R; Kirkham, Jamie J; Nunn, Anthony J; Pirmohamed, Munir

2014-12-17

National Health Service (NHS) hospitals in the UK use a system of coding for patient episodes. The coding system used is the International Classification of Disease (ICD-10). There are ICD-10 codes which may be associated with adverse drug reactions (ADRs) and there is a possibility of using these codes for ADR surveillance. This study aimed to determine whether ADRs prospectively identified in children admitted to a paediatric hospital were coded appropriately using ICD-10. The electronic admission abstract for each patient with at least one ADR was reviewed. A record was made of whether the ADR(s) had been coded using ICD-10. Of 241 ADRs, 76 (31.5%) were coded using at least one ICD-10 ADR code. Of the oncology ADRs, 70/115 (61%) were coded using an ICD-10 ADR code compared with 6/126 (4.8%) non-oncology ADRs (difference in proportions 56%, 95% CI 46.2% to 65.8%; p < 0.001). The majority of ADRs detected in a prospective study at a paediatric centre would not have been identified if the study had relied on ICD-10 codes as a single means of detection. Data derived from administrative healthcare databases are not reliable for identifying ADRs by themselves, but may complement other methods of detection.

PARAMESH: A Parallel Adaptive Mesh Refinement Community Toolkit

NASA Technical Reports Server (NTRS)

MacNeice, Peter; Olson, Kevin M.; Mobarry, Clark; deFainchtein, Rosalinda; Packer, Charles

1999-01-01

In this paper, we describe a community toolkit which is designed to provide parallel support with adaptive mesh capability for a large and important class of computational models, those using structured, logically cartesian meshes. The package of Fortran 90 subroutines, called PARAMESH, is designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement. Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package can provide them with an incremental evolutionary path for their code, converting it first to uniformly refined parallel code, and then later if they so desire, adding adaptivity.

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.

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.

Integrating Geochemical Reactions with a Particle-Tracking Approach to Simulate Nitrogen Transport and Transformation in Aquifers

NASA Astrophysics Data System (ADS)

Cui, Z.; Welty, C.; Maxwell, R. M.

2011-12-01

Lagrangian, particle-tracking models are commonly used to simulate solute advection and dispersion in aquifers. They are computationally efficient and suffer from much less numerical dispersion than grid-based techniques, especially in heterogeneous and advectively-dominated systems. Although particle-tracking models are capable of simulating geochemical reactions, these reactions are often simplified to first-order decay and/or linear, first-order kinetics. Nitrogen transport and transformation in aquifers involves both biodegradation and higher-order geochemical reactions. In order to take advantage of the particle-tracking approach, we have enhanced an existing particle-tracking code SLIM-FAST, to simulate nitrogen transport and transformation in aquifers. The approach we are taking is a hybrid one: the reactive multispecies transport process is operator split into two steps: (1) the physical movement of the particles including the attachment/detachment to solid surfaces, which is modeled by a Lagrangian random-walk algorithm; and (2) multispecies reactions including biodegradation are modeled by coupling multiple Monod equations with other geochemical reactions. The coupled reaction system is solved by an ordinary differential equation solver. In order to solve the coupled system of equations, after step 1, the particles are converted to grid-based concentrations based on the mass and position of the particles, and after step 2 the newly calculated concentration values are mapped back to particles. The enhanced particle-tracking code is capable of simulating subsurface nitrogen transport and transformation in a three-dimensional domain with variably saturated conditions. Potential application of the enhanced code is to simulate subsurface nitrogen loading to the Chesapeake Bay and its tributaries. Implementation details, verification results of the enhanced code with one-dimensional analytical solutions and other existing numerical models will be presented in addition to a discussion of implementation challenges.

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.

A generalized chemistry version of SPARK

NASA Technical Reports Server (NTRS)

Carpenter, Mark H.

1988-01-01

An extension of the reacting H2-air computer code SPARK is presented, which enables the code to be used on any reacting flow problem. Routines are developed calculating in a general fashion, the reaction rates, and chemical Jacobians of any reacting system. In addition, an equilibrium routine is added so that the code will have frozen, finite rate, and equilibrium capabilities. The reaction rate for the species is determined from the law of mass action using Arrhenius expressions for the rate constants. The Jacobian routines are determined by numerically or analytically differentiating the law of mass action for each species. The equilibrium routine is based on a Gibbs free energy minimization routine. The routines are written in FORTRAN 77, with special consideration given to vectorization. Run times for the generalized routines are generally 20 percent slower than reaction specific routines. The numerical efficiency of the generalized analytical Jacobian, however, is nearly 300 percent better than the reaction specific numerical Jacobian used in SPARK.

Visualized kinematics code for two-body nuclear reactions

NASA Astrophysics Data System (ADS)

Lee, E. J.; Chae, K. Y.

2016-05-01

The one or few nucleon transfer reaction has been a great tool for investigating the single-particle properties of a nucleus. Both stable and exotic beams are utilized to study transfer reactions in normal and inverse kinematics, respectively. Because many energy levels of the heavy recoil from the two-body nuclear reaction can be populated by using a single beam energy, identifying each populated state, which is not often trivial owing to high level-density of the nucleus, is essential. For identification of the energy levels, a visualized kinematics code called VISKIN has been developed by utilizing the Java programming language. The development procedure, usage, and application of the VISKIN is reported.

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).

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

New estimation method of neutron skyshine for a high-energy particle accelerator

NASA Astrophysics Data System (ADS)

Oh, Joo-Hee; Jung, Nam-Suk; Lee, Hee-Seock; Ko, Seung-Kook

2016-09-01

A skyshine is the dominant component of the prompt radiation at off-site. Several experimental studies have been done to estimate the neutron skyshine at a few accelerator facilities. In this work, the neutron transports from a source place to off-site location were simulated using the Monte Carlo codes, FLUKA and PHITS. The transport paths were classified as skyshine, direct (transport), groundshine and multiple-shine to understand the contribution of each path and to develop a general evaluation method. The effect of each path was estimated in the view of the dose at far locations. The neutron dose was calculated using the neutron energy spectra obtained from each detector placed up to a maximum of 1 km from the accelerator. The highest altitude of the sky region in this simulation was set as 2 km from the floor of the accelerator facility. The initial model of this study was the 10 GeV electron accelerator, PAL-XFEL. Different compositions and densities of air, soil and ordinary concrete were applied in this calculation, and their dependences were reviewed. The estimation method used in this study was compared with the well-known methods suggested by Rindi, Stevenson and Stepleton, and also with the simple code, SHINE3. The results obtained using this method agreed well with those using Rindi's formula.

CPMC-Lab: A MATLAB package for Constrained Path Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Nguyen, Huy; Shi, Hao; Xu, Jie; Zhang, Shiwei

2014-12-01

We describe CPMC-Lab, a MATLAB program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to ab initio calculations in molecules and solids. The present package implements the full ground-state constrained-path Monte Carlo (CPMC) method in MATLAB with a graphical interface, using the Hubbard model as an example. The package can perform calculations in finite supercells in any dimensions, under periodic or twist boundary conditions. Importance sampling and all other algorithmic details of a total energy calculation are included and illustrated. This open-source tool allows users to experiment with various model and run parameters and visualize the results. It provides a direct and interactive environment to learn the method and study the code with minimal overhead for setup. Furthermore, the package can be easily generalized for auxiliary-field quantum Monte Carlo (AFQMC) calculations in many other models for correlated electron systems, and can serve as a template for developing a production code for AFQMC total energy calculations in real materials. Several illustrative studies are carried out in one- and two-dimensional lattices on total energy, kinetic energy, potential energy, and charge- and spin-gaps.

Modulation of VLF signal amplitudes from 5 different transmitters during a C9.3-class solar flare as observed from a single receiving station in India: modeling with an ion chemistry model and LWPC

NASA Astrophysics Data System (ADS)

Palit, Sourav; Chakrabarti, Sandip Kumar; Pal, Sujay; Das, Bakul; Ray, Suman

2016-07-01

Very Low Frequency (VLF) signal at any location on Earth's surface is strongly dependent on the interference of various modes. The modulation effects on VLF signal due to any terrestrial or extra-terrestrial events vary widely from one propagation path to another depending on the interference patterns along these paths. The task of predicting or reproducing the modulation in the values of signal amplitudes or phase between any two transmitting and receiving stations is challenging. In this work we present results of modeling of the VLF signal amplitudes from five different transmitters as observed at a single receiving station in India during a C9.3 class solar flare. In this model we simulate the ionization rates at lower ionospheric heights from actual flare spectra with the GEANT4 Monte Carlo simulation code and find the equilibrium ion densities with a D-region ion-chemistry model. We find the signal amplitude variation along different propagation paths with the LWPC code. Such efforts are essential for an appropriate understanding of the VLF propagation in Earth's ionosphere waveguide and to achieve desired accuracy while using Earth's ionosphere as an efficient detector of such extra-terrestrial ionization events.

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

Donnelly, H.; Fullwood, R.; Glancy, J.

This is the second volume of a two volume report on the VISA method for evaluating safeguards at fixed-site facilities. This volume contains appendices that support the description of the VISA concept and the initial working version of the method, VISA-1, presented in Volume I. The information is separated into four appendices, each describing details of one of the four analysis modules that comprise the analysis sections of the method. The first appendix discusses Path Analysis methodology, applies it to a Model Fuel Facility, and describes the computer codes that are being used. Introductory material on Path Analysis given inmore » Chapter 3.2.1 and Chapter 4.2.1 of Volume I. The second appendix deals with Detection Analysis, specifically the schemes used in VISA-1 for classifying adversaries and the methods proposed for evaluating individual detection mechanisms in order to build the data base required for detection analysis. Examples of evaluations on identity-access systems, SNM portal monitors, and intrusion devices are provided. The third appendix describes the Containment Analysis overt-segment path ranking, the Monte Carlo engagement model, the network simulation code, the delay mechanism data base, and the results of a sensitivity analysis. The last appendix presents general equations used in Interruption Analysis for combining covert-overt segments and compares them with equations given in Volume I, Chapter 3.« less

Comparison of Calculations and Measurements of the Off-Axis Radiation Dose (SI) in Liquid Nitrogen as a Function of Radiation Length.

DTIC Science & Technology

1984-12-01

radiation lengths. The off-axis dose in Silicon was calculated using the electron/photon transport code CYLTRAN and measured using thermal luminescent...various path lengths out to 2 radiation lengths. The cff-axis dose in Silicon was calculated using the electron/photon transport code CYLTRAN and measured... using thermal luminescent dosimeters (TLD’s). Calculations were performed on a CDC-7600 computer at Los Alamos National Laboratory and measurements

Particle bed reactor modeling

NASA Technical Reports Server (NTRS)

Sapyta, Joe; Reid, Hank; Walton, Lew

1993-01-01

The topics are presented in viewgraph form and include the following: particle bed reactor (PBR) core cross section; PBR bleed cycle; fuel and moderator flow paths; PBR modeling requirements; characteristics of PBR and nuclear thermal propulsion (NTP) modeling; challenges for PBR and NTP modeling; thermal hydraulic computer codes; capabilities for PBR/reactor application; thermal/hydralic codes; limitations; physical correlations; comparison of predicted friction factor and experimental data; frit pressure drop testing; cold frit mask factor; decay heat flow rate; startup transient simulation; and philosophy of systems modeling.

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

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

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.

Ultraviolet Communication for Medical Applications

DTIC Science & Technology

2015-06-01

In the previous Phase I effort, Directed Energy Inc.’s (DEI) parent company Imaging Systems Technology (IST) demonstrated feasibility of several key...accurately model high path loss. Custom photon scatter code was rewritten for parallel execution on a graphics processing unit (GPU). The NVidia CUDA

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.

Communities on the Move: Pedestrian-Oriented Zoning as a Facilitator of Adult Active Travel to Work in the United States.

PubMed

Chriqui, Jamie F; Leider, Julien; Thrun, Emily; Nicholson, Lisa M; Slater, Sandy

2016-01-01

Communities across the United States have been reforming their zoning codes to create pedestrian-friendly neighborhoods with increased street connectivity, mixed use and higher density, open space, transportation infrastructure, and a traditional neighborhood structure. Zoning code reforms include new urbanist zoning such as the SmartCode, form-based codes, transects, transportation and pedestrian-oriented developments, and traditional neighborhood developments. To examine the relationship of zoning code reforms and more active living--oriented zoning provisions with adult active travel to work via walking, biking, or by using public transit. Zoning codes effective as of 2010 were compiled for 3,914 municipal-level jurisdictions located in 471 counties and 2 consolidated cities in 48 states and the District of Columbia, and that collectively covered 72.9% of the U.S. population. Zoning codes were evaluated for the presence of code reform zoning and nine pedestrian-oriented zoning provisions (1 = yes): sidewalks, crosswalks, bike-pedestrian connectivity, street connectivity, bike lanes, bike parking, bike-pedestrian trails/paths, mixed-use development, and other walkability/pedestrian orientation. A zoning scale reflected the number of provisions addressed (out of 10). Five continuous outcome measures were constructed using 2010-2014 American Community Survey municipal-level 5-year estimates to assess the percentage of workers: walking, biking, walking or biking, or taking public transit to work OR engaged in any active travel to work. Regression models controlled for municipal-level socioeconomic characteristics and a GIS-constructed walkability scale and were clustered on county with robust standard errors. Adjusted models indicated that several pedestrian-oriented zoning provisions were statistically associated (p < 0.05 or lower) with increased rates of walking, biking, or engaging in any active travel (walking, biking, or any active travel) to work: code reform zoning, bike parking (street furniture), bike lanes, bike-pedestrian trails/paths, other walkability, mixed-use zoning, and a higher score on the zoning scale. Public transit use was associated with code reform zoning and a number of zoning measures in Southern jurisdictions but not in non-Southern jurisdictions. As jurisdictions revisit their zoning and land use policies, they may want to evaluate the pedestrian-orientation of their zoning codes so that they can plan for pedestrian improvements that will help to encourage active travel to work.

LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 1: Theory and numerical solution procedures

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan

1994-01-01

LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 1 of a series of three reference publications that describe LENS, provide a detailed guide to its usage, and present many example problems. Part 1 derives the governing equations and describes the numerical solution procedures for the types of problems that can be solved. The accuracy and efficiency of LSENS are examined by means of various test problems, and comparisons with other methods and codes are presented. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

Comparison of modelled and empirical atmospheric propagation data

NASA Technical Reports Server (NTRS)

Schott, J. R.; Biegel, J. D.

1983-01-01

The radiometric integrity of TM thermal infrared channel data was evaluated and monitored to develop improved radiometric preprocessing calibration techniques for removal of atmospheric effects. Modelled atmospheric transmittance and path radiance were compared with empirical values derived from aircraft underflight data. Aircraft thermal infrared imagery and calibration data were available on two dates as were corresponding atmospheric radiosonde data. The radiosonde data were used as input to the LOWTRAN 5A code which was modified to output atmospheric path radiance in addition to transmittance. The aircraft data were calibrated and used to generate analogous measurements. These data indicate that there is a tendancy for the LOWTRAN model to underestimate atmospheric path radiance and transmittance as compared to empirical data. A plot of transmittance versus altitude for both LOWTRAN and empirical data is presented.

Fifty year canon of solar eclipses: 1986 - 2035

NASA Technical Reports Server (NTRS)

Espenak, Fred

1987-01-01

A complete catalog is presented, listing the general characteristics of every solar eclipse from 1901 through 2100. To complement this catalog, a detailed set of cylindrical projection world maps shows the umbral paths of every solar eclipse over the 200 year interval. Focusing in on the next 50 years, accurate geodetic path coordinates and local circumstances for the 71 central eclipses from 1987 through 2035 are tabulated. Finally, the geodetic paths of the umbral and penumbral shadows of all 109 solar eclipses in this period are plotted on orthographic projection maps of the Earth. Appendices are included which discuss eclipse geometry, eclipse frequency and occurrence, modern eclipse prediction and time determination. Finally, code for a simple Fortran program is given to predict the occurrence and characteristics of solar eclipses.

Atmospheric radiation model for water surfaces

NASA Technical Reports Server (NTRS)

Turner, R. E.; Gaskill, D. W.; Lierzer, J. R.

1982-01-01

An atmospheric correction model was extended to account for various atmospheric radiation components in remotely sensed data. Components such as the atmospheric path radiance which results from singly scattered sky radiation specularly reflected by the water surface are considered. A component which is referred to as the virtual Sun path radiance, i.e. the singly scattered path radiance which results from the solar radiation which is specularly reflected by the water surface is also considered. These atmospheric radiation components are coded into a computer program for the analysis of multispectral remote sensor data over the Great Lakes of the United States. The user must know certain parameters, such as the visibility or spectral optical thickness of the atmosphere and the geometry of the sensor with respect to the Sun and the target elements under investigation.

LSENS, A General Chemical Kinetics and Sensitivity Analysis Code for Homogeneous Gas-Phase Reactions. Part 2; Code Description and Usage

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1994-01-01

LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part II of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part II describes the code, how to modify it, and its usage, including preparation of the problem data file required to execute LSENS. Code usage is illustrated by several example problems, which further explain preparation of the problem data file and show how to obtain desired accuracy in the computed results. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions. Part I (NASA RP-1328) derives the governing equations and describes the numerical solution procedures for the types of problems that can be solved by LSENS. Part III (NASA RP-1330) explains the kinetics and kinetics-plus-sensitivity-analysis problems supplied with LSENS and presents sample results.

Finite element code development for modeling detonation of HMX composites

NASA Astrophysics Data System (ADS)

Duran, Adam V.; Sundararaghavan, Veera

2017-01-01

In this work, we present a hydrodynamics code for modeling shock and detonation waves in HMX. A stable efficient solution strategy based on a Taylor-Galerkin finite element (FE) discretization was developed to solve the reactive Euler equations. In our code, well calibrated equations of state for the solid unreacted material and gaseous reaction products have been implemented, along with a chemical reaction scheme and a mixing rule to define the properties of partially reacted states. A linear Gruneisen equation of state was employed for the unreacted HMX calibrated from experiments. The JWL form was used to model the EOS of gaseous reaction products. It is assumed that the unreacted explosive and reaction products are in both pressure and temperature equilibrium. The overall specific volume and internal energy was computed using the rule of mixtures. Arrhenius kinetics scheme was integrated to model the chemical reactions. A locally controlled dissipation was introduced that induces a non-oscillatory stabilized scheme for the shock front. The FE model was validated using analytical solutions for SOD shock and ZND strong detonation models. Benchmark problems are presented for geometries in which a single HMX crystal is subjected to a shock condition.

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.

LeRC-HT: NASA Lewis Research Center General Multiblock Navier-Stokes Heat Transfer Code Developed

NASA Technical Reports Server (NTRS)

Heidmann, James D.; Gaugler, Raymond E.

1999-01-01

For the last several years, LeRC-HT, a three-dimensional computational fluid dynamics (CFD) computer code for analyzing gas turbine flow and convective heat transfer, has been evolving at the NASA Lewis Research Center. The code is unique in its ability to give a highly detailed representation of the flow field very close to solid surfaces. This is necessary for an accurate representation of fluid heat transfer and viscous shear stresses. The code has been used extensively for both internal cooling passage flows and hot gas path flows--including detailed film cooling calculations, complex tip-clearance gap flows, and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool (at least 35 technical papers have been published relative to the code and its application), but it should be useful for detailed design analysis. We now plan to make this code available to selected users for further evaluation.

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.

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

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.

Efficient computation of kinship and identity coefficients on large pedigrees.

PubMed

Cheng, En; Elliott, Brendan; Ozsoyoglu, Z Meral

2009-06-01

With the rapidly expanding field of medical genetics and genetic counseling, genealogy information is becoming increasingly abundant. An important computation on pedigree data is the calculation of identity coefficients, which provide a complete description of the degree of relatedness of a pair of individuals. The areas of application of identity coefficients are numerous and diverse, from genetic counseling to disease tracking, and thus, the computation of identity coefficients merits special attention. However, the computation of identity coefficients is not done directly, but rather as the final step after computing a set of generalized kinship coefficients. In this paper, we first propose a novel Path-Counting Formula for calculating generalized kinship coefficients, which is motivated by Wright's path-counting method for computing inbreeding coefficient. We then present an efficient and scalable scheme for calculating generalized kinship coefficients on large pedigrees using NodeCodes, a special encoding scheme for expediting the evaluation of queries on pedigree graph structures. Furthermore, we propose an improved scheme using Family NodeCodes for the computation of generalized kinship coefficients, which is motivated by the significant improvement of using Family NodeCodes for inbreeding coefficient over the use of NodeCodes. We also perform experiments for evaluating the efficiency of our method, and compare it with the performance of the traditional recursive algorithm for three individuals. Experimental results demonstrate that the resulting scheme is more scalable and efficient than the traditional recursive methods for computing generalized kinship coefficients.

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.

Spallation reactions: A successful interplay between modeling and applications

NASA Astrophysics Data System (ADS)

David, J.-C.

2015-06-01

The spallation reactions are a type of nuclear reaction which occur in space by interaction of the cosmic rays with interstellar bodies. The first spallation reactions induced with an accelerator took place in 1947 at the Berkeley cyclotron (University of California) with 200MeV deuterons and 400MeV alpha beams. They highlighted the multiple emission of neutrons and charged particles and the production of a large number of residual nuclei far different from the target nuclei. In the same year, R. Serber described the reaction in two steps: a first and fast one with high-energy particle emission leading to an excited remnant nucleus, and a second one, much slower, the de-excitation of the remnant. In 2010 IAEA organized a workshop to present the results of the most widely used spallation codes within a benchmark of spallation models. If one of the goals was to understand the deficiencies, if any, in each code, one remarkable outcome points out the overall high-quality level of some models and so the great improvements achieved since Serber. Particle transport codes can then rely on such spallation models to treat the reactions between a light particle and an atomic nucleus with energies spanning from few tens of MeV up to some GeV. An overview of the spallation reactions modeling is presented in order to point out the incomparable contribution of models based on basic physics to numerous applications where such reactions occur. Validations or benchmarks, which are necessary steps in the improvement process, are also addressed, as well as the potential future domains of development. Spallation reactions modeling is a representative case of continuous studies aiming at understanding a reaction mechanism and which end up in a powerful tool.

Efficient Skeletonization of Volumetric Objects.

PubMed

Zhou, Yong; Toga, Arthur W

1999-07-01

Skeletonization promises to become a powerful tool for compact shape description, path planning, and other applications. However, current techniques can seldom efficiently process real, complicated 3D data sets, such as MRI and CT data of human organs. In this paper, we present an efficient voxel-coding based algorithm for Skeletonization of 3D voxelized objects. The skeletons are interpreted as connected centerlines. consisting of sequences of medial points of consecutive clusters. These centerlines are initially extracted as paths of voxels, followed by medial point replacement, refinement, smoothness, and connection operations. The voxel-coding techniques have been proposed for each of these operations in a uniform and systematic fashion. In addition to preserving basic connectivity and centeredness, the algorithm is characterized by straightforward computation, no sensitivity to object boundary complexity, explicit extraction of ready-to-parameterize and branch-controlled skeletons, and efficient object hole detection. These issues are rarely discussed in traditional methods. A range of 3D medical MRI and CT data sets were used for testing the algorithm, demonstrating its utility.

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.

KEWPIE2: A cascade code for the study of dynamical decay of excited nuclei

NASA Astrophysics Data System (ADS)

Lü, Hongliang; Marchix, Anthony; Abe, Yasuhisa; Boilley, David

2016-03-01

KEWPIE-a cascade code devoted to investigating the dynamical decay of excited nuclei, specially designed for treating very low probability events related to the synthesis of super-heavy nuclei formed in fusion-evaporation reactions-has been improved and rewritten in C++ programming language to become KEWPIE2. The current version of the code comprises various nuclear models concerning the light-particle emission, fission process and statistical properties of excited nuclei. General features of the code, such as the numerical scheme and the main physical ingredients, are described in detail. Some typical calculations having been performed in the present paper clearly show that theoretical predictions are generally in accordance with experimental data. Furthermore, since the values of some input parameters cannot be determined neither theoretically nor experimentally, a sensibility analysis is presented. To this end, we systematically investigate the effects of using different parameter values and reaction models on the final results. As expected, in the case of heavy nuclei, the fission process has the most crucial role to play in theoretical predictions. This work would be essential for numerical modeling of fusion-evaporation reactions.

Reduced Equations for Calculating the Combustion Rates of Jet-A and Methane Fuel

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2003-01-01

Simplified kinetic schemes for Jet-A and methane fuels were developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) that is being developed at Glenn. These kinetic schemes presented here result in a correlation that gives the chemical kinetic time as a function of initial overall cell fuel/air ratio, pressure, and temperature. The correlations would then be used with the turbulent mixing times to determine the limiting properties and progress of the reaction. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentration of carbon monoxide as a function of fuel air ratio, pressure, and temperature. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates and the values obtained from the equilibrium correlations were then used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide, and NOx were obtained for both Jet-A fuel and methane.

Performance analysis of visible light communication using the STBC-OFDM technique for intelligent transportation systems

NASA Astrophysics Data System (ADS)

Li, Changping; Yi, Ying; Lee, Kyujin; Lee, Kyesan

2014-08-01

Visible light communication (VLC) applied in an intelligent transportation system (ITS) has attracted growing attentions, but it also faces challenges, for example deep path loss and optical multi-path dispersion. In this work, we modelled an actual outdoor optical channel as a Rician channel and further proposed space-time block coding (STBC) orthogonal frequency-division multiplexing (OFDM) technology to reduce the influence of severe optical multi-path dispersion associated with such a mock channel for achieving the effective BER of 10-6 even at a low signal-to-noise ratio (SNR). In this case, the optical signals transmission distance can be extended as long as possible. Through the simulation results of STBC-OFDM and single-input-single-output (SISO) counterparts in bit error rate (BER) performance comparison, we can distinctly observe that the VLC-ITS system using STBC-OFDM technique can obtain a strongly improved BER performance due to multi-path dispersion alleviation.

Office of Biological and Physical Research: Overview Transitioning to the Vision for Space Exploration

NASA Technical Reports Server (NTRS)

Crouch, Roger

2004-01-01

Viewgraphs on NASA's transition to its vision for space exploration is presented. The topics include: 1) Strategic Directives Guiding the Human Support Technology Program; 2) Progressive Capabilities; 3) A Journey to Inspire, Innovate, and Discover; 4) Risk Mitigation Status Technology Readiness Level (TRL) and Countermeasures Readiness Level (CRL); 5) Biological And Physical Research Enterprise Aligning With The Vision For U.S. Space Exploration; 6) Critical Path Roadmap Reference Missions; 7) Rating Risks; 8) Current Critical Path Roadmap (Draft) Rating Risks: Human Health; 9) Current Critical Path Roadmap (Draft) Rating Risks: System Performance/Efficiency; 10) Biological And Physical Research Enterprise Efforts to Align With Vision For U.S. Space Exploration; 11) Aligning with the Vision: Exploration Research Areas of Emphasis; 12) Code U Efforts To Align With The Vision For U.S. Space Exploration; 13) Types of Critical Path Roadmap Risks; and 14) ISS Human Support Systems Research, Development, and Demonstration. A summary discussing the vision for U.S. space exploration is also provided.

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.

Systematic network coding for two-hop lossy transmissions

NASA Astrophysics Data System (ADS)

Li, Ye; Blostein, Steven; Chan, Wai-Yip

2015-12-01

In this paper, we consider network transmissions over a single or multiple parallel two-hop lossy paths. These scenarios occur in applications such as sensor networks or WiFi offloading. Random linear network coding (RLNC), where previously received packets are re-encoded at intermediate nodes and forwarded, is known to be a capacity-achieving approach for these networks. However, a major drawback of RLNC is its high encoding and decoding complexity. In this work, a systematic network coding method is proposed. We show through both analysis and simulation that the proposed method achieves higher end-to-end rate as well as lower computational cost than RLNC for finite field sizes and finite-sized packet transmissions.

SIERRA Code Coupling Module: Arpeggio User Manual Version 4.44

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

Subia, Samuel R.; Overfelt, James R.; Baur, David G.

2017-04-01

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested inmore » coupled applications via simple examples of its usage.« less

Error control techniques for satellite and space communications

NASA Technical Reports Server (NTRS)

Costello, D. J., Jr.

1986-01-01

High rate concatenated coding systems with trellis inner codes and Reed-Solomon (RS) outer codes for application in satellite communication systems are considered. Two types of inner codes are studied: high rate punctured binary convolutional codes which result in overall effective information rates between 1/2 and 1 bit per channel use; and bandwidth efficient signal space trellis codes which can achieve overall effective information rates greater than 1 bit per channel use. Channel capacity calculations with and without side information performed for the concatenated coding system. Concatenated coding schemes are investigated. In Scheme 1, the inner code is decoded with the Viterbi algorithm and the outer RS code performs error-correction only (decoding without side information). In scheme 2, the inner code is decoded with a modified Viterbi algorithm which produces reliability information along with the decoded output. In this algorithm, path metrics are used to estimate the entire information sequence, while branch metrics are used to provide the reliability information on the decoded sequence. This information is used to erase unreliable bits in the decoded output. An errors-and-erasures RS decoder is then used for the outer code. These two schemes are proposed for use on NASA satellite channels. Results indicate that high system reliability can be achieved with little or no bandwidth expansion.

Context-sensitive trace inlining for Java.

PubMed

Häubl, Christian; Wimmer, Christian; Mössenböck, Hanspeter

2013-12-01

Method inlining is one of the most important optimizations in method-based just-in-time (JIT) compilers. It widens the compilation scope and therefore allows optimizing multiple methods as a whole, which increases the performance. However, if method inlining is used too frequently, the compilation time increases and too much machine code is generated. This has negative effects on the performance. Trace-based JIT compilers only compile frequently executed paths, so-called traces, instead of whole methods. This may result in faster compilation, less generated machine code, and better optimized machine code. In the previous work, we implemented a trace recording infrastructure and a trace-based compiler for [Formula: see text], by modifying the Java HotSpot VM. Based on this work, we evaluate the effect of trace inlining on the performance and the amount of generated machine code. Trace inlining has several major advantages when compared to method inlining. First, trace inlining is more selective than method inlining, because only frequently executed paths are inlined. Second, the recorded traces may capture information about virtual calls, which simplify inlining. A third advantage is that trace information is context sensitive so that different method parts can be inlined depending on the specific call site. These advantages allow more aggressive inlining while the amount of generated machine code is still reasonable. We evaluate several inlining heuristics on the benchmark suites DaCapo 9.12 Bach, SPECjbb2005, and SPECjvm2008 and show that our trace-based compiler achieves an up to 51% higher peak performance than the method-based Java HotSpot client compiler. Furthermore, we show that the large compilation scope of our trace-based compiler has a positive effect on other compiler optimizations such as constant folding or null check elimination.

Transfer reaction code with nonlocal interactions

DOE PAGES

Titus, L. J.; Ross, A.; Nunes, F. M.

2016-07-14

We present a suite of codes (NLAT for nonlocal adiabatic transfer) to calculate the transfer cross section for single-nucleon transfer reactions, (d,N)(d,N) or (N,d)(N,d), including nonlocal nucleon–target interactions, within the adiabatic distorted wave approximation. For this purpose, we implement an iterative method for solving the second order nonlocal differential equation, for both scattering and bound states. The final observables that can be obtained with NLAT are differential angular distributions for the cross sections of A(d,N)BA(d,N)B or B(N,d)AB(N,d)A. Details on the implementation of the TT-matrix to obtain the final cross sections within the adiabatic distorted wave approximation method are also provided.more » This code is suitable to be applied for deuteron induced reactions in the range of View the MathML sourceEd=10–70MeV, and provides cross sections with 4% accuracy.« less

Exploring Ultrahigh-Intensity Laser-Plasma Interaction Physics with QED Particle-in-Cell Simulations

NASA Astrophysics Data System (ADS)

Luedtke, S. V.; Yin, L.; Labun, L. A.; Albright, B. J.; Stark, D. J.; Bird, R. F.; Nystrom, W. D.; Hegelich, B. M.

2017-10-01

Next generation high-intensity lasers are reaching intensity regimes where new physics-quantum electrodynamics (QED) corrections to otherwise classical plasma dynamics-becomes important. Modeling laser-plasma interactions in these extreme settings presents a challenge to traditional particle-in-cell (PIC) codes, which either do not have radiation reaction or include only classical radiation reaction. We discuss a semi-classical approach to adding quantum radiation reaction and photon production to the PIC code VPIC. We explore these intensity regimes with VPIC, compare with results from the PIC code PSC, and report on ongoing work to expand the capability of VPIC in these regimes. This work was supported by the U.S. DOE, Los Alamos National Laboratory Science program, LDRD program, NNSA (DE-NA0002008), and AFOSR (FA9550-14-1-0045). HPC resources provided by TACC, XSEDE, and LANL Institutional Computing.

Data acquisition and path selection decision making for an autonomous roving vehicle

NASA Technical Reports Server (NTRS)

Frederick, D. K.; Shen, C. N.; Yerazunis, S. W.

1976-01-01

Problems related to the guidance of an autonomous rover for unmanned planetary exploration were investigated. Topics included in these studies were: simulation on an interactive graphics computer system of the Rapid Estimation Technique for detection of discrete obstacles; incorporation of a simultaneous Bayesian estimate of states and inputs in the Rapid Estimation Scheme; development of methods for estimating actual laser rangefinder errors and their application to date provided by Jet Propulsion Laboratory; and modification of a path selection system simulation computer code for evaluation of a hazard detection system based on laser rangefinder data.

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.

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.

Anaerobic biodegradation of aromatic compounds.

PubMed

Jothimani, P; Kalaichelvan, G; Bhaskaran, A; Selvaseelan, D Augustine; Ramasamy, K

2003-09-01

Many aromatic compounds and their monomers are existing in nature. Besides they are introduced into the environment by human activity. The conversion of these aromatic compounds is mainly an aerobic process because of the involvement of molecular oxygen in ring fission and as an electron acceptor. Recent literatures indicated that ring fission of monomers and obligomers mainly occurs in anaerobic environments through anaerobic respiration with nitrate, sulphate, carbon dioxide or carbonate as electron acceptors. These anaerobic processes will help to work out the better situation for bioremediation of contaminated environments. While there are plenty of efforts to reduce the release of these chemicals to the environment, already contaminated sites need to be remediated not only to restore the sites but to prevent the leachates spreading to nearby environment. Basically microorganisms are better candidates for breakdown of these compounds because of their wider catalytic mechanisms and the ability to act even in the absence of oxygen. These microbes can be grouped based on their energy mechanisms. Normally, the aerobic counterparts employ the enzymes like mono-and-dioxygenases. The end product is basically catechol, which further may be metabolised to CO2 by means of quinones reductases cycles. In the absense of reductases compounds, the reduced catechols tend to become oxidised to form many quinone compounds. The quinone products are more recalcitrant and lead to other aesthetic problems like colour in water, unpleasant odour, etc. On the contrary, in the reducing environment this process is prevented and in a cascade of pathways, the cleaved products are converted to acetyl co-A to be integrated into other central metabolite paths. The central metabolite of anaerobic degradation is invariably co-A thio-esters of benzoic acid or hydroxy benzoic acid. The benzene ring undergoes various substitution and addition reactions to form chloro-, nitro-, methyl- compounds. For complete degradation the side chains must be removed first and then the benzene ring is activated by carboxylation or hydroxylation or co-A thioester formation. In the next step the activated ring is converted to a form that can be collected in the central pool of metabolism. The third step is the channeling reaction in which the products of the catalysis are directed into central metabolite pool. The enzymes involved in these mechanisms are mostly benzyl co-A ligase, benzyl alcohol dehydrogenase. Other enzymes involved in this path are yet to be purified though many of the reactions products that have been theoretically postulated have been identified. This is mainly due to the instability of intermediate compounds as well as the association of the enzyme substrate is femoral and experimental conditions need to be sophisticated further for isolation of these enzymes. The first structural genes of benzoate and hydroxy benzoate ligases were isolated from Rhodopseudomonas palustris. This gene cluster of 30 kb size found in Rhodopseudomonas palustris coded for the Bad A protein. Similarly, some of the bph A,B,C and D cluster of genes coding for the degradation of pentachlorobenzenes were located in Pseudomonas pseudoalgaligenesKF 707.

Color coding of control room displays: the psychocartography of visual layering effects.

PubMed

Van Laar, Darren; Deshe, Ofer

2007-06-01

To evaluate which of three color coding methods (monochrome, maximally discriminable, and visual layering) used to code four types of control room display format (bars, tables, trend, mimic) was superior in two classes of task (search, compare). It has recently been shown that color coding of visual layers, as used in cartography, may be used to color code any type of information display, but this has yet to be fully evaluated. Twenty-four people took part in a 2 (task) x 3 (coding method) x 4 (format) wholly repeated measures design. The dependent variables assessed were target location reaction time, error rates, workload, and subjective feedback. Overall, the visual layers coding method produced significantly faster reaction times than did the maximally discriminable and the monochrome methods for both the search and compare tasks. No significant difference in errors was observed between conditions for either task type. Significantly less perceived workload was experienced with the visual layers coding method, which was also rated more highly than the other coding methods on a 14-item visual display quality questionnaire. The visual layers coding method is superior to other color coding methods for control room displays when the method supports the user's task. The visual layers color coding method has wide applicability to the design of all complex information displays utilizing color coding, from the most maplike (e.g., air traffic control) to the most abstract (e.g., abstracted ecological display).

CSEWG

Science.gov Websites

Nuclear Data Evaluation Co-operation (WPEC) Nuclear Reaction Data Centers, NRDC (IAEA Vienna) EMPIRE , Nuclear Reaction Model Code Atlas of Neutron Resonances The Cross Section Evaluation Working Group (CSEWG

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.

Step-by-Step Simulation of Radiation Chemistry Using Green Functions for Diffusion-Influenced Reactions

NASA Technical Reports Server (NTRS)

Plante, Ianik; Cucinotta, Francis A.

2011-01-01

Radiolytic species are formed approximately 1 ps after the passage of ionizing radiation through matter. After their formation, they diffuse and chemically react with other radiolytic species and neighboring biological molecules, leading to various oxidative damage. Therefore, the simulation of radiation chemistry is of considerable importance to understand how radiolytic species damage biological molecules [1]. The step-by-step simulation of chemical reactions is difficult, because the radiolytic species are distributed non-homogeneously in the medium. Consequently, computational approaches based on Green functions for diffusion-influenced reactions should be used [2]. Recently, Green functions for more complex type of reactions have been published [3-4]. We have developed exact random variate generators of these Green functions [5], which will allow us to use them in radiation chemistry codes. Moreover, simulating chemistry using the Green functions is which is computationally very demanding, because the probabilities of reactions between each pair of particles should be evaluated at each timestep [2]. This kind of problem is well adapted for General Purpose Graphic Processing Units (GPGPU), which can handle a large number of similar calculations simultaneously. These new developments will allow us to include more complex reactions in chemistry codes, and to improve the calculation time. This code should be of importance to link radiation track structure simulations and DNA damage models.

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

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.

A systematic review of validated methods for identifying hypersensitivity reactions other than anaphylaxis (fever, rash, and lymphadenopathy), using administrative and claims data.

PubMed

Schneider, Gary; Kachroo, Sumesh; Jones, Natalie; Crean, Sheila; Rotella, Philip; Avetisyan, Ruzan; Reynolds, Matthew W

2012-01-01

The Food and Drug Administration's Mini-Sentinel pilot program aims to conduct active surveillance to refine safety signals that emerge for marketed medical products. A key facet of this surveillance is to develop and understand the validity of algorithms for identifying health outcomes of interest from administrative and claims data. This article summarizes the process and findings of the algorithm review of hypersensitivity reactions. PubMed and Iowa Drug Information Service searches were conducted to identify citations applicable to the hypersensitivity reactions of health outcomes of interest. Level 1 abstract reviews and Level 2 full-text reviews were conducted to find articles using administrative and claims data to identify hypersensitivity reactions and including validation estimates of the coding algorithms. We identified five studies that provided validated hypersensitivity-reaction algorithms. Algorithm positive predictive values (PPVs) for various definitions of hypersensitivity reactions ranged from 3% to 95%. PPVs were high (i.e. 90%-95%) when both exposures and diagnoses were very specific. PPV generally decreased when the definition of hypersensitivity was expanded, except in one study that used data mining methodology for algorithm development. The ability of coding algorithms to identify hypersensitivity reactions varied, with decreasing performance occurring with expanded outcome definitions. This examination of hypersensitivity-reaction coding algorithms provides an example of surveillance bias resulting from outcome definitions that include mild cases. Data mining may provide tools for algorithm development for hypersensitivity and other health outcomes. Research needs to be conducted on designing validation studies to test hypersensitivity-reaction algorithms and estimating their predictive power, sensitivity, and specificity. Copyright © 2012 John Wiley & Sons, Ltd.

Evaluating and minimizing noise impact due to aircraft flyover

NASA Technical Reports Server (NTRS)

Jacobson, I. D.; Cook, G.

1979-01-01

Existing techniques were used to assess the noise impact on a community due to aircraft operation and to optimize the flight paths of an approaching aircraft with respect to the annoyance produced. Major achievements are: (1) the development of a population model suitable for determining the noise impact, (2) generation of a numerical computer code which uses this population model along with the steepest descent algorithm to optimize approach/landing trajectories, (3) implementation of this optimization code in several fictitious cases as well as for the community surrounding Patrick Henry International Airport, Virginia.

DD-αAMG on QPACE 3

NASA Astrophysics Data System (ADS)

Georg, Peter; Richtmann, Daniel; Wettig, Tilo

2018-03-01

We describe our experience porting the Regensburg implementation of the DD-αAMG solver from QPACE 2 to QPACE 3. We first review how the code was ported from the first generation Intel Xeon Phi processor (Knights Corner) to its successor (Knights Landing). We then describe the modifications in the communication library necessitated by the switch from InfiniBand to Omni-Path. Finally, we present the performance of the code on a single processor as well as the scaling on many nodes, where in both cases the speedup factor is close to the theoretical expectations.

Moments of inclination error distribution computer program

NASA Technical Reports Server (NTRS)

Myler, T. R.

1981-01-01

A FORTRAN coded computer program is described which calculates orbital inclination error statistics using a closed-form solution. This solution uses a data base of trajectory errors from actual flights to predict the orbital inclination error statistics. The Scott flight history data base consists of orbit insertion errors in the trajectory parameters - altitude, velocity, flight path angle, flight azimuth, latitude and longitude. The methods used to generate the error statistics are of general interest since they have other applications. Program theory, user instructions, output definitions, subroutine descriptions and detailed FORTRAN coding information are included.

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.

Glenn-HT: The NASA Glenn Research Center General Multi-Block Navier-Stokes Heat Transfer Code

NASA Technical Reports Server (NTRS)

Gaugler, Raymond E.; Lee, Chi-Miag (Technical Monitor)

2001-01-01

For the last several years, Glenn-HT, a three-dimensional (3D) Computational Fluid Dynamics (CFD) computer code for the analysis of gas turbine flow and convective heat transfer has been evolving at the NASA Glenn Research Center. The code is unique in the ability to give a highly detailed representation of the flow field very close to solid surfaces in order to get accurate representation of fluid heat transfer and viscous shear stresses. The code has been validated and used extensively for both internal cooling passage flow and for hot gas path flows, including detailed film cooling calculations and complex tip clearance gap flow and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool, but it can be useful for detailed design analysis. In this paper, the code is described and examples of its validation and use for complex flow calculations are presented, emphasizing the applicability to turbomachinery for space launch vehicle propulsion systems.

Glenn-HT: The NASA Glenn Research Center General Multi-Block Navier-Stokes Heat Transfer Code

NASA Technical Reports Server (NTRS)

Gaugfer, Raymond E.

2002-01-01

For the last several years, Glenn-HT, a three-dimensional (3D) Computational Fluid Dynamics (CFD) computer code for the analysis of gas turbine flow and convective heat transfer has been evolving at the NASA Glenn Research Center. The code is unique in the ability to give a highly detailed representation of the flow field very close to solid surfaces in order to get accurate representation of fluid heat transfer and viscous shear stresses. The code has been validated and used extensively for both internal cooling passage flow and for hot gas path flows, including detailed film cooling calculations and complex tip clearance gap flow and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool, but it can be useful for detailed design analysis. In this presentation, the code is described and examples of its validation and use for complex flow calculations are presented, emphasizing the applicability to turbomachinery.

Glenn-HT: The NASA Glenn Research Center General Multi-Block Navier Stokes Heat Transfer Code

NASA Technical Reports Server (NTRS)

Gaugler, Raymond E.

2002-01-01

For the last several years, Glenn-HT, a three-dimensional (3D) Computational Fluid Dynamics (CFD) computer code for the analysis of gas turbine flow and convective heat transfer has been evolving at the NASA Glenn Research Center. The code is unique in the ability to give a highly detailed representation of the flow field very close to solid surfaces in order to get accurate representation of fluid beat transfer and viscous shear stresses. The code has been validated and used extensively for both internal cooling passage flow and for hot gas path flows, including detailed film cooling calculations and complex tip clearance gap flow and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool, but it can be useful for detailed design analysis. In this presentation, the code is described and examples of its validation and use for complex flow calculations are presented, emphasizing the applicability to turbomachinery.

Mediators of methylphenidate effects on math performance in children with attention-deficit hyperactivity disorder.

PubMed

Froehlich, Tanya E; Antonini, Tanya N; Brinkman, William B; Langberg, Joshua M; Simon, John O; Adams, Ryan; Fredstrom, Bridget; Narad, Megan E; Kingery, Kathleen M; Altaye, Mekibib; Matheson, Heather; Tamm, Leanne; Epstein, Jeffery N

2014-01-01

Stimulant medications, such as methylphenidate (MPH), improve the academic performance of children with attention-deficit hyperactivity disorder (ADHD). However, the mechanism by which MPH exerts an effect on academic performance is unclear. We examined MPH effects on math performance and investigated possible mediation of MPH effects by changes in time on-task, inhibitory control, selective attention, and reaction time variability. Children with ADHD aged 7 to 11 years (N = 93) completed a timed math worksheet (with problems tailored to each individual's level of proficiency) and 2 neuropsychological tasks (Go/No-Go and Child Attention Network Test) at baseline, then participated in a 4-week, randomized, controlled, titration trial of MPH. Children were then randomly assigned to their optimal MPH dose or placebo for 1 week (administered double-blind) and repeated the math and neuropsychological tasks (posttest). Baseline and posttest videorecordings of children performing the math task were coded to assess time on-task. Children taking MPH completed 23 more math problems at posttest compared to baseline, whereas the placebo group completed 24 fewer problems on posttest versus baseline, but the effects on math accuracy (percent correct) did not differ. Path analyses revealed that only change in time on-task was a significant mediator of MPH's improvements in math productivity. MPH-derived math productivity improvements may be explained in part by increased time spent on-task, rather than improvements in neurocognitive parameters, such as inhibitory control, selective attention, or reaction time variability.

Versatile fusion source integrator AFSI for fast ion and neutron studies in fusion devices

NASA Astrophysics Data System (ADS)

Sirén, Paula; Varje, Jari; Äkäslompolo, Simppa; Asunta, Otto; Giroud, Carine; Kurki-Suonio, Taina; Weisen, Henri; JET Contributors, The

2018-01-01

ASCOT Fusion Source Integrator AFSI, an efficient tool for calculating fusion reaction rates and characterizing the fusion products, based on arbitrary reactant distributions, has been developed and is reported in this paper. Calculation of reactor-relevant D-D, D-T and D-3He fusion reactions has been implemented based on the Bosch-Hale fusion cross sections. The reactions can be calculated between arbitrary particle populations, including Maxwellian thermal particles and minority energetic particles. Reaction rate profiles, energy spectra and full 4D phase space distributions can be calculated for the non-isotropic reaction products. The code is especially suitable for integrated modelling in self-consistent plasma physics simulations as well as in the Serpent neutronics calculation chain. Validation of the model has been performed for neutron measurements at the JET tokamak and the code has been applied to predictive simulations in ITER.

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.

Differential absorption lidar measurements of atmospheric water vapor using a pseudonoise code modulated AlGaAs laser. Thesis

NASA Technical Reports Server (NTRS)

Rall, Jonathan A. R.

1994-01-01

Lidar measurements using pseudonoise code modulated AlGaAs lasers are reported. Horizontal path lidar measurements were made at night to terrestrial targets at ranges of 5 and 13 km with 35 mW of average power and integration times of one second. Cloud and aerosol lidar measurements were made to thin cirrus clouds at 13 km altitude with Rayleigh (molecular) backscatter evident up to 9 km. Average transmitter power was 35 mW and measurement integration time was 20 minutes. An AlGaAs laser was used to characterize spectral properties of water vapor absorption lines at 811.617, 816.024, and 815.769 nm in a multipass absorption cell using derivative spectroscopy techniques. Frequency locking of an AlGaAs laser to a water vapor absorption line was achieved with a laser center frequency stability measured to better than one-fifth of the water vapor Doppler linewidth over several minutes. Differential absorption lidar measurements of atmospheric water vapor were made in both integrated path and range-resolved modes using an externally modulated AlGaAs laser. Mean water vapor number density was estimated from both integrated path and range-resolved DIAL measurements and agreed with measured humidity values to within 6.5 percent and 20 percent, respectively. Error sources were identified and their effects on estimates of water vapor number density calculated.

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.

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.

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.

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.

A MATLAB-based finite-element visualization of quantum reactive scattering. I. Collinear atom-diatom reactions

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

Warehime, Mick; Alexander, Millard H., E-mail: mha@umd.edu

We restate the application of the finite element method to collinear triatomic reactive scattering dynamics with a novel treatment of the scattering boundary conditions. The method provides directly the reactive scattering wave function and, subsequently, the probability current density field. Visualizing these quantities provides additional insight into the quantum dynamics of simple chemical reactions beyond simplistic one-dimensional models. Application is made here to a symmetric reaction (H+H{sub 2}), a heavy-light-light reaction (F+H{sub 2}), and a heavy-light-heavy reaction (F+HCl). To accompany this article, we have written a MATLAB code which is fast, simple enough to be accessible to a wide audience,more » as well as generally applicable to any problem that can be mapped onto a collinear atom-diatom reaction. The code and user's manual are available for download from http://www2.chem.umd.edu/groups/alexander/FEM.« less

Four new topological indices based on the molecular path code.

PubMed

Balaban, Alexandru T; Beteringhe, Adrian; Constantinescu, Titus; Filip, Petru A; Ivanciuc, Ovidiu

2007-01-01

The sequence of all paths pi of lengths i = 1 to the maximum possible length in a hydrogen-depleted molecular graph (which sequence is also called the molecular path code) contains significant information on the molecular topology, and as such it is a reasonable choice to be selected as the basis of topological indices (TIs). Four new (or five partly new) TIs with progressively improved performance (judged by correctly reflecting branching, centricity, and cyclicity of graphs, ordering of alkanes, and low degeneracy) have been explored. (i) By summing the squares of all numbers in the sequence one obtains Sigmaipi(2), and by dividing this sum by one plus the cyclomatic number, a Quadratic TI is obtained: Q = Sigmaipi(2)/(mu+1). (ii) On summing the Square roots of all numbers in the sequence one obtains Sigmaipi(1/2), and by dividing this sum by one plus the cyclomatic number, the TI denoted by S is obtained: S = Sigmaipi(1/2)/(mu+1). (iii) On dividing terms in this sum by the corresponding topological distances, one obtains the Distance-reduced index D = Sigmai{pi(1/2)/[i(mu+1)]}. Two similar formulas define the next two indices, the first one with no square roots: (iv) distance-Attenuated index: A = Sigmai{pi/[i(mu + 1)]}; and (v) the last TI with two square roots: Path-count index: P = Sigmai{pi(1/2)/[i(1/2)(mu + 1)]}. These five TIs are compared for their degeneracy, ordering of alkanes, and performance in QSPR (for all alkanes with 3-12 carbon atoms and for all possible chemical cyclic or acyclic graphs with 4-6 carbon atoms) in correlations with six physical properties and one chemical property.

77 FR 68884 - Petition for Waiver of Compliance

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-16

... petition Docket Number FRA-2012-0060. A copy of the petition, as well as any written communications...] Petition for Waiver of Compliance In accordance with Part 211 of Title 49 Code of Federal Regulations (CFR... equipment overhauls. PATH states that the material and inventory necessary to complete the required...

The Development and Validation of the Inquiry Science Observation Coding Sheet

ERIC Educational Resources Information Center

Brandon, P. R.; Taum, A. K. H.; Young, D. B.; Pottenger, F. M., III

2008-01-01

Evaluation reports increasingly document the degree of program implementation, particularly the extent to which programs adhere to prescribed steps and procedures. Many reports are cursory, however, and few, if any, fully portray the long and winding path taken when developing evaluation instruments, particularly observation instruments. In this…

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

Dillon, Heather E.; Antonopoulos, Chrissi A.; Solana, Amy E.

As the model energy codes are improved to reach efficiency levels 50 percent greater than current codes, use of on-site renewable energy generation is likely to become a code requirement. This requirement will be needed because traditional mechanisms for code improvement, including envelope, mechanical and lighting, have been pressed to the end of reasonable limits. Research has been conducted to determine the mechanism for implementing this requirement (Kaufman 2011). Kaufmann et al. determined that the most appropriate way to structure an on-site renewable requirement for commercial buildings is to define the requirement in terms of an installed power density permore » unit of roof area. This provides a mechanism that is suitable for the installation of photovoltaic (PV) systems on future buildings to offset electricity and reduce the total building energy load. Kaufmann et al. suggested that an appropriate maximum for the requirement in the commercial sector would be 4 W/ft{sup 2} of roof area or 0.5 W/ft{sup 2} of conditioned floor area. As with all code requirements, there must be an alternative compliance path for buildings that may not reasonably meet the renewables requirement. This might include conditions like shading (which makes rooftop PV arrays less effective), unusual architecture, undesirable roof pitch, unsuitable building orientation, or other issues. In the short term, alternative compliance paths including high performance mechanical equipment, dramatic envelope changes, or controls changes may be feasible. These options may be less expensive than many renewable systems, which will require careful balance of energy measures when setting the code requirement levels. As the stringency of the code continues to increase however, efficiency trade-offs will be maximized, requiring alternative compliance options to be focused solely on renewable electricity trade-offs or equivalent programs. One alternate compliance path includes purchase of Renewable Energy Credits (RECs). Each REC represents a specified amount of renewable electricity production and provides an offset of environmental externalities associated with non-renewable electricity production. The purpose of this paper is to explore the possible issues with RECs and comparable alternative compliance options. Existing codes have been examined to determine energy equivalence between the energy generation requirement and the RECs alternative over the life of the building. The price equivalence of the requirement and the alternative are determined to consider the economic drivers for a market decision. This research includes case studies that review how the few existing codes have incorporated RECs and some of the issues inherent with REC markets. Section 1 of the report reviews compliance options including RECs, green energy purchase programs, shared solar agreements and leases, and other options. Section 2 provides detailed case studies on codes that include RECs and community based alternative compliance methods. The methods the existing code requirements structure alternative compliance options like RECs are the focus of the case studies. Section 3 explores the possible structure of the renewable energy generation requirement in the context of energy and price equivalence. The price of RECs have shown high variation by market and over time which makes it critical to for code language to be updated frequently for a renewable energy generation requirement or the requirement will not remain price-equivalent over time. Section 4 of the report provides a maximum case estimate for impact to the PV market and the REC market based on the Kaufmann et al. proposed requirement levels. If all new buildings in the commercial sector complied with the requirement to install rooftop PV arrays, nearly 4,700 MW of solar would be installed in 2012, a major increase from EIA estimates of 640 MW of solar generation capacity installed in 2009. The residential sector could contribute roughly an additional 2,300 MW based on the same code requirement levels of 4 W/ft{sup 2} of roof area. Section 5 of the report provides a basic framework for draft code language recommendations based on the analysis of the alternative compliance levels.« less

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

Analysis of reaction cross-section production in neutron induced fission reactions on uranium isotope using computer code COMPLET.

PubMed

Asres, Yihunie Hibstie; Mathuthu, Manny; Birhane, Marelgn Derso

2018-04-22

This study provides current evidence about cross-section production processes in the theoretical and experimental results of neutron induced reaction of uranium isotope on projectile energy range of 1-100 MeV in order to improve the reliability of nuclear stimulation. In such fission reactions of 235 U within nuclear reactors, much amount of energy would be released as a product that able to satisfy the needs of energy to the world wide without polluting processes as compared to other sources. The main objective of this work is to transform a related knowledge in the neutron-induced fission reactions on 235 U through describing, analyzing and interpreting the theoretical results of the cross sections obtained from computer code COMPLET by comparing with the experimental data obtained from EXFOR. The cross section value of 235 U(n,2n) 234 U, 235 U(n,3n) 233 U, 235 U(n,γ) 236 U, 235 U(n,f) are obtained using computer code COMPLET and the corresponding experimental values were browsed by EXFOR, IAEA. The theoretical results are compared with the experimental data taken from EXFOR Data Bank. Computer code COMPLET has been used for the analysis with the same set of input parameters and the graphs were plotted by the help of spreadsheet & Origin-8 software. The quantification of uncertainties stemming from both experimental data and computer code calculation plays a significant role in the final evaluated results. The calculated results for total cross sections were compared with the experimental data taken from EXFOR in the literature, and good agreement was found between the experimental and theoretical data. This comparison of the calculated data was analyzed and interpreted with tabulation and graphical descriptions, and the results were briefly discussed within the text of this research work. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

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.

Neutron-induced reaction cross-sections of 93Nb with fast neutron based on 9Be(p,n) reaction

NASA Astrophysics Data System (ADS)

Naik, H.; Kim, G. N.; Kim, K.; Zaman, M.; Nadeem, M.; Sahid, M.

2018-02-01

The cross-sections of the 93Nb (n , 2 n)92mNb, 93Nb (n , 3 n)91mNb and 93Nb (n , 4 n)90Nb reactions with the average neutron energies of 14.4 to 34.0 MeV have been determined by using an activation and off-line γ-ray spectrometric technique. The fast neutrons were produced using the 9Be (p , n) reaction with the proton energies of 25-, 35- and 45-MeV from the MC-50 Cyclotron at the Korea Institute of Radiological and Medical Sciences (KIRAMS). The neutron flux-weighted average cross-sections of the 93Nb(n , xn ; x = 2- 4) reactions were also obtained from the mono-energetic neutron-induced reaction cross-sections of 93Nb calculated using the TALYS 1.8 code, and the neutron flux spectrum based on the MCNPX 2.6.0 code. The present results for the 93Nb(n , xn ; x = 2- 4) reactions are compared with the calculated neutron flux-weighted average values and found to be in good agreement.

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

Adaptive format conversion for scalable video coding

NASA Astrophysics Data System (ADS)

Wan, Wade K.; Lim, Jae S.

2001-12-01

The enhancement layer in many scalable coding algorithms is composed of residual coding information. There is another type of information that can be transmitted instead of (or in addition to) residual coding. Since the encoder has access to the original sequence, it can utilize adaptive format conversion (AFC) to generate the enhancement layer and transmit the different format conversion methods as enhancement data. This paper investigates the use of adaptive format conversion information as enhancement data in scalable video coding. Experimental results are shown for a wide range of base layer qualities and enhancement bitrates to determine when AFC can improve video scalability. Since the parameters needed for AFC are small compared to residual coding, AFC can provide video scalability at low enhancement layer bitrates that are not possible with residual coding. In addition, AFC can also be used in addition to residual coding to improve video scalability at higher enhancement layer bitrates. Adaptive format conversion has not been studied in detail, but many scalable applications may benefit from it. An example of an application that AFC is well-suited for is the migration path for digital television where AFC can provide immediate video scalability as well as assist future migrations.

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.

Error control techniques for satellite and space communications

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.

1989-01-01

Two aspects of the work for NASA are examined: the construction of multi-dimensional phase modulation trellis codes and a performance analysis of these codes. A complete list is contained of all the best trellis codes for use with phase modulation. LxMPSK signal constellations are included for M = 4, 8, and 16 and L = 1, 2, 3, and 4. Spectral efficiencies range from 1 bit/channel symbol (equivalent to rate 1/2 coded QPSK) to 3.75 bits/channel symbol (equivalent to 15/16 coded 16-PSK). The parity check polynomials, rotational invariance properties, free distance, path multiplicities, and coding gains are given for all codes. These codes are considered to be the best candidates for implementation of a high speed decoder for satellite transmission. The design of a hardware decoder for one of these codes, viz., the 16-state 3x8-PSK code with free distance 4.0 and coding gain 3.75 dB is discussed. An exhaustive simulation study of the multi-dimensional phase modulation trellis codes is contained. This study was motivated by the fact that coding gains quoted for almost all codes found in literature are in fact only asymptotic coding gains, i.e., the coding gain at very high signal to noise ratios (SNRs) or very low BER. These asymptotic coding gains can be obtained directly from a knowledge of the free distance of the code. On the other hand, real coding gains at BERs in the range of 10(exp -2) to 10(exp -6), where these codes are most likely to operate in a concatenated system, must be done by simulation.

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.

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

NSEG: A segmented mission analysis program for low and high speed aircraft. Volume 3: Demonstration problems

NASA Technical Reports Server (NTRS)

Hague, D. S.; Rozendaal, H. L.

1977-01-01

Program NSEG is a rapid mission analysis code based on the use of approximate flight path equations of motion. Equation form varies with the segment type, for example, accelerations, climbs, cruises, descents, and decelerations. Realistic and detailed vehicle characteristics are specified in tabular form. In addition to its mission performance calculation capabilities, the code also contains extensive flight envelope performance mapping capabilities. For example, rate-of-climb, turn rates, and energy maneuverability parameter values may be mapped in the Mach-altitude plane. Approximate take off and landing analyses are also performed. At high speeds, centrifugal lift effects are accounted for. Extensive turbojet and ramjet engine scaling procedures are incorporated in the code.

Which way and how far? Tracking of translation and rotation information for human path integration.

PubMed

Chrastil, Elizabeth R; Sherrill, Katherine R; Hasselmo, Michael E; Stern, Chantal E

2016-10-01

Path integration, the constant updating of the navigator's knowledge of position and orientation during movement, requires both visuospatial knowledge and memory. This study aimed to develop a systems-level understanding of human path integration by examining the basic building blocks of path integration in humans. To achieve this goal, we used functional imaging to examine the neural mechanisms that support the tracking and memory of translational and rotational components of human path integration. Critically, and in contrast to previous studies, we examined movement in translation and rotation tasks with no defined end-point or goal. Navigators accumulated translational and rotational information during virtual self-motion. Activity in hippocampus, retrosplenial cortex (RSC), and parahippocampal cortex (PHC) increased during both translation and rotation encoding, suggesting that these regions track self-motion information during path integration. These results address current questions regarding distance coding in the human brain. By implementing a modified delayed match to sample paradigm, we also examined the encoding and maintenance of path integration signals in working memory. Hippocampus, PHC, and RSC were recruited during successful encoding and maintenance of path integration information, with RSC selective for tasks that required processing heading rotation changes. These data indicate distinct working memory mechanisms for translation and rotation, which are essential for updating neural representations of current location. The results provide evidence that hippocampus, PHC, and RSC flexibly track task-relevant translation and rotation signals for path integration and could form the hub of a more distributed network supporting spatial navigation. Hum Brain Mapp 37:3636-3655, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Coupled long term simulation of reach scale water and heat fluxes across the river groundwater interface and hyporheic temperature dynamics

NASA Astrophysics Data System (ADS)

Munz, Matthias; Oswald, Sascha E.; Schmidt, Christian

2017-04-01

Flow pattern and seasonal as well as diurnal temperature variations control ecological and biogeochemical conditions in hyporheic sediments. In particular, hyporheic temperatures have a great impact on many microbial processes. In this study we used 3-D coupled water flow and heat transport simulations applying the HydroGeoSphere code in combination with high frequent observations of hydraulic heads and temperatures for quantifying reach scale water and heat flux across the river groundwater interface and hyporheic temperature dynamics of a lowland gravel-bed river. The magnitude and dynamics of simulated temperatures matched the observed with an average mean absolute error of 0.7 °C and an average Nash Sutcliffe Efficiency of 0.87. Our results highlight that the average temperature in the hyporheic zone follows the temperature in the river which is characterized by distinct seasonal and daily temperature cycles. Individual hyporheic flow path temperature substantially varies around the average hyporheic temperature. Hyporheic flow path temperature was found to strongly depend on the flow path residence time and the temperature gradient between river and groundwater; that is, in winter the average flow path temperature of long flow paths is potentially higher compared to short flow paths. Based on the simulation results we derived a general empirical relationship, estimating the influence of hyporheic flow path residence time on hyporheic flow path temperature. Furthermore we used an empirical temperature relationship between effective temperature and respiration rate to estimate the influence of hyporheic flow path residence time and temperature on hyporheic oxygen consumption. This study highlights the relation between complex hyporheic temperature patterns, hyporheic residence times and their implications on temperature sensitive biogeochemical processes.

Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data

PubMed Central

Raju, Hemalatha B.; Tsinoremas, Nicholas F.; Capobianco, Enrico

2016-01-01

Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes and repurposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein-coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parental genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to NP. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN and 8 in DRG), antisense RNA (31 asRNA in SN and 12 in DRG), and pseudogenes (456 in SN and 56 in DRG). In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly identified in protein–protein interaction networks, other connectivity paths were identified between proteins already investigated in studies on disorders, such as Parkinson, Down syndrome, Huntington disease, and Alzheimer. Our findings suggest the importance of reusing gene expression data by meta-analysis approaches. PMID:27803687

Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data.

PubMed

Raju, Hemalatha B; Tsinoremas, Nicholas F; Capobianco, Enrico

2016-01-01

Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes and repurposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein-coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parental genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to NP. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN and 8 in DRG), antisense RNA (31 asRNA in SN and 12 in DRG), and pseudogenes (456 in SN and 56 in DRG). In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly identified in protein-protein interaction networks, other connectivity paths were identified between proteins already investigated in studies on disorders, such as Parkinson, Down syndrome, Huntington disease, and Alzheimer. Our findings suggest the importance of reusing gene expression data by meta-analysis approaches.

Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK

PubMed Central

2014-01-01

Background Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system’s set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This “code-based” approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. Results As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. Conclusions The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming skills, and the graphical interface lends itself to easy modification and use by non-experts. PMID:24725437

Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK.

PubMed

Wang, Kaier; Steyn-Ross, Moira L; Steyn-Ross, D Alistair; Wilson, Marcus T; Sleigh, Jamie W; Shiraishi, Yoichi

2014-04-11

Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system's set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This "code-based" approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming skills, and the graphical interface lends itself to easy modification and use by non-experts.

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.

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.

Two-dimensional implosion simulations with a kinetic particle code [2D implosion simulations with a kinetic particle code

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

Sagert, Irina; Even, Wesley Paul; Strother, Terrance Timothy

Here, we perform two-dimensional implosion simulations using a Monte Carlo kinetic particle code. The application of a kinetic transport code is motivated, in part, by the occurrence of nonequilibrium effects in inertial confinement fusion capsule implosions, which cannot be fully captured by hydrodynamic simulations. Kinetic methods, on the other hand, are able to describe both continuum and rarefied flows. We perform simple two-dimensional disk implosion simulations using one-particle species and compare the results to simulations with the hydrodynamics code rage. The impact of the particle mean free path on the implosion is also explored. In a second study, we focusmore » on the formation of fluid instabilities from induced perturbations. We find good agreement with hydrodynamic studies regarding the location of the shock and the implosion dynamics. Differences are found in the evolution of fluid instabilities, originating from the higher resolution of rage and statistical noise in the kinetic studies.« less

Two-dimensional implosion simulations with a kinetic particle code [2D implosion simulations with a kinetic particle code

DOE PAGES

Sagert, Irina; Even, Wesley Paul; Strother, Terrance Timothy

2017-05-17

Here, we perform two-dimensional implosion simulations using a Monte Carlo kinetic particle code. The application of a kinetic transport code is motivated, in part, by the occurrence of nonequilibrium effects in inertial confinement fusion capsule implosions, which cannot be fully captured by hydrodynamic simulations. Kinetic methods, on the other hand, are able to describe both continuum and rarefied flows. We perform simple two-dimensional disk implosion simulations using one-particle species and compare the results to simulations with the hydrodynamics code rage. The impact of the particle mean free path on the implosion is also explored. In a second study, we focusmore » on the formation of fluid instabilities from induced perturbations. We find good agreement with hydrodynamic studies regarding the location of the shock and the implosion dynamics. Differences are found in the evolution of fluid instabilities, originating from the higher resolution of rage and statistical noise in the kinetic studies.« less

Theoretical evaluation of the reaction rates for {sup 26}Al(n,p){sup 26}Mg and {sup 26}Al(n,{alpha}){sup 23}Na

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

Oginni, B. M.; Iliadis, C.; Champagne, A. E.

2011-02-15

The reactions that destroy {sup 26}Al in massive stars have significance in a number of astrophysical contexts. We evaluate the reaction rates of {sup 26}Al(n,p){sup 26}Mg and {sup 26}Al(n,{alpha}){sup 23}Na using cross sections obtained from the codes empire and talys. These have been compared to the published rates obtained from the non-smoker code and to some experimental data. We show that the results obtained from empire and talys are comparable to those from non-smoker. We also show how the theoretical results vary with respect to changes in the input parameters. Finally, we present recommended rates for these reactions using themore » available experimental data and our new theoretical results.« less

Application of the DART Code for the Assessment of Advanced Fuel Behavior

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

Rest, J.; Totev, T.

2007-07-01

The Dispersion Analysis Research Tool (DART) code is a dispersion fuel analysis code that contains mechanistically-based fuel and reaction-product swelling models, a one dimensional heat transfer analysis, and mechanical deformation models. DART has been used to simulate the irradiation behavior of uranium oxide, uranium silicide, and uranium molybdenum aluminum dispersion fuels, as well as their monolithic counterparts. The thermal-mechanical DART code has been validated against RERTR tests performed in the ATR for irradiation data on interaction thickness, fuel, matrix, and reaction product volume fractions, and plate thickness changes. The DART fission gas behavior model has been validated against UO{sub 2}more » fission gas release data as well as measured fission gas-bubble size distributions. Here DART is utilized to analyze various aspects of the observed bubble growth in U-Mo/Al interaction product. (authors)« less

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.

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

Surface micromachined counter-meshing gears discrimination device

DOEpatents

Polosky, Marc A.; Garcia, Ernest J.; Allen, James J.

2000-12-12

A surface micromachined Counter-Meshing Gears (CMG) discrimination device which functions as a mechanically coded lock. Each of two CMG has a first portion of its perimeter devoted to continuous driving teeth that mesh with respective pinion gears. Each EMG also has a second portion of its perimeter devoted to regularly spaced discrimination gear teeth that extend outwardly on at least one of three levels of the CMG. The discrimination gear teeth are designed so as to pass each other without interference only if the correct sequence of partial rotations of the CMG occurs in response to a coded series of rotations from the pinion gears. A 24 bit code is normally input to unlock the device. Once unlocked, the device provides a path for an energy or information signal to pass through the device. The device is designed to immediately lock up if any portion of the 24 bit code is incorrect.

Fusion PIC code performance analysis on the Cori KNL system

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

Koskela, Tuomas S.; Deslippe, Jack; Friesen, Brian

We study the attainable performance of Particle-In-Cell codes on the Cori KNL system by analyzing a miniature particle push application based on the fusion PIC code XGC1. We start from the most basic building blocks of a PIC code and build up the complexity to identify the kernels that cost the most in performance and focus optimization efforts there. Particle push kernels operate at high AI and are not likely to be memory bandwidth or even cache bandwidth bound on KNL. Therefore, we see only minor benefits from the high bandwidth memory available on KNL, and achieving good vectorization ismore » shown to be the most beneficial optimization path with theoretical yield of up to 8x speedup on KNL. In practice we are able to obtain up to a 4x gain from vectorization due to limitations set by the data layout and memory latency.« less

Total reaction cross sections in CEM and MCNP6 at intermediate energies

DOE PAGES

Kerby, Leslie M.; Mashnik, Stepan G.

2015-05-14

Accurate total reaction cross section models are important to achieving reliable predictions from spallation and transport codes. The latest version of the Cascade Exciton Model (CEM) as incorporated in the code CEM03.03, and the Monte Carlo N-Particle transport code (MCNP6), both developed at Los Alamos National Laboratory (LANL), each use such cross sections. Having accurate total reaction cross section models in the intermediate energy region (50 MeV to 5 GeV) is very important for different applications, including analysis of space environments, use in medical physics, and accelerator design, to name just a few. The current inverse cross sections used inmore » the preequilibrium and evaporation stages of CEM are based on the Dostrovsky et al. model, published in 1959. Better cross section models are now available. Implementing better cross section models in CEM and MCNP6 should yield improved predictions for particle spectra and total production cross sections, among other results.« less

Total reaction cross sections in CEM and MCNP6 at intermediate energies

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

Kerby, Leslie M.; Mashnik, Stepan G.

Accurate total reaction cross section models are important to achieving reliable predictions from spallation and transport codes. The latest version of the Cascade Exciton Model (CEM) as incorporated in the code CEM03.03, and the Monte Carlo N-Particle transport code (MCNP6), both developed at Los Alamos National Laboratory (LANL), each use such cross sections. Having accurate total reaction cross section models in the intermediate energy region (50 MeV to 5 GeV) is very important for different applications, including analysis of space environments, use in medical physics, and accelerator design, to name just a few. The current inverse cross sections used inmore » the preequilibrium and evaporation stages of CEM are based on the Dostrovsky et al. model, published in 1959. Better cross section models are now available. Implementing better cross section models in CEM and MCNP6 should yield improved predictions for particle spectra and total production cross sections, among other results.« less

Codeless GPS Applications to Multi-Path: CGAMP

NASA Technical Reports Server (NTRS)

Macdoran, P. F.; Miller, R. B.; Jenkins, D.; Lemmon, J.; Gold, K.; Schreiner, W.; Snyder, G.

1990-01-01

Cordless Global Positioning System (GPS) Applications to Multi-Path (CGAMP) is meeting the challenge of exploiting the L-band signals from the Global Positioning System (GPS) satellites for the measurement of the impulse response of radio transmission channels over space-Earth paths. This approach was originally suggested by E. K. Smith and has been pursued by J. Lemmon, without an affordable implementation being identifiable. In addition to the high cost of a suitable P code correlating GPS receiver, there is also the major impediment of the often announced Department of Defense policy of selective availability/anti-spoof (SA/AS) that clouds reliable access to the wideband (20 MHz) P channel of the GPS signals without cryptographic access. A technique proposed by MacDoran utilizes codeless methods for exploiting the P channel signals implemented by the use of a pair of antennas and cross correlation signal detection.

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

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.

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.

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.

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part I: Path radiance

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.; Matarrese, Raffaella; Klemm, Frank J., Jr.

2006-09-01

A vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), which enables accounting for radiation polarization, has been developed and validated against a Monte Carlo code, Coulson's tabulated values, and MOBY (Marine Optical Buoy System) water-leaving reflectance measurements. The developed code was also tested against the scalar codes SHARM, DISORT, and MODTRAN to evaluate its performance in scalar mode and the influence of polarization. The obtained results have shown a good agreement of 0.7% in comparison with the Monte Carlo code, 0.2% for Coulson's tabulated values, and 0.001-0.002 for the 400-550 nm region for the MOBY reflectances. Ignoring the effects of polarization led to large errors in calculated top-of-atmosphere reflectances: more than 10% for a molecular atmosphere and up to 5% for an aerosol atmosphere. This new version of 6S is intended to replace the previous scalar version used for calculation of lookup tables in the MODIS (Moderate Resolution Imaging Spectroradiometer) atmospheric correction algorithm.

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part I: path radiance.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F; Matarrese, Raffaella; Klemm, Frank J

2006-09-10

A vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), which enables accounting for radiation polarization, has been developed and validated against a Monte Carlo code, Coulson's tabulated values, and MOBY (Marine Optical Buoy System) water-leaving reflectance measurements. The developed code was also tested against the scalar codes SHARM, DISORT, and MODTRAN to evaluate its performance in scalar mode and the influence of polarization. The obtained results have shown a good agreement of 0.7% in comparison with the Monte Carlo code, 0.2% for Coulson's tabulated values, and 0.001-0.002 for the 400-550 nm region for the MOBY reflectances. Ignoring the effects of polarization led to large errors in calculated top-of-atmosphere reflectances: more than 10% for a molecular atmosphere and up to 5% for an aerosol atmosphere. This new version of 6S is intended to replace the previous scalar version used for calculation of lookup tables in the MODIS (Moderate Resolution Imaging Spectroradiometer) atmospheric correction algorithm.

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.

Code-modulated interferometric imaging system using phased arrays

NASA Astrophysics Data System (ADS)

Chauhan, Vikas; Greene, Kevin; Floyd, Brian

2016-05-01

Millimeter-wave (mm-wave) imaging provides compelling capabilities for security screening, navigation, and bio- medical applications. Traditional scanned or focal-plane mm-wave imagers are bulky and costly. In contrast, phased-array hardware developed for mass-market wireless communications and automotive radar promise to be extremely low cost. In this work, we present techniques which can allow low-cost phased-array receivers to be reconfigured or re-purposed as interferometric imagers, removing the need for custom hardware and thereby reducing cost. Since traditional phased arrays power combine incoming signals prior to digitization, orthogonal code-modulation is applied to each incoming signal using phase shifters within each front-end and two-bit codes. These code-modulated signals can then be combined and processed coherently through a shared hardware path. Once digitized, visibility functions can be recovered through squaring and code-demultiplexing operations. Pro- vided that codes are selected such that the product of two orthogonal codes is a third unique and orthogonal code, it is possible to demultiplex complex visibility functions directly. As such, the proposed system modulates incoming signals but demodulates desired correlations. In this work, we present the operation of the system, a validation of its operation using behavioral models of a traditional phased array, and a benchmarking of the code-modulated interferometer against traditional interferometer and focal-plane arrays.

Scraping EDGAR with Python

ERIC Educational Resources Information Center

Ashraf, Rasha

2017-01-01

This article presents Python codes that can be used to extract data from Securities and Exchange Commission (SEC) filings. The Python program web crawls to obtain URL paths for company filings of required reports, such as Form 10-K. The program then performs a textual analysis and counts the number of occurrences of words in the filing that…

Data-Driven Hint Generation in Vast Solution Spaces: A Self-Improving Python Programming Tutor

ERIC Educational Resources Information Center

Rivers, Kelly; Koedinger, Kenneth R.

2017-01-01

To provide personalized help to students who are working on code-writing problems, we introduce a data-driven tutoring system, ITAP (Intelligent Teaching Assistant for Programming). ITAP uses state abstraction, path construction, and state reification to automatically generate personalized hints for students, even when given states that have not…

Optimal UAV Path Planning for Tracking a Moving Ground Vehicle with a Gimbaled Camera

DTIC Science & Technology

2014-03-27

micro SD card slot to record all video taken at 1080P resolution. This feature allows the team to record the high definition video taken by the...Inequality constraints 64 h=[]; %Equality constraints 104 Bibliography 1. “ DIY Drones: Official ArduPlane Repository”, 2013. URL https://code

[Path analysis of the Influence of Hospital Ethical Climate Perceived by Nurses on Supervisor Trust and Organizational Effectiveness].

PubMed

Noh, Yoon Goo; Jung, Myun Sook

2016-12-01

The purpose of this study was to analyze the paths of influence that a hospital's ethical climate exerts on nurses' organizational commitment and organizational citizenship behavior, with supervisor trust as the mediating factor, and verify compatibility of the models in hospital nurses. The sample consisted of 374 nurses recruited from four hospitals in 3 cities in Korea. The measurements included the Ethical Climate Questionnaire, Supervisor Trust Questionnaire, Organizational Commitment Questionnaire and Organizational Citizenship Behavior Questionnaire. Ethical Climate Questionnaire consisted of 6 factors; benevolence, personal morality, company rules and procedures, laws and professional codes, self-interest and efficiency. Data were analysed using SPSS version 18.0 and AMOS version 18.0. Supervisor trust was explained by benevolence and self-interest (29.8%). Organizational commitment was explained by benevolence, supervisor trust, personal morality, and rules and procedures (40.4%). Organizational citizenship behavior was explained by supervisor trust, laws and codes, and benevolence (21.8%). Findings indicate that managers need to develop a positive hospital ethical climate in order to improve nurses' trust in supervisors, organizational commitment and organizational citizenship behavior.

Study of the solar flares effect on VLF radio signal propagating along NRK-ALG path using LWPC code

NASA Astrophysics Data System (ADS)

Bouderba, Y.; NaitAmor, S.; Tribeche, M.

2016-07-01

The X-ray solar flare emissions penetrate down into the D region of the ionosphere (60-90 km of altitude) and affect the propagating very low frequency (VLF) radio signal. In this paper, we will present the effect of the solar flares on the signal mode composition of the NRK-ALG path during the period from 2007 to 2013. In the Long Wave Propagating Capability (LWPC) code theory, the VLF signal is a sum of discrete modes that propagate to the receiver with different attenuation coefficients. Therefore, an interest is given to the behavior of these coefficients under solar flares. Effectively, from the simulation, we give more explanations about the role of the signal mode composition on the fading displacement since this later is a consequence of the destructive modes interferences. Thus, the sign (positive or negative) of the perturbed signal parameters (amplitude and phase) is found to be depending on the distance between the transmitter and the receiver. Finally, we give the Wait parameters and the electron density variations as a function of solar flares.

Mass transfer effects in a gasification riser

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

Breault, Ronald W.; Li, Tingwen; Nicoletti, Phillip

2013-07-01

In the development of multiphase reacting computational fluid dynamics (CFD) codes, a number of simplifications were incorporated into the codes and models. One of these simplifications was the use of a simplistic mass transfer correlation for the faster reactions and omission of mass transfer effects completely on the moderate speed and slow speed reactions such as those in a fluidized bed gasifier. Another problem that has propagated is that the mass transfer correlation used in the codes is not universal and is being used far from its developed bubbling fluidized bed regime when applied to circulating fluidized bed (CFB) risermore » reactors. These problems are true for the major CFD codes. To alleviate this problem, a mechanistic based mass transfer coefficient algorithm has been developed based upon an earlier work by Breault et al. This fundamental approach uses the local hydrodynamics to predict a local, time varying mass transfer coefficient. The predicted mass transfer coefficients and the corresponding Sherwood numbers agree well with literature data and are typically about an order of magnitude lower than the correlation noted above. The incorporation of the new mass transfer model gives the expected behavior for all the gasification reactions evaluated in the paper. At the expected and typical design values for the solid flow rate in a CFB riser gasifier an ANOVA analysis has shown the predictions from the new code to be significantly different from the original code predictions. The new algorithm should be used such that the conversions are not over predicted. Additionally, its behaviors with changes in solid flow rate are consistent with the changes in the hydrodynamics.« less

Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.

PubMed

Bowsher, Clive G

2011-02-15

Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach. Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input-Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML). The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.

Detonation Velocity Calculations of Explosives with Slowly-Burning Constituents

NASA Astrophysics Data System (ADS)

Howard, W. Michael; Souers, P. Clark; Fried, Laurence E.

1997-07-01

The thermochemical code Equilbrium CHEETAH has been modified to allow partial reaction of constituents and partial flow of heat. Solid or liquid reactants are described by Einstein oscillators, whose temperatures can be changed to allow heat transfer. Hydroxy-terminated-poly-budadiene, mixed with RDX or HMX, does not react, as shown by the effect on the calculated detonation velocity. Aluminum and ammonium perchlorate in composites also do not react. Only partial heat flow also takes place in the unreacted materials. These results show that the usual assumption of total burn in a thermochemical code is probably incorrect, at least in the sonic reaction zone that drives the detonation velocity. A kinetic code would be the logical extension of this work.

Production of energetic light fragments in extensions of the CEM and LAQGSM event generators of the Monte Carlo transport code MCNP6 [Production of energetic light fragments in CEM, LAQGSM, and MCNP6

DOE PAGES

Mashnik, Stepan Georgievich; Kerby, Leslie Marie; Gudima, Konstantin K.; ...

2017-03-23

We extend the cascade-exciton model (CEM), and the Los Alamos version of the quark-gluon string model (LAQGSM), event generators of the Monte Carlo N-particle transport code version 6 (MCNP6), to describe production of energetic light fragments (LF) heavier than 4He from various nuclear reactions induced by particles and nuclei at energies up to about 1 TeV/nucleon. In these models, energetic LF can be produced via Fermi breakup, preequilibrium emission, and coalescence of cascade particles. Initially, we study several variations of the Fermi breakup model and choose the best option for these models. Then, we extend the modified exciton model (MEM)more » used by these codes to account for a possibility of multiple emission of up to 66 types of particles and LF (up to 28Mg) at the preequilibrium stage of reactions. Then, we expand the coalescence model to allow coalescence of LF from nucleons emitted at the intranuclear cascade stage of reactions and from lighter clusters, up to fragments with mass numbers A ≤ 7, in the case of CEM, and A ≤ 12, in the case of LAQGSM. Next, we modify MCNP6 to allow calculating and outputting spectra of LF and heavier products with arbitrary mass and charge numbers. The improved version of CEM is implemented into MCNP6. Lastly, we test the improved versions of CEM, LAQGSM, and MCNP6 on a variety of measured nuclear reactions. The modified codes give an improved description of energetic LF from particle- and nucleus-induced reactions; showing a good agreement with a variety of available experimental data. They have an improved predictive power compared to the previous versions and can be used as reliable tools in simulating applications involving such types of reactions.« less

Production of energetic light fragments in extensions of the CEM and LAQGSM event generators of the Monte Carlo transport code MCNP6 [Production of energetic light fragments in CEM, LAQGSM, and MCNP6

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

Mashnik, Stepan Georgievich; Kerby, Leslie Marie; Gudima, Konstantin K.

We extend the cascade-exciton model (CEM), and the Los Alamos version of the quark-gluon string model (LAQGSM), event generators of the Monte Carlo N-particle transport code version 6 (MCNP6), to describe production of energetic light fragments (LF) heavier than 4He from various nuclear reactions induced by particles and nuclei at energies up to about 1 TeV/nucleon. In these models, energetic LF can be produced via Fermi breakup, preequilibrium emission, and coalescence of cascade particles. Initially, we study several variations of the Fermi breakup model and choose the best option for these models. Then, we extend the modified exciton model (MEM)more » used by these codes to account for a possibility of multiple emission of up to 66 types of particles and LF (up to 28Mg) at the preequilibrium stage of reactions. Then, we expand the coalescence model to allow coalescence of LF from nucleons emitted at the intranuclear cascade stage of reactions and from lighter clusters, up to fragments with mass numbers A ≤ 7, in the case of CEM, and A ≤ 12, in the case of LAQGSM. Next, we modify MCNP6 to allow calculating and outputting spectra of LF and heavier products with arbitrary mass and charge numbers. The improved version of CEM is implemented into MCNP6. Lastly, we test the improved versions of CEM, LAQGSM, and MCNP6 on a variety of measured nuclear reactions. The modified codes give an improved description of energetic LF from particle- and nucleus-induced reactions; showing a good agreement with a variety of available experimental data. They have an improved predictive power compared to the previous versions and can be used as reliable tools in simulating applications involving such types of reactions.« less

Automated Testcase Generation for Numerical Support Functions in Embedded Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Schnieder, Stefan-Alexander

2014-01-01

We present a tool for the automatic generation of test stimuli for small numerical support functions, e.g., code for trigonometric functions, quaternions, filters, or table lookup. Our tool is based on KLEE to produce a set of test stimuli for full path coverage. We use a method of iterative deepening over abstractions to deal with floating-point values. During actual testing the stimuli exercise the code against a reference implementation. We illustrate our approach with results of experiments with low-level trigonometric functions, interpolation routines, and mathematical support functions from an open source UAS autopilot.

Comparison study of photon attenuation characteristics of Lead-Boron Polyethylene by MCNP code, XCOM and experimental data

NASA Astrophysics Data System (ADS)

Zhang, Lei; Jia, Mingchun; Gong, Junjun; Xia, Wenming

2017-08-01

The linear attenuation coefficient, mass attenuation coefficient and mean free path of various Lead-Boron Polyethylene (PbBPE) samples which can be used as the photon shielding materials in marine reactor have been simulated using the Monte Carlo N-Particle (MCNP)-5 code. The MCNP simulation results are in good agreement with the XCOM values and the reported experimental data for source Cesium-137 and Cobalt-60. Thus, this method based on MCNP can be used to simulate the photon attenuation characteristics of various types of PbBPE materials.

Photoneutron Reaction Data for Nuclear Physics and Astrophysics

NASA Astrophysics Data System (ADS)

Utsunomiya, Hiroaki; Renstrøm, Therese; Tveten, Gry Merete; Gheorghe, Ioana; Filipescu, Dan Mihai; Belyshev, Sergey; Stopani, Konstantin; Wang, Hongwei; Fan, Gongtao; Lui, Yiu-Wing; Symochko, Dmytro; Goriely, Stephane; Larsen, Ann-Cecilie; Siem, Sunniva; Varlamov, Vladimir; Ishkhanov, Boris; Glodariu, Tudor; Krzysiek, Mateusz; Takenaka, Daiki; Ari-izumi, Takashi; Amano, Sho; Miyamoto, Shuji

2018-05-01

We discuss the role of photoneutron reaction data in nuclear physics and astrophysics in conjunction with the Coordinated Research Project of the International Atomic Energy Agency with the code F41032 (IAEA-CRP F41032).

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.

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.

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

Finite element code development for modeling detonation of HMX composites

NASA Astrophysics Data System (ADS)

Duran, Adam; Sundararaghavan, Veera

2015-06-01

In this talk, we present a hydrodynamics code for modeling shock and detonation waves in HMX. A stable efficient solution strategy based on a Taylor-Galerkin finite element (FE) discretization was developed to solve the reactive Euler equations. In our code, well calibrated equations of state for the solid unreacted material and gaseous reaction products have been implemented, along with a chemical reaction scheme and a mixing rule to define the properties of partially reacted states. A linear Gruneisen equation of state was employed for the unreacted HMX calibrated from experiments. The JWL form was used to model the EOS of gaseous reaction products. It is assumed that the unreacted explosive and reaction products are in both pressure and temperature equilibrium. The overall specific volume and internal energy was computed using the rule of mixtures. Arrhenius kinetics scheme was integrated to model the chemical reactions. A locally controlled dissipation was introduced that induces a non-oscillatory stabilized scheme for the shock front. The FE model was validated using analytical solutions for sod shock and ZND strong detonation models and then used to perform 2D and 3D shock simulations. We will present benchmark problems for geometries in which a single HMX crystal is subjected to a shock condition. Our current progress towards developing microstructural models of HMX/binder composite will also be discussed.

Dual neutral particle induced transmutation in CINDER2008

NASA Astrophysics Data System (ADS)

Martin, W. J.; de Oliveira, C. R. E.; Hecht, A. A.

2014-12-01

Although nuclear transmutation methods for fission have existed for decades, the focus has been on neutron-induced reactions. Recent novel concepts have sought to use both neutrons and photons for purposes such as active interrogation of cargo to detect the smuggling of highly enriched uranium, a concept that would require modeling the transmutation caused by both incident particles. As photonuclear transmutation has yet to be modeled alongside neutron-induced transmutation in a production code, new methods need to be developed. The CINDER2008 nuclear transmutation code from Los Alamos National Laboratory is extended from neutron applications to dual neutral particle applications, allowing both neutron- and photon-induced reactions for this modeling with a focus on fission. Following standard reaction modeling, the induced fission reaction is understood as a two-part reaction, with an entrance channel to the excited compound nucleus, and an exit channel from the excited compound nucleus to the fission fragmentation. Because photofission yield data-the exit channel from the compound nucleus-are sparse, neutron fission yield data are used in this work. With a different compound nucleus and excitation, the translation to the excited compound state is modified, as appropriate. A verification and validation of these methods and data has been performed. This has shown that the translation of neutron-induced fission product yield sets, and their use in photonuclear applications, is appropriate, and that the code has been extended correctly.

Resident Reactions to Person-Centered Communication by Long-Term Care Staff.

PubMed

Savundranayagam, Marie Y; Sibalija, Jovana; Scotchmer, Emma

2016-09-01

Long-term care staff caregivers who are person centered incorporate the life history, preferences, and feelings of residents with dementia during care interactions. Communication is essential for person-centered care. However, little is known about residents' verbal reactions when staff use person-centered communication. Accordingly, this study investigated the impact of person-centered communication and missed opportunities for such communication by staff on resident reactions. Conversations (N = 46) between staff-resident dyads were audio-recorded during routine care tasks over 12 weeks. Staff utterances were coded for person-centered communication and missed opportunities. Resident utterances were coded for positive reactions, such as cooperation, and negative reactions, such as distress. Linear regression analyses revealed that the more staff used person-centered communication, the more likely that residents reacted positively. Additionally, the more missed opportunities in a conversation, the more likely that the residents reacted negatively. Conversation illustrations elaborate on the quantitative findings and implications for staff training are discussed. © The Author(s) 2016.

Cross section of the 197Au(n,2n)196Au reaction

NASA Astrophysics Data System (ADS)

Kalamara, A.; Vlastou, R.; Kokkoris, M.; Diakaki, M.; Serris, M.; Patronis, N.; Axiotis, M.; Lagoyannis, A.

2017-09-01

The 197Au(n,2n)196Au reaction cross section has been measured at two energies, namely at 17.1 MeV and 20.9 MeV, by means of the activation technique, relative to the 27Al(n,α)24Na reference reaction cross section. Quasi-monoenergetic neutron beams were produced at the 5.5 MV Tandem T11/25 accelerator laboratory of NCSR "Demokritos", by means of the 3H(d,n)4He reaction, implementing a new Ti-tritiated target of ˜ 400 GBq activity. The induced γ-ray activity at the targets and reference foils has been measured with HPGe detectors. The cross section for the population of the second isomeric (12-) state m2 of 196Au was independently determined. Auxiliary Monte Carlo simulations were performed using the MCNP code. The present results are in agreement with previous experimental data and with theoretical calculations of the measured reaction cross sections, which were carried out with the use of the EMPIRE code.

Upgrades of Two Computer Codes for Analysis of Turbomachinery

NASA Technical Reports Server (NTRS)

Chima, Rodrick V.; Liou, Meng-Sing

2005-01-01

Major upgrades have been made in two of the programs reported in "ive Computer Codes for Analysis of Turbomachinery". The affected programs are: Swift -- a code for three-dimensional (3D) multiblock analysis; and TCGRID, which generates a 3D grid used with Swift. Originally utilizing only a central-differencing scheme for numerical solution, Swift was augmented by addition of two upwind schemes that give greater accuracy but take more computing time. Other improvements in Swift include addition of a shear-stress-transport turbulence model for better prediction of adverse pressure gradients, addition of an H-grid capability for flexibility in modeling flows in pumps and ducts, and modification to enable simultaneous modeling of hub and tip clearances. Improvements in TCGRID include modifications to enable generation of grids for more complicated flow paths and addition of an option to generate grids compatible with the ADPAC code used at NASA and in industry. For both codes, new test cases were developed and documentation was updated. Both codes were converted to Fortran 90, with dynamic memory allocation. Both codes were also modified for ease of use in both UNIX and Windows operating systems.

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.

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

Kinetic Effects in Inertial Confinement Fusion

NASA Astrophysics Data System (ADS)

Kagan, Grigory

2014-10-01

Sharp background gradients, inevitably introduced during ICF implosion, are likely responsible for the discrepancy between the predictions of the standard single-fluid rad-hydro codes and the experimental observations. On the one hand, these gradients drive the inter-ion-species transport, so the fuel composition no longer remains constant, unlike what the single-fluid codes assume. On the other hand, once the background scale is comparable to the mean free path, a fluid description becomes invalid. This point takes on special significance in plasmas, where the particle's mean free path scales with the square of this particle's energy. The distribution function of energetic ions may therefore be far from Maxwellian, even if thermal ions are nearly equilibrated. Ironically, it is these energetic, or tail, ions that are supposed to fuse at the onset of ignition. A combination of studies has been conducted to clarify the role of such kinetic effects on ICF performance. First, transport formalism applicable to multi-component plasmas has been developed. In particular, a novel ``electro-diffusion'' mechanism of the ion species separation has been shown to exist. Equally important, in drastic contrast to the classical case of the neutral gas mixture, thermo-diffusion is predicted to be comparable to, or even much larger than, baro-diffusion. By employing the effective potential theory this formalism has then been generalized to the case of a moderately coupled plasma with multiple ion species, making it applicable to the problem of mix at the shell/fuel interface in ICF implosion. Second, distribution function for the energetic ions has been found from first principles and the fusion reactivity reduction has been calculated for hot-spot relevant conditions. A technique for approximate evaluation of the distribution function has been identified. This finding suggests a path to effectively introducing the tail modification effects into mainline rad-hydro codes, while being in good agreement with the first principle based solution. This work was partially supported by the Laboratory Directed Research and Development (LDRD) program of LANL.

PFLOTRAN: Reactive Flow & Transport Code for Use on Laptops to Leadership-Class Supercomputers

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

Hammond, Glenn E.; Lichtner, Peter C.; Lu, Chuan

PFLOTRAN, a next-generation reactive flow and transport code for modeling subsurface processes, has been designed from the ground up to run efficiently on machines ranging from leadership-class supercomputers to laptops. Based on an object-oriented design, the code is easily extensible to incorporate additional processes. It can interface seamlessly with Fortran 9X, C and C++ codes. Domain decomposition parallelism is employed, with the PETSc parallel framework used to manage parallel solvers, data structures and communication. Features of the code include a modular input file, implementation of high-performance I/O using parallel HDF5, ability to perform multiple realization simulations with multiple processors permore » realization in a seamless manner, and multiple modes for multiphase flow and multicomponent geochemical transport. Chemical reactions currently implemented in the code include homogeneous aqueous complexing reactions and heterogeneous mineral precipitation/dissolution, ion exchange, surface complexation and a multirate kinetic sorption model. PFLOTRAN has demonstrated petascale performance using 2{sup 17} processor cores with over 2 billion degrees of freedom. Accomplishments achieved to date include applications to the Hanford 300 Area and modeling CO{sub 2} sequestration in deep geologic formations.« less

Comparison of distributed acceleration and standard models of cosmic-ray transport

NASA Technical Reports Server (NTRS)

Letaw, J. R.; Silberberg, R.; Tsao, C. H.

1995-01-01

Recent cosmic-ray abundance measurements for elements in the range 3 less than or equal to Z less than or equal to 28 and energies 10 MeV/n less than or equal to E less than or equal to 1 TeV/n have been analyzed with computer transport modeling. About 500 elemental and isotopic measurements have been explored in this analysis. The transport code includes the effects of ionization losses, nuclear spallation reactions (including those of secondaries), all nuclear decay modes, stripping and attachment of electrons, escape from the Galaxy, weak reacceleration and solar modulation. Four models of reacceleration (with several submodels of various reacceleration strengths) were explored. A chi (exp 2) analysis show that the reacceleration models yield at least equally good fits to the data as the standard propagation model. However, with reacceleration, the ad hoc assumptions of the standard model regarding discontinuities in the energy dependence of the mean path length traversed by cosmic rays, and in the momentum spectrum of the cosmic-ray source spectrum are eliminated. Futhermore, the difficulty between rigidity dependent leakage and energy independent anisotropy below energies of 10(exp 14) eV is alleviated.

Measurement and resonance analysis of the 33S(n ,α )30Si cross section at the CERN n_TOF facility in the energy region from 10 to 300 keV

NASA Astrophysics Data System (ADS)

Praena, J.; Sabaté-Gilarte, M.; Porras, I.; Quesada, J. M.; Altstadt, S.; Andrzejewski, J.; Audouin, L.; Bécares, V.; Barbagallo, M.; Bečvář, F.; Belloni, F.; Berthoumieux, E.; Billowes, J.; Boccone, V.; Bosnar, D.; Brugger, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Carrapiço, C.; Cerutti, F.; Chiaveri, E.; Chin, M.; Colonna, N.; Cortés, G.; Cortés-Giraldo, M. A.; Diakaki, M.; Dietz, M.; Domingo-Pardo, C.; Dressler, R.; Durán, I.; Eleftheriadis, C.; Ferrari, A.; Fraval, K.; Furman, V.; Göbel, K.; Gómez-Hornillos, M. B.; Ganesan, S.; García, A. R.; Giubrone, G.; Gonçalves, I. F.; González-Romero, E.; Goverdovski, A.; Griesmayer, E.; Guerrero, C.; Gunsing, F.; Heftrich, T.; Hernández-Prieto, A.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Karadimos, D.; Katabuchi, T.; Ketlerov, V.; Khryachkov, V.; Kivel, N.; Koehler, P.; Kokkoris, M.; Kroll, J.; Krtička, M.; Lampoudis, C.; Langer, C.; Leal-Cidoncha, E.; Lederer-Woods, C.; Leeb, H.; Leong, L. S.; Lerendegui-Marco, J.; Losito, R.; Mallick, A.; Manousos, A.; Marganiec, J.; Martínez, T.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Mondelaers, W.; Paradela, C.; Pavlik, A.; Perkowski, J.; Plompen, A. J. M.; Rauscher, T.; Reifarth, R.; Riego-Perez, A.; Robles, M.; Rubbia, C.; Ryan, J. A.; Sarmento, R.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tarrío, D.; Tassan-Got, L.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vermeulen, M. J.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Ware, T.; Weigand, M.; Weiss, C.; Wright, T.; Žugec, P.; n TOF Collaboration

2018-06-01

The 33S(n ,α )30Si cross section has been measured at the neutron time-of-flight (n _TOF ) facility at CERN in the neutron energy range from 10 to 300 keV relative to the 10B(n ,α )7Li cross-section standard. Both reactions were measured simultaneously with a set of micromegas detectors. The flight path of 185 m has allowed us to obtain the cross section with high-energy resolution. An accurate description of the resonances has been performed by means of the multilevel multichannel R -matrix code sammy. The results show a significantly higher area of the biggest resonance (13.45 keV) than the unique high-resolution (n ,α ) measurement. The new parametrization of the 13.45-keV resonance is similar to that of the unique transmission measurement. This resonance is a matter of research in neutron-capture therapy. The 33S(n ,α )30Si cross section has been studied in previous works because of its role in the production of 36S in stars, which is currently overproduced in stellar models compared to observations.

Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins

NASA Astrophysics Data System (ADS)

Seyler, Sean L.

In a typical living cell, millions to billions of proteins--nanomachines that fluctuate and cycle among many conformational states--convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible. Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)--an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project--developing a hybrid atomistic-continuum method--is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.

Role of Off-Line-of-Sight Propagation in Geomagnetic EMP Formation

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

Kruger, Hans W.

The author’s synchrotron radiation based 3D geomagnetic EMP code MACSYNC has been used to explore the impact on pulse rise time and air conductivity of EMP propagation paths to the observer that are located off the direct line-of-sight (LOS) between gamma source and observer. This geometry is always present because, for an isotropic source, most the gammas are emitted at an angle with respect to the LOS. Computations for a 1 kt near-surface burst observed from space yield two principal findings: 1. The rise time is generated by the combined actions of a) electron spreading along the LOS due tomore » the Compton electron emission angular distribution folded with electron multiple scattering effects, and b) radiation arrival time spreading due to length differences for different off-LOS propagation paths. The pulse rise time does not depend on the rise time of the conductivity. The conductivity rise time determines the pulse amplitude. 2. One-dimensional legacy EMP codes are inherently incapable of producing the correct pulse shape because they cannot treat the dependence of the conductivity on two dimensions, i.e. the radius from the source and the angle of the propagation path with the LOS. This divergence from one-dimensionality begins at a small fraction of a nanosecond for a sea-level burst. This effect will also be present in high-altitude bursts, however, determination of its onset time and magnitude requires high-altitude computations which have not yet been done.« less

Tow-Steered Panels With Holes Subjected to Compression or Shear Loads

NASA Technical Reports Server (NTRS)

Jegley, Dawn C.; Tatting, Brian F.; Guerdal, Zafer

2005-01-01

Tailoring composite laminates to vary the fiber orientations within a fiber layer of a laminate to address non-uniform stress states and provide structural advantages such as the alteration of principal load paths has potential application to future low-cost, light-weight structures for commercial transport aircraft. Evaluation of this approach requires the determination of the effectiveness of stiffness tailoring through the use of curvilinear fiber paths in flat panels including the reduction of stress concentrations around the holes and the increase in load carrying capability. Panels were designed through the use of an optimization code using a genetic algorithm and fabricated using a tow-steering approach. Manufacturing limitations, such as the radius of curvature of tows the machine could support, avoidance of wrinkling of fibers and minimization of gaps between fibers were considered in the design process. Variable stiffness tow-steered panels constructed with curvilinear fiber paths were fabricated so that the design methodology could be verified through experimentation. Finite element analysis where each element s stacking sequence was accurately defined is used to verify the behavior predicted based on the design code. Experiments on variable stiffness flat panels with central circular holes were conducted with the panels loaded in axial compression or shear. Tape and tow-steered panels are used to demonstrate the buckling, post-buckling and failure behavior of elastically tailored panels. The experimental results presented establish the buckling performance improvements attainable by elastic tailoring of composite laminates.

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.

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.

Resolving the Multi-scale Behavior of Geochemical Weathering in the Critical Zone Using High Resolution Hydro-geochemical Models

NASA Astrophysics Data System (ADS)

Pandey, S.; Rajaram, H.

2015-12-01

This work investigates hydrologic and geochemical interactions in the Critical Zone (CZ) using high-resolution reactive transport modeling. Reactive transport models can be used to predict the response of geochemical weathering and solute fluxes in the CZ to changes in a dynamic environment, such as those pertaining to human activities and climate change in recent years. The scales of hydrology and geochemistry in the CZ range from days to eons in time and centimeters to kilometers in space. Here, we present results of a multi-dimensional, multi-scale hydro-geochemical model to investigate the role of subsurface heterogeneity on the formation of mineral weathering fronts in the CZ, which requires consideration of many of these spatio-temporal scales. The model is implemented using the reactive transport code PFLOTRAN, an open source subsurface flow and reactive transport code that utilizes parallelization over multiple processing nodes and provides a strong framework for simulating weathering in the CZ. The model is set up to simulate weathering dynamics in the mountainous catchments representative of the Colorado Front Range. Model parameters were constrained based on hydrologic, geochemical, and geophysical observations from the Boulder Creek Critical Zone Observatory (BcCZO). Simulations were performed in fractured rock systems and compared with systems of heterogeneous and homogeneous permeability fields. Tracer simulations revealed that the mean residence time of solutes was drastically accelerated as fracture density increased. In simulations that include mineral reactions, distinct signatures of transport limitations on weathering arose when discrete flow paths were included. This transport limitation was related to both advective and diffusive processes in the highly heterogeneous systems (i.e. fractured media and correlated random permeability fields with σlnk > 3). The well-known time-dependence of mineral weathering rates was found to be the most pronounced in the fractured systems, with a departure from the maximum system-averaged dissolution rate occurring after ~100 kyr followed by a gradual decrease in the reaction rate with time that persists beyond 104 kyr.

Probing Trapped Ion Energies Via Ion-Molecule Reaction Kinetics: Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

DTIC Science & Technology

1992-05-28

ORGANIZATION (if applicable) Office of Naval Research N00014-87- j - 1248 Bc. ADDRESS (City, State, and ZIP Code) 10. SOURCE OF FUNDING NUMBERS 800 N. Quincy St...RESEARCH Grant NOOO14-87- J -1248 R & T Code 4134052 TECHNICAL REPORT NO. 36 Probing Trapped Ion Energies Via Ion-Molecule Reaction Kinetics: Fourier...reactivity (for charge transfer with N2) of the higher energy J =1/2 state is approximately three times that of the J =3/2 state at collision energies

A Graphical User Interface for a Method to Infer Kinetics and Network Architecture (MIKANA)

PubMed Central

Mourão, Márcio A.; Srividhya, Jeyaraman; McSharry, Patrick E.; Crampin, Edmund J.; Schnell, Santiago

2011-01-01

One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis–Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1). PMID:22096591

A graphical user interface for a method to infer kinetics and network architecture (MIKANA).

PubMed

Mourão, Márcio A; Srividhya, Jeyaraman; McSharry, Patrick E; Crampin, Edmund J; Schnell, Santiago

2011-01-01

One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis-Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1).

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.

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.

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.

Efficient simultaneous dense coding and teleportation with two-photon four-qubit cluster states

NASA Astrophysics Data System (ADS)

Zhang, Cai; Situ, Haozhen; Li, Qin; He, Guang Ping

2016-08-01

We firstly propose a simultaneous dense coding protocol with two-photon four-qubit cluster states in which two receivers can simultaneously get their respective classical information sent by a sender. Because each photon has two degrees of freedom, the protocol will achieve a high transmittance. The security of the simultaneous dense coding protocol has also been analyzed. Secondly, we investigate how to simultaneously teleport two different quantum states with polarization and path degree of freedom using cluster states to two receivers, respectively, and discuss its security. The preparation and transmission of two-photon four-qubit cluster states is less difficult than that of four-photon entangled states, and it has been experimentally generated with nearly perfect fidelity and high generation rate. Thus, our protocols are feasible with current quantum techniques.

Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1983-01-01

A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

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).

Making your code citable with the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; DuPrie, Kimberly; Schmidt, Judy; Berriman, G. Bruce; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

2016-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. With nearly 1,200 codes, it is the largest indexed resource for astronomy codes in existence. Established in 1999, it offers software authors a path to citation of their research codes even without publication of a paper describing the software, and offers scientists a way to find codes used in refereed publications, thus improving the transparency of the research. It also provides a method to quantify the impact of source codes in a fashion similar to the science metrics of journal articles. Citations using ASCL IDs are accepted by major astronomy journals and if formatted properly are tracked by ADS and other indexing services. The number of citations to ASCL entries increased sharply from 110 citations in January 2014 to 456 citations in September 2015. The percentage of code entries in ASCL that were cited at least once rose from 7.5% in January 2014 to 17.4% in September 2015. The ASCL's mid-2014 infrastructure upgrade added an easy entry submission form, more flexible browsing, search capabilities, and an RSS feeder for updates. A Changes/Additions form added this past fall lets authors submit links for papers that use their codes for addition to the ASCL entry even if those papers don't formally cite the codes, thus increasing the transparency of that research and capturing the value of their software to the community.

Leadership Class Configuration Interaction Code - Status and Opportunities

NASA Astrophysics Data System (ADS)

Vary, James

2011-10-01

With support from SciDAC-UNEDF (www.unedf.org) nuclear theorists have developed and are continuously improving a Leadership Class Configuration Interaction Code (LCCI) for forefront nuclear structure calculations. The aim of this project is to make state-of-the-art nuclear structure tools available to the entire community of researchers including graduate students. The project includes codes such as NuShellX, MFDn and BIGSTICK that run a range of computers from laptops to leadership class supercomputers. Codes, scripts, test cases and documentation have been assembled, are under continuous development and are scheduled for release to the entire research community in November 2011. A covering script that accesses the appropriate code and supporting files is under development. In addition, a Data Base Management System (DBMS) that records key information from large production runs and archived results of those runs has been developed (http://nuclear.physics.iastate.edu/info/) and will be released. Following an outline of the project, the code structure, capabilities, the DBMS and current efforts, I will suggest a path forward that would benefit greatly from a significant partnership between researchers who use the codes, code developers and the National Nuclear Data efforts. This research is supported in part by DOE under grant DE-FG02-87ER40371 and grant DE-FC02-09ER41582 (SciDAC-UNEDF).

Spatio-Temporal Structure, Path Characteristics, and Perceptual Grouping in Immediate Serial Spatial Recall

PubMed Central

De Lillo, Carlo; Kirby, Melissa; Poole, Daniel

2016-01-01

Immediate serial spatial recall measures the ability to retain sequences of locations in short-term memory and is considered the spatial equivalent of digit span. It is tested by requiring participants to reproduce sequences of movements performed by an experimenter or displayed on a monitor. Different organizational factors dramatically affect serial spatial recall but they are often confounded or underspecified. Untangling them is crucial for the characterization of working-memory models and for establishing the contribution of structure and memory capacity to spatial span. We report five experiments assessing the relative role and independence of factors that have been reported in the literature. Experiment 1 disentangled the effects of spatial clustering and path-length by manipulating the distance of items displayed on a touchscreen monitor. Long-path sequences segregated by spatial clusters were compared with short-path sequences not segregated by clusters. Recall was more accurate for sequences segregated by clusters independently from path-length. Experiment 2 featured conditions where temporal pauses were introduced between or within cluster boundaries during the presentation of sequences with the same paths. Thus, the temporal structure of the sequences was either consistent or inconsistent with a hierarchical representation based on segmentation by spatial clusters but the effect of structure could not be confounded with effects of path-characteristics. Pauses at cluster boundaries yielded more accurate recall, as predicted by a hierarchical model. In Experiment 3, the systematic manipulation of sequence structure, path-length, and presence of path-crossings of sequences showed that structure explained most of the variance, followed by the presence/absence of path-crossings, and path-length. Experiments 4 and 5 replicated the results of the previous experiments in immersive virtual reality navigation tasks where the viewpoint of the observer changed dynamically during encoding and recall. This suggested that the effects of structure in spatial span are not dependent on perceptual grouping processes induced by the aerial view of the stimulus array typically afforded by spatial recall tasks. These results demonstrate the independence of coding strategies based on structure from effects of path characteristics and perceptual grouping in immediate serial spatial recall. PMID:27891101

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.

Thermal-Flow Code for Modeling Gas Dynamics and Heat Transfer in Space Shuttle Solid Rocket Motor Joints

NASA Technical Reports Server (NTRS)

Wang, Qunzhen; Mathias, Edward C.; Heman, Joe R.; Smith, Cory W.

2000-01-01

A new, thermal-flow simulation code, called SFLOW. has been developed to model the gas dynamics, heat transfer, as well as O-ring and flow path erosion inside the space shuttle solid rocket motor joints by combining SINDA/Glo, a commercial thermal analyzer. and SHARPO, a general-purpose CFD code developed at Thiokol Propulsion. SHARP was modified so that friction, heat transfer, mass addition, as well as minor losses in one-dimensional flow can be taken into account. The pressure, temperature and velocity of the combustion gas in the leak paths are calculated in SHARP by solving the time-dependent Navier-Stokes equations while the heat conduction in the solid is modeled by SINDA/G. The two codes are coupled by the heat flux at the solid-gas interface. A few test cases are presented and the results from SFLOW agree very well with the exact solutions or experimental data. These cases include Fanno flow where friction is important, Rayleigh flow where heat transfer between gas and solid is important, flow with mass addition due to the erosion of the solid wall, a transient volume venting process, as well as some transient one-dimensional flows with analytical solutions. In addition, SFLOW is applied to model the RSRM nozzle joint 4 subscale hot-flow tests and the predicted pressures, temperatures (both gas and solid), and O-ring erosions agree well with the experimental data. It was also found that the heat transfer between gas and solid has a major effect on the pressures and temperatures of the fill bottles in the RSRM nozzle joint 4 configuration No. 8 test.

Development and Demonstration of an Ada Test Generation System

NASA Technical Reports Server (NTRS)

1996-01-01

In this project we have built a prototype system that performs Feasible Path Analysis on Ada programs: given a description of a set of control flow paths through a procedure, and a predicate at a program point feasible path analysis determines if there is input data which causes execution to flow down some path in the collection reaching the point so that tile predicate is true. Feasible path analysis can be applied to program testing, program slicing, array bounds checking, and other forms of anomaly checking. FPA is central to most applications of program analysis. But, because this problem is formally unsolvable, syntactic-based approximations are used in its place. For example, in dead-code analysis the problem is to determine if there are any input values which cause execution to reach a specified program point. Instead an approximation to this problem is computed: determine whether there is a control flow path from the start of the program to the point. This syntactic approximation is efficiently computable and conservative: if there is no such path the program point is clearly unreachable, but if there is such a path, the analysis is inconclusive, and the code is assumed to be live. Such conservative analysis too often yields unsatisfactory results because the approximation is too weak. As another example, consider data flow analysis. A du-pair is a pair of program points such that the first point is a definition of a variable and the second point a use and for which there exists a definition-free path from the definition to the use. The sharper, semantic definition of a du-pair requires that there be a feasible definition-free path from the definition to the use. A compiler using du-pairs for detecting dead variables may miss optimizations by not considering feasibility. Similarly, a program analyzer computing program slices to merge parallel versions may report conflicts where none exist. In the context of software testing, feasibility analysis plays an important role in identifying testing requirements which are infeasible. This is especially true for data flow testing and modified condition/decision coverage. Our system uses in an essential way symbolic analysis and theorem proving technology, and we believe this work represents one of the few successful uses of a theorem prover working in a completely automatic fashion to solve a problem of practical interest. We believe this work anticipates an important trend away from purely syntactic-based methods for program analysis to semantic methods based on symbolic processing and inference technology. Other results demonstrating the practical use of automatic inference is being reported in hardware verification, although there are significant differences between the hardware work and ours. However, what is common and important is that general purpose theorem provers are being integrated with more special-purpose decision procedures to solve problems in analysis and verification. We are pursuina commercial opportunities for this work, and will use and extend the work in other projects we are engaged in. Ultimately we would like to rework the system to analyze C, C++, or Java as a key step toward commercialization.

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.

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.

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.

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

Simplified, inverse, ejector design tool

NASA Technical Reports Server (NTRS)

Dechant, Lawrence J.

1993-01-01

A simple lumped parameter based inverse design tool has been developed which provides flow path geometry and entrainment estimates subject to operational, acoustic, and design constraints. These constraints are manifested through specification of primary mass flow rate or ejector thrust, fully-mixed exit velocity, and static pressure matching. Fundamentally, integral forms of the conservation equations coupled with the specified design constraints are combined to yield an easily invertible linear system in terms of the flow path cross-sectional areas. Entrainment is computed by back substitution. Initial comparison with experimental and analogous one-dimensional methods show good agreement. Thus, this simple inverse design code provides an analytically based, preliminary design tool with direct application to High Speed Civil Transport (HSCT) design studies.

Specification and Error Pattern Based Program Monitoring

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Johnson, Scott; Rosu, Grigore; Clancy, Daniel (Technical Monitor)

2001-01-01

We briefly present Java PathExplorer (JPAX), a tool developed at NASA Ames for monitoring the execution of Java programs. JPAX can be used not only during program testing to reveal subtle errors, but also can be applied during operation to survey safety critical systems. The tool facilitates automated instrumentation of a program in order to properly observe its execution. The instrumentation can be either at the bytecode level or at the source level when the source code is available. JPaX is an instance of a more general project, called PathExplorer (PAX), which is a basis for experiments rather than a fixed system, capable of monitoring various programming languages and experimenting with other logics and analysis techniques

PathScore: a web tool for identifying altered pathways in cancer data.

PubMed

Gaffney, Stephen G; Townsend, Jeffrey P

2016-12-01

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects. Web application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at: github.com/sggaffney/pathscore with a GPLv3 license. stephen.gaffney@yale.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Electro-Optic Propagation

DTIC Science & Technology

2002-09-30

Electro - Optic Propagation Stephen Doss-Hammel SPAWARSYSCEN San Diego code 2858 49170 Propagation Path San Diego, CA 92152-7385 phone: (619...OBJECTIVES The electro - optical propagation objectives are: 1) The acquisition and analysis of mid-wave and long-wave infrared transmission and...elements to the electro - optical propagation model development. The first element is the design and execution of field experiments to generate useful

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).

Report of experiments and evidence for ASC L2 milestone 4467 : demonstration of a legacy application's path to exascale.

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

Curry, Matthew L.; Ferreira, Kurt Brian; Pedretti, Kevin Thomas Tauke

2012-03-01

This report documents thirteen of Sandia's contributions to the Computational Systems and Software Environment (CSSE) within the Advanced Simulation and Computing (ASC) program between fiscal years 2009 and 2012. It describes their impact on ASC applications. Most contributions are implemented in lower software levels allowing for application improvement without source code changes. Improvements are identified in such areas as reduced run time, characterizing power usage, and Input/Output (I/O). Other experiments are more forward looking, demonstrating potential bottlenecks using mini-application versions of the legacy codes and simulating their network activity on Exascale-class hardware. The purpose of this report is to provemore » that the team has completed milestone 4467-Demonstration of a Legacy Application's Path to Exascale. Cielo is expected to be the last capability system on which existing ASC codes can run without significant modifications. This assertion will be tested to determine where the breaking point is for an existing highly scalable application. The goal is to stretch the performance boundaries of the application by applying recent CSSE RD in areas such as resilience, power, I/O, visualization services, SMARTMAP, lightweight LWKs, virtualization, simulation, and feedback loops. Dedicated system time reservations and/or CCC allocations will be used to quantify the impact of system-level changes to extend the life and performance of the ASC code base. Finally, a simulation of anticipated exascale-class hardware will be performed using SST to supplement the calculations. Determine where the breaking point is for an existing highly scalable application: Chapter 15 presented the CSSE work that sought to identify the breaking point in two ASC legacy applications-Charon and CTH. Their mini-app versions were also employed to complete the task. There is no single breaking point as more than one issue was found with the two codes. The results were that applications can expect to encounter performance issues related to the computing environment, system software, and algorithms. Careful profiling of runtime performance will be needed to identify the source of an issue, in strong combination with knowledge of system software and application source code.« less

Preserving Envelope Efficiency in Performance Based Code Compliance

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

Thornton, Brian A.; Sullivan, Greg P.; Rosenberg, Michael I.

2015-06-20

The City of Seattle 2012 Energy Code (Seattle 2014), one of the most progressive in the country, is under revision for its 2015 edition. Additionally, city personnel participate in the development of the next generation of the Washington State Energy Code and the International Energy Code. Seattle has pledged carbon neutrality by 2050 including buildings, transportation and other sectors. The United States Department of Energy (DOE), through Pacific Northwest National Laboratory (PNNL) provided technical assistance to Seattle in order to understand the implications of one potential direction for its code development, limiting trade-offs of long-lived building envelope components less stringentmore » than the prescriptive code envelope requirements by using better-than-code but shorter-lived lighting and heating, ventilation, and air-conditioning (HVAC) components through the total building performance modeled energy compliance path. Weaker building envelopes can permanently limit building energy performance even as lighting and HVAC components are upgraded over time, because retrofitting the envelope is less likely and more expensive. Weaker building envelopes may also increase the required size, cost and complexity of HVAC systems and may adversely affect occupant comfort. This report presents the results of this technical assistance. The use of modeled energy code compliance to trade-off envelope components with shorter-lived building components is not unique to Seattle and the lessons and possible solutions described in this report have implications for other jurisdictions and energy codes.« less

Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

DTIC Science & Technology

2017-03-24

NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for