Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

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Mark A Olson

Full Text Available A central problem of computational structural biology is the refinement of modeled protein structures taken from either comparative modeling or knowledge-based methods. Simulations are commonly used to achieve higher resolution of the structures at the all-atom level, yet methodologies that consistently yield accurate results remain elusive. In this work, we provide an assessment of an adaptive temperature-based replica exchange simulation method where the temperature clients dynamically walk in temperature space to enrich their population and exchanges near steep energetic barriers. This approach is compared to earlier work of applying the conventional method of static temperature clients to refine a dataset of conformational decoys. Our results show that, while an adaptive method has many theoretical advantages over a static distribution of client temperatures, only limited improvement was gained from this strategy in excursions of the downhill refinement regime leading to an increase in the fraction of native contacts. To illustrate the sampling differences between the two simulation methods, energy landscapes are presented along with their temperature client profiles.

Designed-walk replica-exchange method for simulations of complex systems

OpenAIRE

Urano, Ryo; Okamoto, Yuko

2015-01-01

We propose a new implementation of the replica-exchange method (REM) in which replicas follow a pre-planned route in temperature space instead of a random walk. Our method satisfies the detailed balance condition in the proposed route. The method forces tunneling events between the highest and lowest temperatures to happen with an almost constant period. The number of tunneling counts is proportional to that of the random-walk REM multiplied by the square root of moving distance in temperatur...

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

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Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor

2018-03-01

The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.

Bayesian ensemble refinement by replica simulations and reweighting

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Hummer, Gerhard; Köfinger, Jürgen

2015-12-01

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation.

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Sidler, Dominik; Schwaninger, Arthur; Riniker, Sereina

2016-10-21

In molecular dynamics (MD) simulations, free-energy differences are often calculated using free energy perturbation or thermodynamic integration (TI) methods. However, both techniques are only suited to calculate free-energy differences between two end states. Enveloping distribution sampling (EDS) presents an attractive alternative that allows to calculate multiple free-energy differences in a single simulation. In EDS, a reference state is simulated which "envelopes" the end states. The challenge of this methodology is the determination of optimal reference-state parameters to ensure equal sampling of all end states. Currently, the automatic determination of the reference-state parameters for multiple end states is an unsolved issue that limits the application of the methodology. To resolve this, we have generalised the replica-exchange EDS (RE-EDS) approach, introduced by Lee et al. [J. Chem. Theory Comput. 10, 2738 (2014)] for constant-pH MD simulations. By exchanging configurations between replicas with different reference-state parameters, the complexity of the parameter-choice problem can be substantially reduced. A new robust scheme to estimate the reference-state parameters from a short initial RE-EDS simulation with default parameters was developed, which allowed the calculation of 36 free-energy differences between nine small-molecule inhibitors of phenylethanolamine N-methyltransferase from a single simulation. The resulting free-energy differences were in excellent agreement with values obtained previously by TI and two-state EDS simulations.

Replica Exchange Simulations of the Thermodynamics of Aβ Fibril Growth

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Takeda, Takako; Klimov, Dmitri K.

2009-01-01

Abstract Replica exchange molecular dynamics and an all-atom implicit solvent model are used to probe the thermodynamics of deposition of Alzheimer's Aβ monomers on preformed amyloid fibrils. Consistent with the experiments, two deposition stages have been identified. The docking stage occurs over a wide temperature range, starting with the formation of the first peptide-fibril interactions at 500 K. Docking is completed when a peptide fully adsorbs on the fibril edge at the temperature of 380 K. The docking transition appears to be continuous, and occurs without free energy barriers or intermediates. During docking, incoming Aβ monomer adopts a disordered structure on the fibril edge. The locking stage occurs at the temperature of ≈360 K and is characterized by the rugged free energy landscape. Locking takes place when incoming Aβ peptide forms a parallel β-sheet structure on the fibril edge. Because the β-sheets formed by locked Aβ peptides are typically off-registry, the structure of the locked phase differs from the structure of the fibril interior. The study also reports that binding affinities of two distinct fibril edges with respect to incoming Aβ peptides are different. The peptides bound to the concave edge have significantly lower free energy compared to those bound on the convex edge. Comparison with the available experimental data is discussed. PMID:19167295

Conformational Ensembles of α-Synuclein Derived Peptide with Different Osmolytes from Temperature Replica Exchange Sampling

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Salma Jamal

2017-12-01

Full Text Available Intrinsically disordered proteins (IDP are a class of proteins that do not have a stable three-dimensional structure and can adopt a range of conformations playing various vital functional role. Alpha-synuclein is one such IDP which can aggregate into toxic protofibrils and has been associated largely with Parkinson's disease (PD along with other neurodegenerative diseases. Osmolytes are small organic compounds that can alter the environment around the proteins by acting as denaturants or protectants for the proteins. In the present study, we have conducted a series of replica exchange molecular dynamics simulations to explore the role of osmolytes, urea which is a denaturant and TMAO (trimethylamine N-oxide, a protecting osmolyte, in aggregation and conformations of the synuclein peptide. We observed that both the osmolytes have significantly distinct impacts on the peptide and led to transitions of the conformations of the peptide from one state to other. Our findings highlighted that urea attenuated peptide aggregation and resulted in the formation of extended peptide structures whereas TMAO led to compact and folded forms of the peptide.

Difficult Sudoku Puzzles Created by Replica Exchange Monte Carlo Method

OpenAIRE

Watanabe, Hiroshi

2013-01-01

An algorithm to create difficult Sudoku puzzles is proposed. An Ising spin-glass like Hamiltonian describing difficulty of puzzles is defined, and difficult puzzles are created by minimizing the energy of the Hamiltonian. We adopt the replica exchange Monte Carlo method with simultaneous temperature adjustments to search lower energy states efficiently, and we succeed in creating a puzzle which is the world hardest ever created in our definition, to our best knowledge. (Added on Mar. 11, the ...

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

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Lu, Qing; Kim, Jaegil; Straub, John E

2013-03-14

The generalized Replica Exchange Method (gREM) is extended into the isobaric-isothermal ensemble, and applied to simulate a vapor-liquid phase transition in Lennard-Jones fluids. Merging an optimally designed generalized ensemble sampling with replica exchange, gREM is particularly well suited for the effective simulation of first-order phase transitions characterized by "backbending" in the statistical temperature. While the metastable and unstable states in the vicinity of the first-order phase transition are masked by the enthalpy gap in temperature replica exchange method simulations, they are transformed into stable states through the parameterized effective sampling weights in gREM simulations, and join vapor and liquid phases with a succession of unimodal enthalpy distributions. The enhanced sampling across metastable and unstable states is achieved without the need to identify a "good" order parameter for biased sampling. We performed gREM simulations at various pressures below and near the critical pressure to examine the change in behavior of the vapor-liquid phase transition at different pressures. We observed a crossover from the first-order phase transition at low pressure, characterized by the backbending in the statistical temperature and the "kink" in the Gibbs free energy, to a continuous second-order phase transition near the critical pressure. The controlling mechanisms of nucleation and continuous phase transition are evident and the coexistence properties and phase diagram are found in agreement with literature results.

Effects of the Pathogenic Mutation A117V and the Protective Mutation H111S on the Folding and Aggregation of PrP106-126: Insights from Replica Exchange Molecular Dynamics Simulations.

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Lulu Ning

Full Text Available The fragment 106-126 of prion protein exhibits similar properties to full-length prion. Experiments have shown that the A117V mutation enhances the aggregation of PrP106-126, while the H111S mutation abolishes the assembly. However, the mechanism of the change in the aggregation behavior of PrP106-126 upon the two mutations is not fully understood. In this study, replica exchange molecular dynamics simulations were performed to investigate the conformational ensemble of the WT PrP106-126 and its two mutants A117V and H111S. The obtained results indicate that the three species are all intrinsically disordered but they have distinct morphological differences. The A117V mutant has a higher propensity to form β-hairpin structures than the WT, while the H111S mutant has a higher population of helical structures. Furthermore, the A117V mutation increases the hydrophobic solvent accessible surface areas of PrP106-126 and the H111S mutation reduces the exposure of hydrophobic residues. It can be concluded that the difference in populations of β-hairpin structures and the change of hydrophobic solvent accessible areas may induce the different aggregation behaviors of the A117V and the H111S mutated PrP106-126. Understanding why the two mutations have contrary effects on the aggregation of PrP106-126 is very meaningful for further elucidation of the mechanism underlying aggregation and design of inhibitor against aggregation process.

Long-time atomistic simulations with the Parallel Replica Dynamics method

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Perez, Danny

Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

Fast Optimal Replica Placement with Exhaustive Search Using Dynamically Reconfigurable Processor

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Hidetoshi Takeshita

2011-01-01

Full Text Available This paper proposes a new replica placement algorithm that expands the exhaustive search limit with reasonable calculation time. It combines a new type of parallel data-flow processor with an architecture tuned for fast calculation. The replica placement problem is to find a replica-server set satisfying service constraints in a content delivery network (CDN. It is derived from the set cover problem which is known to be NP-hard. It is impractical to use exhaustive search to obtain optimal replica placement in large-scale networks, because calculation time increases with the number of combinations. To reduce calculation time, heuristic algorithms have been proposed, but it is known that no heuristic algorithm is assured of finding the optimal solution. The proposed algorithm suits parallel processing and pipeline execution and is implemented on DAPDNA-2, a dynamically reconfigurable processor. Experiments show that the proposed algorithm expands the exhaustive search limit by the factor of 18.8 compared to the conventional algorithm search limit running on a Neumann-type processor.

Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.

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Wang, Hongrui; Liu, Hongwei; Cai, Leixin; Wang, Caixia; Lv, Qiang

2017-07-10

In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein-small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (MC) and REMC sampling methods, these methods use multi-objective optimization Pareto front information to facilitate the selection of replicas for exchange. The Pareto front information generated to select lower energy conformations as representative conformation structure replicas can facilitate the convergence of the available conformational space, including available near-native structures. Furthermore, our approach directly provides min-min scenario Pareto optimal solutions, as well as a hybrid of the min-min and max-min scenario Pareto optimal solutions with lower energy conformations for use as structure templates in the REMC sampling method. These methods were validated based on a thorough analysis of a benchmark data set containing 16 benchmark test cases. An in-depth comparison between MC, REMC, multi-objective optimization-REMC (MO-REMC), and hybrid MO-REMC (HMO-REMC) sampling methods was performed to illustrate the differences between the four conformational search strategies. Our findings demonstrate that the MO-REMC and HMO-REMC conformational sampling methods are powerful approaches for obtaining protein-small molecule docking conformational predictions based on the binding energy of complexes in RosettaLigand.

Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

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Khavrutskii, Ilja V; Wallqvist, Anders

2010-11-09

This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.

Dynamical self-arrest in symmetric and asymmetric diblock copolymer melts using a replica approach within a local theory.

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Wu, Sangwook

2009-03-01

We investigate dynamical self-arrest in a diblock copolymer melt using a replica approach within a self-consistent local method based on dynamical mean-field theory (DMFT). The local replica approach effectively predicts (chiN)_{A} for dynamical self-arrest in a block copolymer melt for symmetric and asymmetric cases. We discuss the competition of the cubic and quartic interactions in the Landau free energy for a block copolymer melt in stabilizing a glassy state depending on the chain length. Our local replica theory provides a universal value for the dynamical self-arrest in block copolymer melts with (chiN)_{A} approximately 10.5+64N;{-3/10} for the symmetric case.

New force replica exchange method and protein folding pathways probed by force-clamp technique.

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Kouza, Maksim; Hu, Chin-Kun; Li, Mai Suan

2008-01-28

We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. This new approach was applied to obtain the force-temperature phase diagram and other thermodynamical quantities of the three-domain ubiquitin. Using the C(alpha)-Go model and the Langevin dynamics, we have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multidomain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the polyubiquitin or a single domain with the C terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiquitin, using the microscopic theory for the dependence of unfolding time on the external force. The linkage between residue Lys48 and the C terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multidomain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations.

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Capelli, Riccardo; Tiana, Guido; Camilloni, Carlo

2018-05-14

Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimental data, and it has been shown that replica-averaged simulations, restrained using a static potential, are a practical and powerful implementation of such a principle. Here we show that replica-averaged simulations restrained using a time-dependent potential are equivalent to the principle of maximum caliber, the dynamic version of the principle of maximum entropy, and thus may allow us to integrate time-resolved data in molecular dynamics simulations. We provide an analytical proof of the equivalence as well as a computational validation making use of simple models and synthetic data. Some limitations and possible solutions are also discussed.

Folding very short peptides using molecular dynamics.

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Bosco K Ho

2006-04-01

Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins.

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Lee, Kuo Hao; Chen, Jianhan

2017-11-15

Recasting temperature replica exchange (T-RE) as a special case of Gibbs sampling has led to a simple and efficient scheme for enhanced mixing (Chodera and Shirts, J. Chem. Phys., 2011, 135, 194110). To critically examine if T-RE with independence sampling (T-REis) improves conformational sampling, we performed T-RE and T-REis simulations of ordered and disordered proteins using coarse-grained and atomistic models. The results demonstrate that T-REis effectively increase the replica mobility in temperatures space with minimal computational overhead, especially for folded proteins. However, enhanced mixing does not translate well into improved conformational sampling. The convergences of thermodynamic properties interested are similar, with slight improvements for T-REis of ordered systems. The study re-affirms the efficiency of T-RE does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational re-arrangements. Due to its simplicity and efficacy of enhanced mixing, T-REis is expected to be more effective when incorporated with various Hamiltonian-RE protocols. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Color molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Hatsuda, Tetsuo

2000-01-01

We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

Systematic expansion in the order parameter for replica theory of the dynamical glass transition.

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Jacquin, Hugo; Zamponi, Francesco

2013-03-28

It has been shown recently that predictions from mode-coupling theory for the glass transition of hard-spheres become increasingly bad when dimensionality increases, whereas replica theory predicts a correct scaling. Nevertheless if one focuses on the regime around the dynamical transition in three dimensions, mode-coupling results are far more convincing than replica theory predictions. It seems thus necessary to reconcile the two theoretic approaches in order to obtain a theory that interpolates between low-dimensional, mode-coupling results, and "mean-field" results from replica theory. Even though quantitative results for the dynamical transition issued from replica theory are not accurate in low dimensions, two different approximation schemes--small cage expansion and replicated hyper-netted-chain (RHNC)--provide the correct qualitative picture for the transition, namely, a discontinuous jump of a static order parameter from zero to a finite value. The purpose of this work is to develop a systematic expansion around the RHNC result in powers of the static order parameter, and to calculate the first correction in this expansion. Interestingly, this correction involves the static three-body correlations of the liquid. More importantly, we separately demonstrate that higher order terms in the expansion are quantitatively relevant at the transition, and that the usual mode-coupling kernel, involving two-body direct correlation functions of the liquid, cannot be recovered from static computations.

Sensitivity of molecular vibrational dynamics to energy exchange rate constants

International Nuclear Information System (INIS)

Billing, G D; Coletti, C; Kurnosov, A K; Napartovich, A P

2003-01-01

The sensitivity of molecular vibrational population dynamics, governing the CO laser operated in fundamental and overtone transitions, to vibration-to-vibration rate constants is investigated. With this aim, three rate constant sets have been used, differing in their completeness (i.e. accounting for single-quantum exchange only, or for multi-quantum exchange with a limited number of rate constants obtained by semiclassical calculations, and, finally, with an exhaustive set of rate constants including asymmetric exchange processes, as well) and in the employed interaction potential. The most complete set among these three is introduced in this paper. An existing earlier kinetic model was updated to include the latter new data. Comparison of data produced by kinetic modelling with the above mentioned sets of rate constants shows that the vibrational distribution function, and, in particular, the CO overtone laser characteristics, are very sensitive to the choice of the model. The most complete model predicts slower evolution of the vibrational distribution, in qualitative agreement with experiments

Phonon replica dynamics in high quality GaN epilayers and AlGaN/GaN quantum wells

Energy Technology Data Exchange (ETDEWEB)

Alderighi, D.; Vinattieri, A.; Colocci, M. [Ist. Nazionale Fisica della Materia, Firenze (Italy); Dipt. di Fisica and LENS, Firenze (Italy); Bogani, F. [Ist. Nazionale Fisica della Materia, Firenze (Italy); Dipt. di Energetica, Firenze (Italy); Gottardo, S. [Dipt. di Fisica and LENS, Firenze (Italy); Grandjean, N.; Massies, J. [Centre de Recherche sur l' Hetero-Epitaxie et ses Applications, CNRS, Valbonne (France)

2001-01-01

We present an experimental study of the exciton and phonon replica dynamics in high quality GaN epilayers and AlGaN/GaN quantum wells (QW) by means of picosecond time-resolved photoluminescence (PL) measurements. A non-exponential decay is observed both at the zero phonon line (ZPL) and at the n = 1 LO replica. Time-resolved spectra unambiguously assign the replica to the free exciton A recombination. Optical migration effects are detected both in the epilayer and the QWs samples and disappear as the temperature increases up to 60-90 K. Even though the sample quality is comparable to state-of-the-art samples, localization effects dominate the exciton dynamics at low temperature in the studied GaN based structures. (orig.)

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

Science.gov (United States)

Paschek, Dietmar; Nymeyer, Hugh; García, Angel E

2007-03-01

We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

Calculation of absolute protein-ligand binding free energy using distributed replica sampling.

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Rodinger, Tomas; Howell, P Lynne; Pomès, Régis

2008-10-21

Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

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Wallace, Jason A; Shen, Jana K

2012-11-14

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

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Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

2015-10-26

Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

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Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

Dynamics of ligand exchange mechanism at Cu(II) in water: an ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region.

Science.gov (United States)

Moin, Syed Tarique; Hofer, Thomas S; Weiss, Alexander K H; Rode, Bernd M

2013-07-07

Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment.

Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region

International Nuclear Information System (INIS)

Moin, Syed Tarique; Hofer, Thomas S.; Weiss, Alexander K. H.; Rode, Bernd M.

2013-01-01

Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

Science.gov (United States)

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

On the coupling between molecular diffusion and solvation shell exchange

DEFF Research Database (Denmark)

Møller, Klaus Braagaard; Rey, Rossend; Masia, Marco

2005-01-01

The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li+ and Na+ ions, and for liquid argon. First, two methods...

Ultrafast dynamics of hydrogen bond exchange in aqueous ionic solutions.

Science.gov (United States)

Park, Sungnam; Odelius, Michael; Gaffney, Kelly J

2009-06-04

The structural and dynamical properties of aqueous ionic solutions influence a wide range of natural and biological processes. In these solutions, water has the opportunity to form hydrogen bonds with other water molecules and anions. Knowing the time scale with which these configurations interconvert represents a key factor to understanding the influence of molecular scale heterogeneity on chemical events in aqueous ionic solutions. We have used ultrafast IR spectroscopy and Car-Parrinello molecular dynamics (CPMD) simulations to investigate the hydrogen bond (H-bond) structural dynamics in aqueous 6 M sodium perchlorate (NaClO4) solution. We have measured the H-bond exchange dynamics between spectrally distinct water-water and water-anion H-bond configurations with 2DIR spectroscopy and the orientational relaxation dynamics of water molecules in different H-bond configurations with polarization-selective IR pump-probe experiments. The experimental H-bond exchange time correlates strongly with the experimental orientational relaxation time of water molecules. This agrees with prior observations in water and aqueous halide solutions, and has been interpreted within the context of an orientational jump model for the H-bond exchange. The CPMD simulations performed on aqueous 6 M NaClO4 solution clearly demonstrate that water molecules organize into two radially and angularly distinct structural subshells within the first solvation shell of the perchlorate anion, with one subshell possessing the majority of the water molecules that donate H-bonds to perchlorate anions and the other subshell possessing predominantly water molecules that donate two H-bonds to other water molecules. Due to the high ionic concentration used in the simulations, essentially all water molecules reside in the first ionic solvation shells. The CPMD simulations also demonstrate that the molecular exchange between these two structurally distinct subshells proceeds more slowly than the H

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States); Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States)

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

Directory of Open Access Journals (Sweden)

Moye Wang

2016-04-01

Full Text Available As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

Replicas Strategy and Cache Optimization of Video Surveillance Systems Based on Cloud Storage

Directory of Open Access Journals (Sweden)

Rongheng Li

2018-04-01

Full Text Available With the rapid development of video surveillance technology, especially the popularity of cloud-based video surveillance applications, video data begins to grow explosively. However, in the cloud-based video surveillance system, replicas occupy an amount of storage space. Also, the slow response to video playback constrains the performance of the system. In this paper, considering the characteristics of video data comprehensively, we propose a dynamic redundant replicas mechanism based on security levels that can dynamically adjust the number of replicas. Based on the location correlation between cameras, this paper also proposes a data cache strategy to improve the response speed of data reading. Experiments illustrate that: (1 our dynamic redundant replicas mechanism can save storage space while ensuring data security; (2 the cache mechanism can predict the playback behaviors of the users in advance and improve the response speed of data reading according to the location and time correlation of the front-end cameras; and (3 in terms of cloud-based video surveillance, our proposed approaches significantly outperform existing methods.

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

Science.gov (United States)

Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

2017-09-30

GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A Multicontrolled Enamine Configurational Switch Undergoing Dynamic Constitutional Exchange.

Science.gov (United States)

Ren, Yansong; Svensson, Per H; Ramström, Olof

2018-05-22

A multiresponsive enamine-based molecular switch is presented, in which forward/backward configurational rotation around the C=C bond could be precisely controlled by the addition of an acid/base or metal ions. Fluorescence turn-on/off effects and large Stokes shifts were observed while regulating the switching process with Cu II . The enamine functionality furthermore enabled double dynamic regimes, in which configurational switching could operate in conjunction with constitutional enamine exchange of the rotor part. This behavior was used to construct a prototypical dynamic covalent switch system through enamine exchange with primary amines. The dynamic exchange process could be readily turned on/off by regulating the switch status with pH. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamical replica analysis of processes on finitely connected random graphs: II. Dynamics in the Griffiths phase of the diluted Ising ferromagnet

International Nuclear Information System (INIS)

Mozeika, A; Coolen, A C C

2009-01-01

We study the Glauber dynamics of Ising spin models with random bonds, on finitely connected random graphs. We generalize a recent dynamical replica theory with which to predict the evolution of the joint spin-field distribution, to include random graphs with arbitrary degree distributions. The theory is applied to Ising ferromagnets on randomly diluted Bethe lattices, where we study the evolution of the magnetization and the internal energy. It predicts a prominent slowing down of the flow in the Griffiths phase, it suggests a further dynamical transition at lower temperatures within the Griffiths phase, and it is verified quantitatively by the results of Monte Carlo simulations

Exploring biomolecular dynamics and interactions using advanced sampling methods

International Nuclear Information System (INIS)

Luitz, Manuel; Bomblies, Rainer; Ostermeir, Katja; Zacharias, Martin

2015-01-01

Molecular dynamics (MD) and Monte Carlo (MC) simulations have emerged as a valuable tool to investigate statistical mechanics and kinetics of biomolecules and synthetic soft matter materials. However, major limitations for routine applications are due to the accuracy of the molecular mechanics force field and due to the maximum simulation time that can be achieved in current simulations studies. For improving the sampling a number of advanced sampling approaches have been designed in recent years. In particular, variants of the parallel tempering replica-exchange methodology are widely used in many simulation studies. Recent methodological advancements and a discussion of specific aims and advantages are given. This includes improved free energy simulation approaches and conformational search applications. (topical review)

Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

International Nuclear Information System (INIS)

Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

2014-01-01

Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle

DEFF Research Database (Denmark)

Grabon, Aby; Orłowski, Adam; Tripathi, Ashutosh

2017-01-01

. However, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics simulations of the mammalian StART-like PtdIns/phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical...... analyses that tested key aspects of the hypotheses generated by the molecular dynamics simulations. These studies provided five key insights into the PITPα lipid exchange cycle: (i) interaction of PITPα with the membrane is spontaneous and mediated by four specific protein substructures; (ii) the ability......Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling...

Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal.

Science.gov (United States)

Neale, Chris; Madill, Chris; Rauscher, Sarah; Pomès, Régis

2013-08-13

All molecular dynamics simulations are susceptible to sampling errors, which degrade the accuracy and precision of observed values. The statistical convergence of simulations containing atomistic lipid bilayers is limited by the slow relaxation of the lipid phase, which can exceed hundreds of nanoseconds. These long conformational autocorrelation times are exacerbated in the presence of charged solutes, which can induce significant distortions of the bilayer structure. Such long relaxation times represent hidden barriers that induce systematic sampling errors in simulations of solute insertion. To identify optimal methods for enhancing sampling efficiency, we quantitatively evaluate convergence rates using generalized ensemble sampling algorithms in calculations of the potential of mean force for the insertion of the ionic side chain analog of arginine in a lipid bilayer. Umbrella sampling (US) is used to restrain solute insertion depth along the bilayer normal, the order parameter commonly used in simulations of molecular solutes in lipid bilayers. When US simulations are modified to conduct random walks along the bilayer normal using a Hamiltonian exchange algorithm, systematic sampling errors are eliminated more rapidly and the rate of statistical convergence of the standard free energy of binding of the solute to the lipid bilayer is increased 3-fold. We compute the ratio of the replica flux transmitted across a defined region of the order parameter to the replica flux that entered that region in Hamiltonian exchange simulations. We show that this quantity, the transmission factor, identifies sampling barriers in degrees of freedom orthogonal to the order parameter. The transmission factor is used to estimate the depth-dependent conformational autocorrelation times of the simulation system, some of which exceed the simulation time, and thereby identify solute insertion depths that are prone to systematic sampling errors and estimate the lower bound of the

Marriage exchanges, seed exchanges, and the dynamics of manioc diversity.

Science.gov (United States)

Delêtre, Marc; McKey, Doyle B; Hodkinson, Trevor R

2011-11-08

The conservation of crop genetic resources requires understanding the different variables-cultural, social, and economic-that impinge on crop diversity. In small-scale farming systems, seed exchanges represent a key mechanism in the dynamics of crop genetic diversity, and analyzing the rules that structure social networks of seed exchange between farmer communities can help decipher patterns of crop genetic diversity. Using a combination of ethnobotanical and molecular genetic approaches, we investigated the relationships between regional patterns of manioc genetic diversity in Gabon and local networks of seed exchange. Spatially explicit Bayesian clustering methods showed that geographical discontinuities of manioc genetic diversity mirror major ethnolinguistic boundaries, with a southern matrilineal domain characterized by high levels of varietal diversity and a northern patrilineal domain characterized by low varietal diversity. Borrowing concepts from anthropology--kinship, bridewealth, and filiation--we analyzed the relationships between marriage exchanges and seed exchange networks in patrilineal and matrilineal societies. We demonstrate that, by defining marriage prohibitions, kinship systems structure social networks of exchange between farmer communities and influence the movement of seeds in metapopulations, shaping crop diversity at local and regional levels.

Validation of the replica trick for simple models

Science.gov (United States)

Shinzato, Takashi

2018-04-01

We discuss the replica analytic continuation using several simple models in order to prove mathematically the validity of the replica analysis, which is used in a wide range of fields related to large-scale complex systems. While replica analysis consists of two analytical techniques—the replica trick (or replica analytic continuation) and the thermodynamical limit (and/or order parameter expansion)—we focus our study on replica analytic continuation, which is the mathematical basis of the replica trick. We apply replica analysis to solve a variety of analytical models, and examine the properties of replica analytic continuation. Based on the positive results for these models we propose that replica analytic continuation is a robust procedure in replica analysis.

Increasing the power of accelerated molecular dynamics methods and plans to exploit the coming exascale

Science.gov (United States)

Voter, Arthur

Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.

Slow molecular dynamics in the β relaxation of semicrystalline polymers studied by pure exchange 13C solid state NMR

International Nuclear Information System (INIS)

Azevedo, Eduardo R. de; Becker-Guedes, Fabio; Bonagamba, Tito J.; Schmidt-Rohr, Klaus; Iowa State University, Ames, IA

2001-01-01

The dynamics in the amorphous regions of semicrystalline polymers exert important influences on mechanical properties, but have been notoriously difficult to characterize. Two new solid-state NMR techniques, PUREX (pure exchange) and CODEX (center band-only detection of exchange) NMR, make it possible to analyze the molecular motions near the glass transition in the amorphous regions of semicrystalline polymers. This is achieved by selectively suppressing the otherwise dominant signals of the static segments in the crystallites. We have applied both NMR techniques to study the slow motions near the glass transition in semicrystalline polymers (β relaxation) and in fully amorphous samples for reference. The studied polymers were isotactic poly(1-butene) (iPB1) (form I), syndiotactic and atactic polypropylenes (sPP, and aPP, respectively), as well as polyisobutylene (PIB). We have analyzed the geometry and time scale of the slow molecular motion for all samples and determined the apparent activation energies. (author)

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

Czech Academy of Sciences Publication Activity Database

Šponer, Jiří; Banáš, P.; Jurečka, P.; Zgarbová, M.; Kührová, P.; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, M.

2014-01-01

Roč. 5, č. 10 (2014), s. 1771-1782 ISSN 1948-7185 R&D Projects: GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : DELTA-VIRUS RIBOZYME * AMBER FORCE-FIELD * REPLICA-EXCHANGE METHOD Subject RIV: BO - Biophysics Impact factor: 7.458, year: 2014

Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

International Nuclear Information System (INIS)

Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

2014-01-01

In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW 12 O 40 3− , as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

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

Science.gov (United States)

Wang, Ting; Plecháč, Petr

2017-12-01

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

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

Science.gov (United States)

Wang, Ting; Plecháč, Petr

2017-12-21

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

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

Science.gov (United States)

Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

2018-01-01

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield

Merging constitutional and motional covalent dynamics in reversible imine formation and exchange processes.

Science.gov (United States)

Kovaříček, Petr; Lehn, Jean-Marie

2012-06-06

The formation and exchange processes of imines of salicylaldehyde, pyridine-2-carboxaldehyde, and benzaldehyde have been studied, showing that the former has features of particular interest for dynamic covalent chemistry, displaying high efficiency and fast rates. The monoimines formed with aliphatic α,ω-diamines display an internal exchange process of self-transimination type, inducing a local motion of either "stepping-in-place" or "single-step" type by bond interchange, whose rate decreases rapidly with the distance of the terminal amino groups. Control of the speed of the process over a wide range may be achieved by substituents, solvent composition, and temperature. These monoimines also undergo intermolecular exchange, thus merging motional and constitutional covalent behavior within the same molecule. With polyamines, the monoimines formed execute internal motions that have been characterized by extensive one-dimensional, two-dimensional, and EXSY proton NMR studies. In particular, with linear polyamines, nondirectional displacement occurs by shifting of the aldehyde residue along the polyamine chain serving as molecular track. Imines thus behave as simple prototypes of systems displaying relative motions of molecular moieties, a subject of high current interest in the investigation of synthetic and biological molecular motors. The motional processes described are of dynamic covalent nature and take place without change in molecular constitution. They thus represent a category of dynamic covalent motions, resulting from reversible covalent bond formation and dissociation. They extend dynamic covalent chemistry into the area of molecular motions. A major further step will be to achieve control of directionality. The results reported here for imines open wide perspectives, together with other chemical groups, for the implementation of such features in multifunctional molecules toward the design of molecular devices presenting a complex combination of

Hyper-V Replica essentials

CERN Document Server

Krstevski, Vangel

2013-01-01

a in various deployment scenarios.Hyper-V Replica Essentials is for Windows Server administrators who want to improve their system availability and speed up disaster recovery. You will need experience in Hyper-V deployment because Hyper-V Replica is built in the Hyper-V platform.

Replica treatment of the Calogero-Sutherland model

International Nuclear Information System (INIS)

Gangardt, Dimitry M.; Kamenev, Alex

2001-01-01

Employing Forrester-Ha method of Jack polynomials, we derive an integral identity connecting certain N-fold coordinate average of the Calogero-Sutherland model with the n-fold replica integral. Subsequent analytical continuation in n leads to asymptotic expressions for the (static and dynamic) density-density correlation function of the model as well as the Green's function for an arbitrary coupling constant λ

A replica exchange transition interface sampling method with multiple interface sets for investigating networks of rare events

Science.gov (United States)

Swenson, David W. H.; Bolhuis, Peter G.

2014-07-01

The multiple state transition interface sampling (TIS) framework in principle allows the simulation of a large network of complex rare event transitions, but in practice suffers from convergence problems. To improve convergence, we combine multiple state TIS [J. Rogal and P. G. Bolhuis, J. Chem. Phys. 129, 224107 (2008)] with replica exchange TIS [T. S. van Erp, Phys. Rev. Lett. 98, 268301 (2007)]. In addition, we introduce multiple interface sets, which allow more than one order parameter to be defined for each state. We illustrate the methodology on a model system of multiple independent dimers, each with two states. For reaction networks with up to 64 microstates, we determine the kinetics in the microcanonical ensemble, and discuss the convergence properties of the sampling scheme. For this model, we find that the kinetics depend on the instantaneous composition of the system. We explain this dependence in terms of the system's potential and kinetic energy.

Molecular dynamics simulation of radiation grafted FEP films as proton exchange membranes: Effects of the side chain length

DEFF Research Database (Denmark)

Li, Xue; Zhao, Yang; Li, Weiwei

2017-01-01

In order to study the microstructure of the prepared potential proton exchange membrane (PEM), molecular dynamics (MD) simulations were used to lucubrate the transport behavior of water molecules and hydronium ions inside the hydrated sulfonated styrene grafted fluorinated ethylene propylene (FEP...... whereas larger water clusters formed. The results of the mean square displacements (MSDs) show that the proton conductivities of the membranes with the proposed side chain lengths were about three fifths of the experimental data, of which the membrane with side chain length of 7 sulfonic styrene units...... was supposed to exhibit the highest proton conductivity, that is 115.69 mS cm-1. All of the supposed membrane models presented good proton conductivity that could definitely meet the application requirements of the proton exchange membranes. The MD simulations can provide an insight to the chain structure...

A Validation Study of the Impression Replica Technique.

Science.gov (United States)

Segerström, Sofia; Wiking-Lima de Faria, Johanna; Braian, Michael; Ameri, Arman; Ahlgren, Camilla

2018-04-17

To validate the well-known and often-used impression replica technique for measuring fit between a preparation and a crown in vitro. The validation consisted of three steps. First, a measuring instrument was validated to elucidate its accuracy. Second, a specimen consisting of male and female counterparts was created and validated by the measuring instrument. Calculations were made for the exact values of three gaps between the male and female. Finally, impression replicas were produced of the specimen gaps and sectioned into four pieces. The replicas were then measured with the use of a light microscope. The values received from measuring the specimen were then compared with the values received from the impression replicas, and the technique was thereby validated. The impression replica technique overvalued all measured gaps. Depending on location of the three measuring sites, the difference between the specimen and the impression replicas varied from 47 to 130 μm. The impression replica technique overestimates gaps within the range of 2% to 11%. The validation of the replica technique enables the method to be used as a reference when testing other methods for evaluating fit in dentistry. © 2018 by the American College of Prosthodontists.

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

Science.gov (United States)

Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

2017-10-12

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

Replica scaling studies of hard missile impacts on reinforced concrete

International Nuclear Information System (INIS)

Barr, P.; Carter, P.G.; Howe, W.D.; Neilson, A.J.

1982-01-01

Missile and target combinations at three different liners scales have been used in an experimental assessment of the applicability of replica scaling to the dynamic behaviour of reinforced concrete structures impacted by rigid missiles. Experimental results are presented for models with relative linear scales of 1, 0.37 and 0.12. (orig.) [de

Modeling Vocal Fold Intravascular Flow using Synthetic Replicas

Science.gov (United States)

Terry, Aaron D.; Ricks, Matthew T.; Thomson, Scott L.

2017-11-01

Vocal fold vibration that is induced by air flowing from the lungs is believed to decrease blood flow through the vocal folds. This is important due to the critical role of blood flow in maintaining tissue health. However, the precise mechanical relationships between vocal fold vibration and blood perfusion remain understudied. A platform for studying liquid perfusion in a synthetic, life-size, self-oscillating vocal fold replica has recently been developed. The replicas are fabricated using molded silicone with material properties comparable to those of human vocal fold tissues and that include embedded microchannels through which liquid is perfused. The replicas are mounted on an air flow supply tube to initiate flow-induced vibration. A liquid reservoir is attached to the microchannel to cause liquid to perfuse through replica in the anterior-posterior direction. As replica vibration is initiated and amplitude increases, perfusion flow rate decreases. In this presentation, the replica design will be presented, along with data quantifying the relationships between parameters such as replica vibration amplitude, stiffness, microchannel diameter, and perfusion flow rate. This work was supported by Grant NIDCD R01DC005788 from the National Institutes of Health.

Functional Dynamics of Hexameric Helicase Probed by Hydrogen Exchange and Simulation

Science.gov (United States)

Radou, Gaël; Dreyer, Frauke N.; Tuma, Roman; Paci, Emanuele

2014-01-01

The biological function of large macromolecular assemblies depends on their structure and their dynamics over a broad range of timescales; for this reason, it is a significant challenge to investigate these assemblies using conventional experimental techniques. One of the most promising experimental techniques is hydrogen-deuterium exchange detected by mass spectrometry. Here, we describe to our knowledge a new computational method for quantitative interpretation of deuterium exchange kinetics and apply it to a hexameric viral helicase P4 that unwinds and translocates RNA into a virus capsid at the expense of ATP hydrolysis. Room-temperature dynamics probed by a hundred nanoseconds of all-atom molecular dynamics simulations is sufficient to predict the exchange kinetics of most sequence fragments and provide a residue-level interpretation of the low-resolution experimental results. The strategy presented here is also a valuable tool to validate experimental data, e.g., assignments, and to probe mechanisms that cannot be observed by x-ray crystallography, or that occur over timescales longer than those that can be realistically simulated, such as the opening of the hexameric ring. PMID:25140434

From cellulose to kerogen: molecular simulation of a geological process.

Science.gov (United States)

Atmani, Lea; Bichara, Christophe; Pellenq, Roland J-M; Van Damme, Henri; van Duin, Adri C T; Raza, Zamaan; Truflandier, Lionel A; Obliger, Amaël; Kralert, Paul G; Ulm, Franz J; Leyssale, Jean-Marc

2017-12-01

The process by which organic matter decomposes deep underground to form petroleum and its underlying kerogen matrix has so far remained a no man's land to theoreticians, largely because of the geological (Myears) timescale associated with the process. Using reactive molecular dynamics and an accelerated simulation framework, the replica exchange molecular dynamics method, we simulate the full transformation of cellulose into kerogen and its associated fluid phase under prevailing geological conditions. We observe in sequence the fragmentation of the cellulose crystal and production of water, the development of an unsaturated aliphatic macromolecular phase and its aromatization. The composition of the solid residue along the maturation pathway strictly follows what is observed for natural type III kerogen and for artificially matured samples under confined conditions. After expulsion of the fluid phase, the obtained microporous kerogen possesses the structure, texture, density, porosity and stiffness observed for mature type III kerogen and a microporous carbon obtained by saccharose pyrolysis at low temperature. As expected for this variety of precursor, the main resulting hydrocarbon is methane. The present work thus demonstrates that molecular simulations can now be used to assess, almost quantitatively, such complex chemical processes as petrogenesis in fossil reservoirs and, more generally, the possible conversion of any natural product into bio-sourced materials and/or fuel.

Molecular digital pathology: progress and potential of exchanging molecular data.

Science.gov (United States)

Roy, Somak; Pfeifer, John D; LaFramboise, William A; Pantanowitz, Liron

2016-09-01

Many of the demands to perform next generation sequencing (NGS) in the clinical laboratory can be resolved using the principles of telepathology. Molecular telepathology can allow facilities to outsource all or a portion of their NGS operation such as cloud computing, bioinformatics pipelines, variant data management, and knowledge curation. Clinical pathology laboratories can electronically share diverse types of molecular data with reference laboratories, technology service providers, and/or regulatory agencies. Exchange of electronic molecular data allows laboratories to perform validation of rare diseases using foreign data, check the accuracy of their test results against benchmarks, and leverage in silico proficiency testing. This review covers the emerging subject of molecular telepathology, describes clinical use cases for the appropriate exchange of molecular data, and highlights key issues such as data integrity, interoperable formats for massive genomic datasets, security, malpractice and emerging regulations involved with this novel practice.

Impact of exchange-correlation effects on the IV characteristics of a molecular junction

DEFF Research Database (Denmark)

Thygesen, Kristian Sommer

2008-01-01

The role of exchange-correlation effects in nonequilibrium quantum transport through molecular junctions is assessed by analyzing the IV curve of a generic two-level model using self-consistent many-body perturbation theory (second Born and GW approximations) on the Keldysh contour. It is demonst...... of dynamic correlations introduces quasiparticle (QP) scattering which in turn broadens the molecular resonances. The broadening increases strongly with bias and can have a large impact on the calculated IV characteristic....

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids

Science.gov (United States)

Shinoda, Wataru; Hatanaka, Yuta; Hirakawa, Masashi; Okazaki, Susumu; Tsuzuki, Seiji; Ueno, Kazuhide; Watanabe, Masayoshi

2018-05-01

Equimolar mixtures of glymes and organic lithium salts are known to produce solvate ionic liquids, in which the stability of the [Li(glyme)]+ complex plays an important role in determining the ionic dynamics. Since these mixtures have attractive physicochemical properties for application as electrolytes, it is important to understand the dependence of the stability of the [Li(glyme)]+ complex on the ion dynamics. A series of microsecond molecular dynamics simulations has been conducted to investigate the dynamic properties of these solvate ionic liquids. Successful solvate ionic liquids with high stability of the [Li(glyme)]+ complex have been shown to have enhanced ion dynamics. Li-glyme pair exchange rarely occurs: its characteristic time is longer than that of ion diffusion by one or two orders of magnitude. Li-glyme pair exchange most likely occurs through cluster formation involving multiple [Li(glyme)]+ pairs. In this process, multiple exchanges likely take place in a concerted manner without the production of energetically unfavorable free glyme or free Li+ ions.

Replica Fourier Transform: Properties and applications

International Nuclear Information System (INIS)

Crisanti, A.; De Dominicis, C.

2015-01-01

The Replica Fourier Transform is the generalization of the discrete Fourier Transform to quantities defined on an ultrametric tree. It finds use in conjunction of the replica method used to study thermodynamics properties of disordered systems such as spin glasses. Its definition is presented in a systematic and simple form and its use illustrated with some representative examples. In particular we give a detailed discussion of the diagonalization in the Replica Fourier Space of the Hessian matrix of the Gaussian fluctuations about the mean field saddle point of spin glass theory. The general results are finally discussed for a generic spherical spin glass model, where the Hessian can be computed analytically

Replica consistency in a Data Grid

International Nuclear Information System (INIS)

Domenici, Andrea; Donno, Flavia; Pucciani, Gianni; Stockinger, Heinz; Stockinger, Kurt

2004-01-01

A Data Grid is a wide area computing infrastructure that employs Grid technologies to provide storage capacity and processing power to applications that handle very large quantities of data. Data Grids rely on data replication to achieve better performance and reliability by storing copies of data sets on different Grid nodes. When a data set can be modified by applications, the problem of maintaining consistency among existing copies arises. The consistency problem also concerns metadata, i.e., additional information about application data sets such as indices, directories, or catalogues. This kind of metadata is used both by the applications and by the Grid middleware to manage the data. For instance, the Replica Management Service (the Grid middleware component that controls data replication) uses catalogues to find the replicas of each data set. Such catalogues can also be replicated and their consistency is crucial to the correct operation of the Grid. Therefore, metadata consistency generally poses stricter requirements than data consistency. In this paper we report on the development of a Replica Consistency Service based on the middleware mainly developed by the European Data Grid Project. The paper summarises the main issues in the replica consistency problem, and lays out a high-level architectural design for a Replica Consistency Service. Finally, results from simulations of different consistency models are presented

Effect of sequence and stereochemistry reversal on p53 peptide mimicry.

Directory of Open Access Journals (Sweden)

Alessio Atzori

Full Text Available Peptidomimetics effective in modulating protein-protein interactions and resistant to proteolysis have potential in therapeutic applications. An appealing yet underperforming peptidomimetic strategy is to employ D-amino acids and reversed sequences to mimic a lead peptide conformation, either separately or as the combined retro-inverso peptide. In this work, we examine the conformations of inverse, reverse and retro-inverso peptides of p53(15-29 using implicit solvent molecular dynamics simulation and circular dichroism spectroscopy. In order to obtain converged ensembles for the peptides, we find enhanced sampling is required via the replica exchange molecular dynamics method. From these replica exchange simulations, the D-peptide analogues of p53(15-29 result in a predominantly left-handed helical conformation. When the parent sequence is reversed sequence as either the L-peptide and D-peptide, these peptides display a greater helical propensity, feature reflected by NMR and CD studies in TFE/water solvent. The simulations also indicate that, while approximately similar orientations of the side-chains are possible by the peptide analogues, their ability to mimic the parent peptide is severely compromised by backbone orientation (for D-amino acids and side-chain orientation (for reversed sequences. A retro-inverso peptide is disadvantaged as a mimic in both aspects, and further chemical modification is required to enable this concept to be used fruitfully in peptidomimetic design. The replica exchange molecular simulation approach adopted here, with its ability to provide detailed conformational insights into modified peptides, has potential as a tool to guide structure-based design of new improved peptidomimetics.

Production of entropy on simplified dynamics in spin glass systems

CERN Document Server

Saakyan, D B

2001-01-01

In models of spin glasses one eliminates condition of extreme based on one of the order parameters. On the basis of the available expression for static sum one derived the effective hamiltonian for parameter and the appropriate energy. Relaxation of the system is studied as energy exchange between the degree of freedom related to the order slow parameter and with the rest of the system. At that level one may indicate point of glass capture within phase space on the basis of the static solutions. One studies p-spin model without magnetic field in case of replica symmetry violation. One studies dynamics of p-spin glass in magnetic field in replica-symmetrical phase. One studied model of spins with quadratic interaction when dynamic constants had temperature differing from temperature of space

Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle.

Science.gov (United States)

Grabon, Aby; Orłowski, Adam; Tripathi, Ashutosh; Vuorio, Joni; Javanainen, Matti; Róg, Tomasz; Lönnfors, Max; McDermott, Mark I; Siebert, Garland; Somerharju, Pentti; Vattulainen, Ilpo; Bankaitis, Vytas A

2017-09-01

Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling. However, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics simulations of the mammalian StART-like PtdIns/phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical analyses that tested key aspects of the hypotheses generated by the molecular dynamics simulations. These studies provided five key insights into the PITPα lipid exchange cycle: (i) interaction of PITPα with the membrane is spontaneous and mediated by four specific protein substructures; (ii) the ability of PITPα to initiate closure around the PtdCho ligand is accompanied by loss of flexibility of two helix/loop regions, as well as of the C-terminal helix; (iii) the energy barrier of phospholipid extraction from the membrane is lowered by a network of hydrogen bonds between the lipid molecule and PITPα; (iv) the trajectory of PtdIns or PtdCho into and through the lipid-binding pocket is chaperoned by sets of PITPα residues conserved throughout the StART-like PITP family; and (v) conformational transitions in the C-terminal helix have specific functional involvements in PtdIns transfer activity. Taken together, these findings provide the first mechanistic description of key aspects of the PITPα PtdIns/PtdCho exchange cycle and offer a rationale for the high conservation of particular sets of residues across evolutionarily distant members of the metazoan StART-like PITP family. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Simulated tempering distributed replica sampling: A practical guide to enhanced conformational sampling

Energy Technology Data Exchange (ETDEWEB)

Rauscher, Sarah; Pomes, Regis, E-mail: pomes@sickkids.ca

2010-11-01

Simulated tempering distributed replica sampling (STDR) is a generalized-ensemble method designed specifically for simulations of large molecular systems on shared and heterogeneous computing platforms [Rauscher, Neale and Pomes (2009) J. Chem. Theor. Comput. 5, 2640]. The STDR algorithm consists of an alternation of two steps: (1) a short molecular dynamics (MD) simulation; and (2) a stochastic temperature jump. Repeating these steps thousands of times results in a random walk in temperature, which allows the system to overcome energetic barriers, thereby enhancing conformational sampling. The aim of the present paper is to provide a practical guide to applying STDR to complex biomolecular systems. We discuss the details of our STDR implementation, which is a highly-parallel algorithm designed to maximize computational efficiency while simultaneously minimizing network communication and data storage requirements. Using a 35-residue disordered peptide in explicit water as a test system, we characterize the efficiency of the STDR algorithm with respect to both diffusion in temperature space and statistical convergence of structural properties. Importantly, we show that STDR provides a dramatic enhancement of conformational sampling compared to a canonical MD simulation.

An integrate-over-temperature approach for enhanced sampling.

Science.gov (United States)

Gao, Yi Qin

2008-02-14

A simple method is introduced to achieve efficient random walking in the energy space in molecular dynamics simulations which thus enhances the sampling over a large energy range. The approach is closely related to multicanonical and replica exchange simulation methods in that it allows configurations of the system to be sampled in a wide energy range by making use of Boltzmann distribution functions at multiple temperatures. A biased potential is quickly generated using this method and is then used in accelerated molecular dynamics simulations.

Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

Science.gov (United States)

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

A replica exchange Monte Carlo algorithm for protein folding in the HP model

Directory of Open Access Journals (Sweden)

Shmygelska Alena

2007-09-01

Full Text Available Abstract Background The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of the most important and challenging problems in biochemistry, molecular biology and biophysics. The ab initio protein folding problem is computationally challenging and has been shown to be NP MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaat0uy0HwzTfgDPnwy1egaryqtHrhAL1wy0L2yHvdaiqaacqWFneVtcqqGqbauaaa@3961@-hard even when conformations are restricted to a lattice. In this work, we implement and evaluate the replica exchange Monte Carlo (REMC method, which has already been applied very successfully to more complex protein models and other optimization problems with complex energy landscapes, in combination with the highly effective pull move neighbourhood in two widely studied Hydrophobic Polar (HP lattice models. Results We demonstrate that REMC is highly effective for solving instances of the square (2D and cubic (3D HP protein folding problem. When using the pull move neighbourhood, REMC outperforms current state-of-the-art algorithms for most benchmark instances. Additionally, we show that this new algorithm provides a larger ensemble of ground-state structures than the existing state-of-the-art methods. Furthermore, it scales well with sequence length, and it finds significantly better conformations on long biological sequences and sequences with a provably unique ground-state structure, which is believed to be a characteristic of real proteins. We also present evidence that our REMC algorithm can fold sequences which exhibit significant interaction between termini in the hydrophobic core relatively easily. Conclusion We demonstrate that REMC utilizing the pull move

Extensions to the Dynamic Aerospace Vehicle Exchange Markup Language

Science.gov (United States)

Brian, Geoffrey J.; Jackson, E. Bruce

2011-01-01

The Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML) is a syntactical language for exchanging flight vehicle dynamic model data. It provides a framework for encoding entire flight vehicle dynamic model data packages for exchange and/or long-term archiving. Version 2.0.1 of DAVE-ML provides much of the functionality envisioned for exchanging aerospace vehicle data; however, it is limited in only supporting scalar time-independent data. Additional functionality is required to support vector and matrix data, abstracting sub-system models, detailing dynamics system models (both discrete and continuous), and defining a dynamic data format (such as time sequenced data) for validation of dynamics system models and vehicle simulation packages. Extensions to DAVE-ML have been proposed to manage data as vectors and n-dimensional matrices, and record dynamic data in a compatible form. These capabilities will improve the clarity of data being exchanged, simplify the naming of parameters, and permit static and dynamic data to be stored using a common syntax within a single file; thereby enhancing the framework provided by DAVE-ML for exchanging entire flight vehicle dynamic simulation models.

Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Federica Chiappori

Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

Molecular dynamics simulations of proton-ordered water confined in low-diameter carbon nanotubes.

Science.gov (United States)

Li, Shujuan; Schmidt, Burkhard

2015-03-21

The present work deals with molecular dynamics simulations of water confined in single-walled carbon nanotubes (CNTs), with emphasis on the proton-ordering of water and its polarization. First, the water occupancy of open-ended armchair and zigzag CNTs immersed in water under ambient NPT conditions is calculated for various water models, and for varying Lennard-Jones parameters of the water-carbon interaction. As a function of the CNT diameter, the water density displays several oscillations before converging to the bulk value. Based on these results, the water structures encapsulated in 10 nm long armchair CNTs (n,n) with 5 ≤ n ≤ 10, are investigated under NVT conditions. Inside the smallest nanotubes (n = 5, 6) highly ferroelectric (FE), quasi-one-dimensional water chains are found while inside the other CNTs water molecules assemble into single-walled ice nanotubes (INTs). There are several, near-degenerate minimum energy INT structures: single helical structures were found for 7 ≤ n ≤ 10, in all cases in FE arrangement. In addition, a double helical INT structure was found for n = 8 with an even higher polarization. Prism-like structures were found only for 8 ≤ n ≤ 10 with various FE, ferrielectric (FI), and antiferroelectric (AF, n = 9, 10) proton ordering. The coexistence of the nearly iso-energetic FE, FI, and AF INT structures separated by high barriers renders the molecular dynamics highly metastable, typically with nanosecond timescales at room temperature. Hence, the replica exchange simulation method is used to obtain populations of different INT states at finite temperatures. Many of the FE INT structures confined in low-diameter CNTs are still prevalent at room temperature. Both helix-helix and helix-prism structural transitions are detected which can be either continuous (around 470 K for n = 8) or discontinuous (at 218 K for n = 9). Also melting-like transitions are found in which the INT structures are disrupted leading to a loss of FE

Broken symmetry in the mean field theory of the ising spin glass: replica way and no replica way

International Nuclear Information System (INIS)

De Dominicis, C.

1983-06-01

We review the type of symmetry breaking involved in the solution discovered by Parisi and in the static derivation of the solution first introduced via dynamics by Sompolinsky. We turn to a formulation of the problem due to Thouless, Anderson and Palmer (TAP) that put a set of equations for the magnetization. A probability law for the magnetization is then built. We consider two cases: (i) a canonical distribution which is shown to give indentical results to the Hamiltonian formulation under a weak and physical assumption and (ii) a white distribution characterized by two matrices and a response. We show what symmetry breaking is necessary to recover Sompolinsky free energy. In section III we supplement replica indices in the Hamiltonian approach by ''time'' indices ans show in particular that the analytic continuation involved in Sompolinsky's equilibrium derivation, is trying to mimick a translational symmetry breaking in ''time'' that incorporates Sompolinsky's ansatz of a long time scale sequence. In section IV we apply the same treatment to the white average approach and show that, replicas can be altogether discorded and replaced by ''time''. Finally, we briefly discuss the attribution of distinct answers for the standard spin glass order parameter depending on the physical situation: equilibrium or non equilibrium associated with canonical or white (non canonical) initial conditions and density matrices

SRF Cavity Surface Topography Characterization Using Replica Techniques

Energy Technology Data Exchange (ETDEWEB)

C. Xu, M.J. Kelley, C.E. Reece

2012-07-01

To better understand the roll of topography on SRF cavity performance, we seek to obtain detailed topographic information from the curved practical cavity surfaces. Replicas taken from a cavity interior surface provide internal surface molds for fine Atomic Force Microscopy (AFM) and stylus profilometry. In this study, we confirm the replica resolution both on surface local defects such as grain boundary and etching pits and compare the surface uniform roughness with the aid of Power Spectral Density (PSD) where we can statistically obtain roughness parameters at different scales. A series of sampling locations are at the same magnetic field chosen at the same latitude on a single cell cavity to confirm the uniformity. Another series of sampling locations at different magnetic field amplitudes are chosen for this replica on the same cavity for later power loss calculation. We also show that application of the replica followed by rinsing does not adversely affect the cavity performance.

Molecular dynamics simulations of solutions at constant chemical potential

Science.gov (United States)

Perego, C.; Salvalaglio, M.; Parrinello, M.

2015-04-01

Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

Neurovascular Modeling: Small-Batch Manufacturing of Silicone Vascular Replicas

Science.gov (United States)

Chueh, J.Y.; Wakhloo, A.K.; Gounis, M.J.

2009-01-01

BACKGROUND AND PURPOSE Realistic, population based cerebrovascular replicas are required for the development of neuroendovascular devices. The objective of this work was to develop an efficient methodology for manufacturing realistic cerebrovascular replicas. MATERIALS AND METHODS Brain MR angiography data from 20 patients were acquired. The centerline of the vasculature was calculated, and geometric parameters were measured to describe quantitatively the internal carotid artery (ICA) siphon. A representative model was created on the basis of the quantitative measurements. Using this virtual model, we designed a mold with core-shell structure and converted it into a physical object by fused-deposit manufacturing. Vascular replicas were created by injection molding of different silicones. Mechanical properties, including the stiffness and luminal coefficient of friction, were measured. RESULTS The average diameter, length, and curvature of the ICA siphon were 4.15 ± 0.09 mm, 22.60 ± 0.79 mm, and 0.34 ± 0.02 mm-1 (average ± standard error of the mean), respectively. From these image datasets, we created a median virtual model, which was transformed into a physical replica by an efficient batch-manufacturing process. The coefficient of friction of the luminal surface of the replica was reduced by up to 55% by using liquid silicone rubber coatings. The modulus ranged from 0.67 to 1.15 MPa compared with 0.42 MPa from human postmortem studies, depending on the material used to make the replica. CONCLUSIONS Population-representative, smooth, and true-to-scale silicone arterial replicas with uniform wall thickness were successfully built for in vitro neurointerventional device-testing by using a batch-manufacturing process. PMID:19321626

Replica Fourier Tansforms on Ultrametric Trees, and Block-Diagonalizing Multi-Replica Matrices

Science.gov (United States)

de Dominicis, C.; Carlucci, D. M.; Temesvári, T.

1997-01-01

The analysis of objects living on ultrametric trees, in particular the block-diagonalization of 4-replica matrices M^{α β;γ^δ}, is shown to be dramatically simplified through the introduction of properly chosen operations on those objects. These are the Replica Fourier Transforms on ultrametric trees. Those transformations are defined and used in the present work. On montre que l'analyse d'objets vivant sur un arbre ultramétrique, en particulier, la diagonalisation par blocs d'une matrice M^{α β;γ^δ} dépendant de 4-répliques, se simplifie de façon dramatique si l'on introduit les opérations appropriées sur ces objets. Ce sont les Transformées de Fourier de Répliques sur un arbre ultramétrique. Ces transformations sont définies et utilisées dans le présent travail.

A single disulfide bond disruption in the β3 integrin subunit promotes thiol/disulfide exchange, a molecular dynamics study.

Directory of Open Access Journals (Sweden)

Lihie Levin

Full Text Available The integrins are a family of membrane receptors that attach a cell to its surrounding and play a crucial function in cell signaling. The combination of internal and external stimuli alters a folded non-active state of these proteins to an extended active configuration. The β3 subunit of the platelet αIIbβ3 integrin is made of well-structured domains rich in disulfide bonds. During the activation process some of the disulfides are re-shuffled by a mechanism requiring partial reduction of some of these bonds; any disruption in this mechanism can lead to inherent blood clotting diseases. In the present study we employed Molecular Dynamics simulations for tracing the sequence of structural fluctuations initiated by a single cysteine mutation in the β3 subunit of the receptor. These simulations showed that in-silico protein mutants exhibit major conformational deformations leading to possible disulfide exchange reactions. We suggest that any mutation that prevents Cys560 from reacting with one of the Cys(567-Cys(581 bonded pair, thus disrupting its ability to participate in a disulfide exchange reaction, will damage the activation mechanism of the integrin. This suggestion is in full agreement with previously published experiments. Furthermore, we suggest that rearrangement of disulfide bonds could be a part of a natural cascade of thiol/disulfide exchange reactions in the αIIbβ3 integrin, which are essential for the native activation process.

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

Science.gov (United States)

Rapaport, D C

2009-04-01

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

Liquid-vapor coexistence by molecular dynamics simulation

International Nuclear Information System (INIS)

Baranyai, Andras; Cummings, Peter T.

2000-01-01

We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics

A concurrent multiscale micromorphic molecular dynamics

International Nuclear Information System (INIS)

Li, Shaofan; Tong, Qi

2015-01-01

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities

International Nuclear Information System (INIS)

Hirata, So; Ivanov, Stanislav; Bartlett, Rodney J.; Grabowski, Ireneusz

2005-01-01

Time-dependent density-functional theory (TDDFT) employing the exact-exchange functional has been formulated on the basis of the optimized-effective-potential (OEP) method of Talman and Shadwick for second-order molecular properties and implemented into a Gaussian-basis-set, trial-vector algorithm. The only approximation involved, apart from the lack of correlation effects and the use of Gaussian-type basis functions, was the consistent use of the adiabatic approximation in the exchange kernel and in the linear response function. The static and dynamic polarizabilities and their anisotropy predicted by the TDDFT with exact exchange (TDOEP) agree accurately with the corresponding values from time-dependent Hartree-Fock theory, the exact-exchange counterpart in the wave function theory. The TDOEP is free from the nonphysical asymptotic decay of the exchange potential of most conventional density functionals or from any other manifestations of the incomplete cancellation of the self-interaction energy. The systematic overestimation of the absolute values and dispersion of polarizabilities that plagues most conventional TDDFT cannot be seen in the TDOEP

Second-order quadrupolar line shapes under molecular dynamics: An additional transition in the extremely fast regime.

Science.gov (United States)

Hung, Ivan; Wu, Gang; Gan, Zhehong

NMR spectroscopy is a powerful tool for probing molecular dynamics. For the classic case of two-site exchange, NMR spectra go through the transition from exchange broadening through coalescence and then motional narrowing as the exchange rate increases passing through the difference between the resonance frequencies of the two sites. For central-transition spectra of half-integer quadrupolar nuclei in solids, line shape change due to molecular dynamics occurs in two stages. The first stage occurs when the exchange rate is comparable to the second-order quadrupolar interaction. The second spectral transition comes at a faster exchange rate which approaches the Larmor frequency and generally reduces the isotropic quadrupolar shift. Such a two-stage transition phenomenon is unique to half-integer quadrupolar nuclei. A quantum mechanical formalism in full Liouville space is presented to explain the physical origin of the two-stage phenomenon and for use in spectral simulations. Variable-temperature 17 O NMR of solid NaNO 3 in which the NO 3 - ion undergoes 3-fold jumps confirms the two-stage transition process. The spectra of NaNO 3 acquired in the temperature range of 173-413K agree well with simulations using the quantum mechanical formalism. The rate constants for the 3-fold NO 3 - ion jumps span eight orders of magnitude (10 2 -10 10 s -1 ) covering both transitions of the dynamic 17 O line shape. Copyright © 2016 Elsevier Inc. All rights reserved.

Replica calibration artefacts for optical 3D scanning of micro parts

DEFF Research Database (Denmark)

De Chiffre, Leonardo; Carmignato, S.; Cantatore, Angela

2009-01-01

This work deals with development of calibration artefacts produced by using hard replica materials, achieving high quality geometrical reproduction of suitable reference artefacts, high stability, and high surface cooperativeness. An investigation was carried out using a replica material for dental...... applications to reproduce the geometry of a step artefact, a miniature step gauge, and a curve standard for optical measuring machines. The replica artefacts were calibrated using a tactile coordinate measuring machine and measured on two different optical scanners. Replication quality and applicability...... of the artefacts to verify the accuracy of optical measurements as well as thermal expansion coefficient and stability of the replica artefacts over time were documented....

Molecular mechanics of silk nanostructures under varied mechanical loading.

Science.gov (United States)

Bratzel, Graham; Buehler, Markus J

2012-06-01

Spider dragline silk is a self-assembling tunable protein composite fiber that rivals many engineering fibers in tensile strength, extensibility, and toughness, making it one of the most versatile biocompatible materials and most inviting for synthetic mimicry. While experimental studies have shown that the peptide sequence and molecular structure of silk have a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies, in particular, under variations of genetic sequences have been reported. In this study, atomistic-level structures of wildtype as well as modified MaSp1 protein from the Nephila clavipes spider dragline silk sequences, obtained using an in silico approach based on replica exchange molecular dynamics and explicit water molecular dynamics, are subjected to simulated nanomechanical testing using different force-control loading conditions including stretch, pull-out, and peel. The authors have explored the effects of the poly-alanine length of the N. clavipes MaSp1 peptide sequence and identify differences in nanomechanical loading conditions on the behavior of a unit cell of 15 strands with 840-990 total residues used to represent a cross-linking β-sheet crystal node in the network within a fibril of the dragline silk thread. The specific loading condition used, representing concepts derived from the protein network connectivity at larger scales, have a significant effect on the mechanical behavior. Our analysis incorporates stretching, pull-out, and peel testing to connect biochemical features to mechanical behavior. The method used in this study could find broad applications in de novo design of silk-like tunable materials for an array of applications. Copyright © 2011 Wiley Periodicals, Inc.

Application of extraction replicas and analytical electron microscopy to precipitate phase studies

International Nuclear Information System (INIS)

Kenik, E.A.; Maziasz, P.J.

1984-01-01

Extraction replicas provide a powerful extension of AEM techniques for analysis of fine precipitates. In many cases, replicas allow more accurate analyses to be performed and, in some cases, allow unique analyses which cannot be performed in-foil. However, there are limitations to the use of extraction replicas in AEM, of which the analyst must be aware. Many can be eliminated by careful preparation. Often, combined AEM studies of precipitates in-foil and on extraction replicas provide complementary and corroborative information for the fullest analysis of precipitate phases

Exchange Rate and Inflation Dynamics

OpenAIRE

Eatzaz Ahmad; Saima Ahmed Ali

1999-01-01

This paper studies simultaneous determination of nominal exchange rate and domestic price level in Pakistan. The estimated model contains sufficient built-in dynamics to trace the pattern and speed of adjustment in the two variables in response to temporary or permanent shocks. The two domestic shocks considered in the paper are monetary and real shocks, while the three external shocks considered are import price, export price and foreign exchange reserves shocks. The study finds that the imp...

Simulated dynamic response of a multi-stage compressor with variable molecular weight flow medium

Science.gov (United States)

Babcock, Dale A.

1995-01-01

A mathematical model of a multi-stage compressor with variable molecular weight flow medium is derived. The modeled system consists of a five stage, six cylinder, double acting, piston type compressor. Each stage is followed by a water cooled heat exchanger which serves to transfer the heat of compression from the gas. A high molecular weight gas (CFC-12) mixed with air in varying proportions is introduced to the suction of the compressor. Condensation of the heavy gas may occur in the upper stage heat exchangers. The state equations for the system are integrated using the Advanced Continuous Simulation Language (ACSL) for determining the system's dynamic and steady state characteristics under varying operating conditions.

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide.

Science.gov (United States)

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH 2 ). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD 3 CD in H 2 O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide

Science.gov (United States)

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD3CD in H2O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

Accuracy of three-dimensional printing for manufacturing replica teeth.

Science.gov (United States)

Lee, Keun-Young; Cho, Jin-Woo; Chang, Na-Young; Chae, Jong-Moon; Kang, Kyung-Hwa; Kim, Sang-Cheol; Cho, Jin-Hyoung

2015-09-01

Three-dimensional (3D) printing is a recent technological development that may play a significant role in orthodontic diagnosis and treatment. It can be used to fabricate skull models or study models, as well as to make replica teeth in autotransplantation or tooth impaction cases. The aim of this study was to evaluate the accuracy of fabrication of replica teeth made by two types of 3D printing technologies. Fifty extracted molar teeth were selected as samples. They were scanned to generate high-resolution 3D surface model stereolithography files. These files were converted into physical models using two types of 3D printing technologies: Fused deposition modeling (FDM) and PolyJet technology. All replica teeth were scanned and 3D images generated. Computer software compared the replica teeth to the original teeth with linear measurements, volumetric measurements, and mean deviation measurements with best-fit alignment. Paired t-tests were used to statistically analyze the measurements. Most measurements of teeth formed using FDM tended to be slightly smaller, while those of the PolyJet replicas tended to be slightly larger, than those of the extracted teeth. Mean deviation measurements with best-fit alignment of FDM and PolyJet group were 0.047 mm and 0.038 mm, respectively. Although there were statistically significant differences, they were regarded as clinically insignificant. This study confirms that FDM and PolyJet technologies are accurate enough to be usable in orthodontic diagnosis and treatment.

A critical inventory of preoperative skull replicas.

Science.gov (United States)

Fasel, J H D; Beinemann, J; Schaller, K; Gailloud, P

2013-09-01

Physical replicas of organs are used increasingly for preoperative planning. The quality of these models is generally accepted by surgeons. In view of the strong trend towards minimally invasive and personalised surgery, however, the aim of this investigation was to assess qualitatively the accuracy of such replicas, using skull models as an example. Skull imaging was acquired for three cadavers by computed tomography using clinical routine parameters. After digital three-dimensional (3D) reconstruction, physical replicas were produced by 3D printing. The facsimilia were analysed systematically and compared with the best gold standard possible: the macerated skull itself. The skull models were far from anatomically accurate. Non-conforming rendering was observed in particular for foramina, sutures, notches, fissures, grooves, channels, tuberosities, thin-walled structures, sharp peaks and crests, and teeth. Surgeons should be aware that preoperative models may not yet render the exact anatomy of the patient under consideration and are advised to continue relying, in specific conditions, on their own analysis of the native computed tomography or magnetic resonance imaging.

Generalized ensemble method applied to study systems with strong first order transitions

Science.gov (United States)

Małolepsza, E.; Kim, J.; Keyes, T.

2015-09-01

At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub [1], where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM). This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. The method is illustrated in a study of the very strong solid/liquid transition in water.

Influence of molecular packing and phospholipid type on rates of cholesterol exchange

International Nuclear Information System (INIS)

Lund-Katz, S.; Laboda, H.M.; McLean, L.R.; Phillips, M.C.

1988-01-01

The rates of [ 14 C]cholesterol transfer from small unilamellar vesicles containing cholesterol dissolved in bilayers of different phospholipids have been determined to examine the influence of phospholipid-cholesterol interactions on the rate of cholesterol desorption from the lipid-water interface. At 37 0 C, for vesicles containing 10 mol % cholesterol, the half-times for exchange are about 1, 13, and 80 h, respectively, for unsaturated PC, saturated PC, and SM. In order to probe how differences in molecular packing in the bilayers cause the rate constants for cholesterol desorption to be in the order unsaturated PC > saturated PC > SM, nuclear magnetic resonance (NMR) and monolayer methods were used to evaluate the cholesterol physical state and interactions with phospholipid. The NMR relaxation parameters for [4- 13 C] cholesterol reveal no differences in molecular dynamics in the above bilayers. The greater van der Waals interaction in the SM monolayer (or bilayer) compared to PC gives rise to a larger condensation by cholesterol. This is a direct demonstration of the greater interaction of cholesterol with SM compared to PC. An estimate of the van der Waals interactions between cholesterol and these phospholipids has been used to derive a relationship between the ratio of the rate constants for cholesterol desorption and the relative molecular areas (lateral packing density) in two bilayers. This analysis suggests that differences in cholesterol-phospholipid van der Waals interaction energy are an important cause of varying rates of cholesterol exchange from different host phospholipid bilayers

Storing files in a parallel computing system using list-based index to identify replica files

Science.gov (United States)

Faibish, Sorin; Bent, John M.; Tzelnic, Percy; Zhang, Zhenhua; Grider, Gary

2015-07-21

Improved techniques are provided for storing files in a parallel computing system using a list-based index to identify file replicas. A file and at least one replica of the file are stored in one or more storage nodes of the parallel computing system. An index for the file comprises at least one list comprising a pointer to a storage location of the file and a storage location of the at least one replica of the file. The file comprises one or more of a complete file and one or more sub-files. The index may also comprise a checksum value for one or more of the file and the replica(s) of the file. The checksum value can be evaluated to validate the file and/or the file replica(s). A query can be processed using the list.

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

International Nuclear Information System (INIS)

Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

Fabrication of the replica templated from butterfly wing scales with complex light trapping structures

Science.gov (United States)

Han, Zhiwu; Li, Bo; Mu, Zhengzhi; Yang, Meng; Niu, Shichao; Zhang, Junqiu; Ren, Luquan

2015-11-01

The polydimethylsiloxane (PDMS) positive replica templated twice from the excellent light trapping surface of butterfly Trogonoptera brookiana wing scales was fabricated by a simple and promising route. The exact SiO2 negative replica was fabricated by using a synthesis method combining a sol-gel process and subsequent selective etching. Afterwards, a vacuum-aided process was introduced to make PDMS gel fill into the SiO2 negative replica, and the PDMS gel was solidified in an oven. Then, the SiO2 negative replica was used as secondary template and the structures in its surface was transcribed onto the surface of PDMS. At last, the PDMS positive replica was obtained. After comparing the PDMS positive replica and the original bio-template in terms of morphology, dimensions and reflectance spectra and so on, it is evident that the excellent light trapping structures of butterfly wing scales were inherited by the PDMS positive replica faithfully. This bio-inspired route could facilitate the preparation of complex light trapping nanostructure surfaces without any assistance from other power-wasting and expensive nanofabrication technologies.

Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution.

Science.gov (United States)

Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P

2016-07-14

The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.

Data Sets Replicas Placements Strategy from Cost-Effective View in the Cloud

Directory of Open Access Journals (Sweden)

Xiuguo Wu

2016-01-01

Full Text Available Replication technology is commonly used to improve data availability and reduce data access latency in the cloud storage system by providing users with different replicas of the same service. Most current approaches largely focus on system performance improvement, neglecting management cost in deciding replicas number and their store places, which cause great financial burden for cloud users because the cost for replicas storage and consistency maintenance may lead to high overhead with the number of new replicas increased in a pay-as-you-go paradigm. In this paper, towards achieving the approximate minimum data sets management cost benchmark in a practical manner, we propose a replicas placements strategy from cost-effective view with the premise that system performance meets requirements. Firstly, we design data sets management cost models, including storage cost and transfer cost. Secondly, we use the access frequency and the average response time to decide which data set should be replicated. Then, the method of calculating replicas’ number and their store places with minimum management cost is proposed based on location problem graph. Both the theoretical analysis and simulations have shown that the proposed strategy offers the benefits of lower management cost with fewer replicas.

Fabrication of free-standing replicas of fragile, laminar, chitinous biotemplates

Energy Technology Data Exchange (ETDEWEB)

Lakhtakia, Akhlesh; Motyka, Michael A [Materials Research Institute and Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802 (United States); MartIn-Palma, Raul J; Pantano, Carlo G [Materials Research Institute and Department of Materials Science and Engineering, Pennsylvania State University, University Park, PA 16802 (United States)], E-mail: akhlesh@psu.edu

2009-09-01

The conformal-evaporated-film-by-rotation technique, followed by the dissolution of chitin in an aqueous solution of orthophosphoric acid, can be used to fabricate free-standing replicas of fragile, laminar, chitinous biotemplates. This novel approach was demonstrated using butterfly wings as biotemplates and GeSeSb chalcogenide glass for replicas. (communication)

Fabrication of free-standing replicas of fragile, laminar, chitinous biotemplates

International Nuclear Information System (INIS)

Lakhtakia, Akhlesh; Motyka, Michael A; MartIn-Palma, Raul J; Pantano, Carlo G

2009-01-01

The conformal-evaporated-film-by-rotation technique, followed by the dissolution of chitin in an aqueous solution of orthophosphoric acid, can be used to fabricate free-standing replicas of fragile, laminar, chitinous biotemplates. This novel approach was demonstrated using butterfly wings as biotemplates and GeSeSb chalcogenide glass for replicas. (communication)

Nonadiabatic exchange dynamics during adiabatic frequency sweeps.

Science.gov (United States)

Barbara, Thomas M

2016-04-01

A Bloch equation analysis that includes relaxation and exchange effects during an adiabatic frequency swept pulse is presented. For a large class of sweeps, relaxation can be incorporated using simple first order perturbation theory. For anisochronous exchange, new expressions are derived for exchange augmented rotating frame relaxation. For isochronous exchange between sites with distinct relaxation rate constants outside the extreme narrowing limit, simple criteria for adiabatic exchange are derived and demonstrate that frequency sweeps commonly in use may not be adiabatic with regard to exchange unless the exchange rates are much larger than the relaxation rates. Otherwise, accurate assessment of the sensitivity to exchange dynamics will require numerical integration of the rate equations. Examples of this situation are given for experimentally relevant parameters believed to hold for in-vivo tissue. These results are of significance in the study of exchange induced contrast in magnetic resonance imaging. Copyright © 2016 Elsevier Inc. All rights reserved.

Replica approach to mean-variance portfolio optimization

Science.gov (United States)

Varga-Haszonits, Istvan; Caccioli, Fabio; Kondor, Imre

2016-12-01

We consider the problem of mean-variance portfolio optimization for a generic covariance matrix subject to the budget constraint and the constraint for the expected return, with the application of the replica method borrowed from the statistical physics of disordered systems. We find that the replica symmetry of the solution does not need to be assumed, but emerges as the unique solution of the optimization problem. We also check the stability of this solution and find that the eigenvalues of the Hessian are positive for r  =  N/T  optimal in-sample variance is found to vanish at the critical point inversely proportional to the divergent estimation error.

Molecular (Feshbach) treatment of charge exchange Li3++He collisions. I. Energies and couplings

International Nuclear Information System (INIS)

Martin, F.; Riera, A.; Yanez, M.

1986-01-01

We point out a fundamental difference between the molecular treatment of charge exchange X/sup n/++H(1s) and X/sup n/++He(1s 2 ) collisions, which is that the latter process involves molecular states that are formally autoionizing. Then standard ab initio methods do not, in general, yield the relevant wave functions that are needed in the collision treatment, irrespective of whether quasimolecular autoionization be significant or not during the collision. We implement a particularly simple and useful form of the Feshbach formalism to calculate the energies of those two electron systems, and a method to evaluate the corresponding dynamical couplings is presented for the first time. Our implementation of this formalism together with the new computational techniques involved are presented in detail

Long-memory exchange rate dynamics in the euro era

International Nuclear Information System (INIS)

Barkoulas, John T.; Barilla, Anthony G.; Wells, William

2016-01-01

We investigate the long-run dynamics of a system of eight major exchange rates in the euro era using both integer and fractional cointegration methodologies. Contrary to the fragile evidence in the pre-euro era, robust evidence of linear cointegratedness is obtained in the foreign exchange market during the euro era. Upon closer examination, deviations from the cointegrating relationship exhibit nonstationary, long-memory dynamic behavior (Joseph effect). We find the long-memory evidence to be temporally stable in the most recent era. Finally, the foreign exchange system dynamics appears to be characterized by less persistence (smaller fractional exponent) in the euro era (as compared to pre-euro time periods), potentially indicating increased policy coordination by central banks in the recent period.

Lanthanide paramagnetic probes for NMR spectroscopic studies of fast molecular conformational dynamics and temperature control. Effective six-site proton exchange in 18-crown-6 by exchange spectroscopy.

Science.gov (United States)

Babailov, Sergey P

2012-02-06

(1)H and (13)C NMR measurements are reported for the CDCl(3) and CD(2)Cl(2) solutions of [La(18-crown-6)(NO(3))(3)] (I), [Pr(18-crown-6) (NO(3))(3)] (II), [Ce(18-crown-6)(NO(3))(3)] (III), and [Nd(18-crown-6)(NO(3))(3)] (IV) complexes. Temperature dependencies of the (1)H NMR spectra of paramagnetic II-IV have been analyzed using the dynamic NMR (DNMR) methods for six-site exchange. Two types of conformational dynamic processes were identified (the first one is conditioned by interconversion of complex enantiomeric forms and pseudorotation of a macrocycle molecule upon the C(2) symmetry axis; the second one is conditioned by macrocycle molecule inversion). Application of exchange spectroscopy (2D-EXSY) of DNMR for investigation of this dynamic system (II-IV) simplifies the assignment of the NMR signals and represents the first experimental study of multisite exchange. In the present work, the methodology of paramagnetic 4f (Ce, Pr, and Nd) probe applications for the study of free-energy, enthalpy, and entropy changes in chemical exchange processes, as well as the advantages of this method in a comparison with DNMR studies of diamagnetic substances, is discussed. In particular, as a result of paramagnetic chemical shifts in 4f complexes, the range of measurable rate constants expands considerably compared to the analogous range in diamagnetic compounds. Coordination compounds investigated in the paper represent new types of thermometric NMR sensors and lanthanide paramagnetic probes for in situ temperature control in solution.

Controlled Folding, Motional, and Constitutional Dynamic Processes of Polyheterocyclic Molecular Strands.

Science.gov (United States)

Barboiu, Mihail; Stadler, Adrian-Mihail; Lehn, Jean-Marie

2016-03-18

General design principles have been developed for the control of the structural features of polyheterocyclic strands and their effector-modulated shape changes. Induced defined molecular motions permit designed enforcement of helical as well as linear molecular shapes. The ability of such molecular strands to bind metal cations allows the generation of coiling/uncoiling processes between helically folded and extended linear states. Large molecular motions are produced on coordination of metal ions, which may be made reversible by competition with an ancillary complexing agent and fueled by sequential acid/base neutralization energy. The introduction of hydrazone units into the strands confers upon them constitutional dynamics, whereby interconversion between different strand compositions is achieved through component exchange. These features have relevance for nanomechanical devices. We present a morphological and functional analysis of such systems developed in our laboratories. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Patrol Detection for Replica Attacks on Wireless Sensor Networks

OpenAIRE

Wang, Liang-Min; Shi, Yang

2011-01-01

Replica attack is a critical concern in the security of wireless sensor networks. We employ mobile nodes as patrollers to detect replicas distributed in different zones in a network, in which a basic patrol detection protocol and two detection algorithms for stationary and mobile modes are presented. Then we perform security analysis to discuss the defense strategies against the possible attacks on the proposed detection protocol. Moreover, we show the advantages of the proposed protocol by d...

Reconstruction of Monte Carlo replicas from Hessian parton distributions

Energy Technology Data Exchange (ETDEWEB)

Hou, Tie-Jiun [Department of Physics, Southern Methodist University,Dallas, TX 75275-0181 (United States); Gao, Jun [INPAC, Shanghai Key Laboratory for Particle Physics and Cosmology,Department of Physics and Astronomy, Shanghai Jiao-Tong University, Shanghai 200240 (China); High Energy Physics Division, Argonne National Laboratory,Argonne, Illinois, 60439 (United States); Huston, Joey [Department of Physics and Astronomy, Michigan State University,East Lansing, MI 48824 (United States); Nadolsky, Pavel [Department of Physics, Southern Methodist University,Dallas, TX 75275-0181 (United States); Schmidt, Carl; Stump, Daniel [Department of Physics and Astronomy, Michigan State University,East Lansing, MI 48824 (United States); Wang, Bo-Ting; Xie, Ke Ping [Department of Physics, Southern Methodist University,Dallas, TX 75275-0181 (United States); Dulat, Sayipjamal [Department of Physics and Astronomy, Michigan State University,East Lansing, MI 48824 (United States); School of Physics Science and Technology, Xinjiang University,Urumqi, Xinjiang 830046 (China); Center for Theoretical Physics, Xinjiang University,Urumqi, Xinjiang 830046 (China); Pumplin, Jon; Yuan, C.P. [Department of Physics and Astronomy, Michigan State University,East Lansing, MI 48824 (United States)

2017-03-20

We explore connections between two common methods for quantifying the uncertainty in parton distribution functions (PDFs), based on the Hessian error matrix and Monte-Carlo sampling. CT14 parton distributions in the Hessian representation are converted into Monte-Carlo replicas by a numerical method that reproduces important properties of CT14 Hessian PDFs: the asymmetry of CT14 uncertainties and positivity of individual parton distributions. The ensembles of CT14 Monte-Carlo replicas constructed this way at NNLO and NLO are suitable for various collider applications, such as cross section reweighting. Master formulas for computation of asymmetric standard deviations in the Monte-Carlo representation are derived. A correction is proposed to address a bias in asymmetric uncertainties introduced by the Taylor series approximation. A numerical program is made available for conversion of Hessian PDFs into Monte-Carlo replicas according to normal, log-normal, and Watt-Thorne sampling procedures.

Molecular dynamics as a method to gain understanding in questions concerning montmorillonite

International Nuclear Information System (INIS)

Seppaelae, A.; Vaari, J.; Puhakka, E.; Tanhua-Tyrkkoe, M.; Olin, M.; Kasa, S.

2012-01-01

Document available in extended abstract form only. Bentonite is one of the main material components to be used in the KBS-3 concept for safe disposal of spent nuclear fuel. The functional material in bentonite giving its beneficial properties is montmorillonite mineral. Montmorillonite consists of two completely different components: one nano-metre thick and approximately 200-400 nano-metres wide mineral layers carrying constant charge and charge compensating cations very near the mineral surfaces. The first component is more of a passive component while the second can absorb water molecules and change the cationic composition. In addition to montmorillonite bentonite usually contains some salts dissolved into water and accessory minerals. Any bulk bentonite is formed from these components via many scales of which structure is not yet fully known to science. Therefore the beneficial macroscopic properties of bentonite are assumed to follow from the nano-level structure and reactions. In safety studies of spent fuel disposal the time span to be considered extends beyond a hundred thousand years making any straightforward experimenting impossible. However, by modelling it is possible to study even very long periods of time. Unfortunately the model data and reactions are at least implicitly based on our short term experiments and may therefore be biased in some way. One possible solution to this may be the application of molecular chemistry or dynamics to construct the basis for our modelling studies. We have applied molecular chemistry on surface properties of kaolinite clay and biotite mineral but molecular dynamics is a new type of modelling for us. We believe that (during the coming ten years) molecular dynamics could make it easier to understand for example the following topics: How do charge compensating (exchanged) and aqueous cations interact? Why does water expand montmorillonite during wetting? Exact mechanism? How does water leave montmorillonite during

Variations in calcite growth kinetics with surface topography: molecular dynamics simulations and process-based growth kinetics modelling

NARCIS (Netherlands)

Wolthers, M.; Di Tommaso, D.; Du, Zhimei; de Leeuw, Nora H.

2013-01-01

It is generally accepted that cation dehydration is the rate-limiting step to crystal growth from aqueous solution. Here we employ classical molecular dynamics simulations to show that the water exchange frequency at structurally distinct calcium sites in the calcite surface varies by about two

Accuracy of three-dimensional printing for manufacturing replica teeth

OpenAIRE

Lee, Keun-Young; Cho, Jin-Woo; Chang, Na-Young; Chae, Jong-Moon; Kang, Kyung-Hwa; Kim, Sang-Cheol; Cho, Jin-Hyoung

2015-01-01

Objective Three-dimensional (3D) printing is a recent technological development that may play a significant role in orthodontic diagnosis and treatment. It can be used to fabricate skull models or study models, as well as to make replica teeth in autotransplantation or tooth impaction cases. The aim of this study was to evaluate the accuracy of fabrication of replica teeth made by two types of 3D printing technologies. Methods Fifty extracted molar teeth were selected as samples. They were sc...

How Well Does BODIPY-Cholesteryl Ester Mimic Unlabeled Cholesteryl Esters in High Density Lipoprotein Particles?

DEFF Research Database (Denmark)

Karilainen, Topi; Vuorela, Timo; Vattulainen, Ilpo

2015-01-01

We compare the behavior of unlabeled and BODIPY-labeled cholesteryl ester (CE) in high density lipoprotein by atomistic molecular dynamics simulations. We find through replica exchange umbrella sampling and unbiased molecular dynamics simulations that BODIPY labeling has no significant effect...... on the partitioning of CE between HDL and the water phase. However, BODIPY-CE was observed to diffuse more slowly and locate itself closer to the HDL-water interface than CE due to the BODIPY probe that is constrained to the surface region, and because the CE body in BODIPY-CE prefers to align itself away from...... the HDL surface. The implications as to the suitability of BODIPY to explore lipoprotein properties are discussed....

Molecular (Feshbach) treatment of charge exchange Li/sup 3 +/+He collisions. I. Energies and couplings

Energy Technology Data Exchange (ETDEWEB)

Martin, F.; Riera, A.; Yanez, M.

1986-05-15

We point out a fundamental difference between the molecular treatment of charge exchange X/sup n/++H(1s) and X/sup n/++He(1s/sup 2/) collisions, which is that the latter process involves molecular states that are formally autoionizing. Then standard ab initio methods do not, in general, yield the relevant wave functions that are needed in the collision treatment, irrespective of whether quasimolecular autoionization be significant or not during the collision. We implement a particularly simple and useful form of the Feshbach formalism to calculate the energies of those two electron systems, and a method to evaluate the corresponding dynamical couplings is presented for the first time. Our implementation of this formalism together with the new computational techniques involved are presented in detail.

The added value of the replica simulators in the exploitation of nuclear power plants; El valor anadido de los simuladores replica en la explotacion de las centrales nucleares

Energy Technology Data Exchange (ETDEWEB)

Diaz Giron, P. a.; Ortega, F.; Rivero, N.

2011-07-01

Nuclear power plants full scope replica simulators were in the past solely designed following operational personnel training criteria. Nevertheless, these simulators not only feature a high replica control room but also provide an accurate process response. Control room replica simulators are presently based on complex technological platforms permitting highest physical and functional fidelity, allowing to be used as versatile and value added tools in diverse plants operation and maintenance activities. In recent years. Tecnatom has extended the use of such simulators to different engineering applications. this article intends to identify the simulators use in training and other applications beyond training. (Author)

Internal structure analysis of particle-double network gels used in a gel organ replica

Science.gov (United States)

Abe, Mei; Arai, Masanori; Saito, Azusa; Sakai, Kazuyuki; Kawakami, Masaru; Furukawa, Hidemitsu

2016-04-01

In recent years, the fabrication of patient organ replicas using 3D printers has been attracting a great deal of attention in medical fields. However, the cost of these organ replicas is very high as it is necessary to employ very expensive 3D printers and printing materials. Here we present a new gel organ replica, of human kidney, fabricated with a conventional molding technique, using a particle-double network hydrogel (P-DN gel). The replica is transparent and has the feel of a real kidney. It is expected that gel organ replicas produced this way will be a useful tool for the education of trainee surgeons and clinical ultrasonography technologists. In addition to developing a gel organ replica, the internal structure of the P-DN gel used is also discussed. Because the P-DN gel has a complex structure comprised of two different types of network, it has not been possible to investigate them internally in detail. Gels have an inhomogeneous network structure. If it is able to get a more uniform structure, it is considered that this would lead to higher strength in the gel. In the present study we investigate the structure of P-DN gel, using the gel organ replica. We investigated the internal structure of P-DN gel using Scanning Microscopic Light Scattering (SMILS), a non-contacting and non-destructive.

A model of lipid-free apolipoprotein A-I revealed by iterative molecular dynamics simulation.

Directory of Open Access Journals (Sweden)

Xing Zhang

Full Text Available Apolipoprotein A-I (apo A-I, the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS. Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipid-free apo A-I, which contains a bundled four-helix N-terminal domain (1-192 that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193-243. This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.

Erbium(III) in aqueous solution: an ab initio molecular dynamics study.

Science.gov (United States)

Canaval, Lorenz R; Sakwarathorn, Theerathad; Rode, Bernd M; Messner, Christoph B; Lutz, Oliver M D; Bonn, Günther K

2013-12-05

Structural and dynamical properties of the erbium(III) ion in water have been obtained by means of ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations for the ground state and an excited state. The quality of the simulations has been monitored by recording UV/vis and Raman spectra of dilute solutions of ErCl3 and Er(NO3)3 in water and by comparison with EXAFS data from literature. Slight deviations between these data can be mainly attributed to relativistic effects, which are not sufficiently considered by the methodological framework. In both simulations, a mixture of coordination numbers eight and nine and a ligand exchange on the picosecond range are observed. The strength of the Er-ligand bond is considerably lower than that of trivalent transition metal ions but higher than that for La(III) and Ce(III) in aqueous solution. The main difference between ground state and excited state is the ligand exchange rate of the first shell. The second hydration shell is stable in both cases but with significantly different properties.

Replica symmetry breaking solution for two-sublattice fermionic Ising spin glass models in a transverse field

International Nuclear Information System (INIS)

Zimmer, F.M.; Magalhaes, S.G.

2007-01-01

The one-step replica symmetry breaking is used to study the competition between spin glass (SG) and antiferromagnetic order (AF) in two-sublattice fermionic Ising SG models in the presence of a transverse Γ and a parallel H magnetic fields. Inter- and intra-sublattice exchange interactions following Gaussian distributions are considered. The problem is formulated in a Grassmann path integral formalism within the static ansatz. Results show that H favors the non-ergodic mixed phase (AF+SG) and it destroys the AF. The Γ suppresses the magnetic orders, and the intra-sublattice interaction can introduce a discontinuous phase transition

Nonequilibrium molecular dynamics: The first 25 years

International Nuclear Information System (INIS)

Hoover, W.G.

1992-08-01

Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments

Patrol Detection for Replica Attacks on Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Yang Shi

2011-02-01

Full Text Available Replica attack is a critical concern in the security of wireless sensor networks. We employ mobile nodes as patrollers to detect replicas distributed in different zones in a network, in which a basic patrol detection protocol and two detection algorithms for stationary and mobile modes are presented. Then we perform security analysis to discuss the defense strategies against the possible attacks on the proposed detection protocol. Moreover, we show the advantages of the proposed protocol by discussing and comparing the communication cost and detection probability with some existing methods.

Lattice dynamics and molecular dynamics simulation of complex materials

International Nuclear Information System (INIS)

Chaplot, S.L.

1997-01-01

In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

Replica methods for loopy sparse random graphs

International Nuclear Information System (INIS)

Coolen, ACC

2016-01-01

I report on the development of a novel statistical mechanical formalism for the analysis of random graphs with many short loops, and processes on such graphs. The graphs are defined via maximum entropy ensembles, in which both the degrees (via hard constraints) and the adjacency matrix spectrum (via a soft constraint) are prescribed. The sum over graphs can be done analytically, using a replica formalism with complex replica dimensions. All known results for tree-like graphs are recovered in a suitable limit. For loopy graphs, the emerging theory has an appealing and intuitive structure, suggests how message passing algorithms should be adapted, and what is the structure of theories describing spin systems on loopy architectures. However, the formalism is still largely untested, and may require further adjustment and refinement. (paper)

Current Account and Real Exchange Rate Dynamics in Indonesia

Directory of Open Access Journals (Sweden)

Firman Mochtar

2015-07-01

Full Text Available We analyze the role of both permanent and temporary factors in affecting the Indonesian current account and real exchange dynamics before and after 2000. Adopting Lee and Chinn (1998; 2006 approach as well as Chinn et al. (2007, two results stand out. First, we confirm that the behavior of the real exchange rate has altered since 2000. Identifications show that permanent shocks are the primary causes for the movement of the real exchange rate after 2000, while in the period before 2000, the Indonesian real exchange rate changes are characterized by greater dominance of temporary shocks. The apparent change in the real exchange rate behavior may be strongly justified by the implementation of free-floating exchange rate system since August 1997. Second, the shift of the real exchange rate behavior after 2000 does not necessarily affect the current account dynamics. Empirical evidence confirms that the variance of current account post 2000 remains largely due to temporary shocks. Albeit having increasing influence, permanent shocks have insignificant effect in explaining fluctuations of the current account. In this sense, the current account surplus after 2000 is attributed largely to nominal variables such as price increase, while the impact of productivity improvement is still limited.

Popularity framework to process dataset traces and its application on dynamic replica reduction in the ATLAS experiment

International Nuclear Information System (INIS)

Molfetas, Angelos; Megino, Fernando Barreiro; Tykhonov, Andrii; Lassnig, Mario; Garonne, Vincent; Barisits, Martin; Campana, Simone; Dimitrov, Gancho; Jezequel, Stephane; Ueda, Ikuo; Viegas, Florbela Tique Aires

2011-01-01

The ATLAS experiment's data management system is constantly tracing file movement operations that occur on the Worldwide LHC Computing Grid (WLCG). Due to the large scale of the WLCG, statistical analysis of the traces is infeasible in real-time. Factors that contribute to the scalability problems include the capability for users to initiate on-demand queries, high dimensionality of tracer entries combined with very low cardinality parameters, and the large size of the namespace. These scalability issues are alleviated through the adoption of an incremental model that aggregates data for all combinations occurring in selected tracer fields on a daily basis. Using this model it is possible to query on-demand relevant statistics about system usage. We present an implementation of this popularity model in the experiment's distributed data management system, DQ2, and describe a direct application example of the popularity framework, an automated cleaning system, which uses the statistics to dynamically detect and reduce unpopular replicas from grid sites. This paper describes the architecture employed by the cleaning system and reports on the results collected from a prototype during the first months of the ATLAS collision data taking.

Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

PyRETIS: A well-done, medium-sized python library for rare events.

Science.gov (United States)

Lervik, Anders; Riccardi, Enrico; van Erp, Titus S

2017-10-30

Transition path sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, for example, chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. PyRETIS is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The folding mechanism and key metastable state identification of the PrP127-147 monomer studied by molecular dynamics simulations and Markov state model analysis.

Science.gov (United States)

Zhou, Shuangyan; Wang, Qianqian; Wang, Yuwei; Yao, Xiaojun; Han, Wei; Liu, Huanxiang

2017-05-10

The structural transition of prion proteins from a native α-helix (PrP C ) to a misfolded β-sheet-rich conformation (PrP Sc ) is believed to be the main cause of a number of prion diseases in humans and animals. Understanding the molecular basis of misfolding and aggregation of prion proteins will be valuable for unveiling the etiology of prion diseases. However, due to the limitation of conventional experimental techniques and the heterogeneous property of oligomers, little is known about the molecular architecture of misfolded PrP Sc and the mechanism of structural transition from PrP C to PrP Sc . The prion fragment 127-147 (PrP127-147) has been reported to be a critical region for PrP Sc formation in Gerstmann-Straussler-Scheinker (GSS) syndrome and thus has been used as a model for the study of prion aggregation. In the present study, we employ molecular dynamics (MD) simulation techniques to study the conformational change of this fragment that could be relevant to the PrP C -PrP Sc transition. Employing extensive replica exchange molecular dynamics (REMD) and conventional MD simulations, we sample a huge number of conformations of PrP127-147. Using the Markov state model (MSM), we identify the metastable conformational states of this fragment and the kinetic network of transitions between the states. The resulting MSM reveals that disordered random-coiled conformations are the dominant structures. A key metastable folded state with typical extended β-sheet structures is identified with Pro137 being located in a turn region, consistent with a previous experimental report. Conformational analysis reveals that intrapeptide hydrophobic interaction and two key residue interactions, including Arg136-His140 and Pro137-His140, contribute a lot to the formation of ordered extended β-sheet states. However, network pathway analysis from the most populated disordered state indicates that the formation of extended β-sheet states is quite slow (at the millisecond

Microlens fabrication by replica molding of frozen laser-printed droplets

Science.gov (United States)

Surdo, Salvatore; Diaspro, Alberto; Duocastella, Martí

2017-10-01

In this work, we synergistically combine laser-induced forward transfer (LIFT) and replica molding for the fabrication of microlenses with control of their geometry and size independent of the material or substrate used. Our approach is based on a multistep process in which liquid microdroplets of an aqueous solution are first printed on a substrate by LIFT. Following a freezing step, the microdroplets are used as a master to fabricate a polydimethylsiloxane (PDMS) mold. A subsequent replica molding step enables the creation of microlenses and microlens arrays on arbitrary selected substrates and by using different curable polymers. Thus, our method combines the rapid fabrication capabilities of LIFT and the perfectively smooth surface quality of the generated microdroplets, with the advantages of replica molding in terms of parallelization and materials flexibility. We demonstrate our strategy by generating microlenses of different photocurable polymers and by characterizing their optical and morphological properties.

Substructured multibody molecular dynamics.

Energy Technology Data Exchange (ETDEWEB)

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Replica symmetry breaking in short range spin glasses: A review of the theoretical foundations and of the numerical evidence

International Nuclear Information System (INIS)

Marinari, E.; Zuliani, F.; Parisi, G.; Ricci-Tersenghi, F.; Ruiz-Lorenzo, J.J.

2000-04-01

We discuss Replica Symmetry Breaking (RSB) in Spin Glasses. We present an update about the state of the matter, both from the analytical and from the numerical point of view. We put a particular attention in discussing the difficulties stressed by Newman and Stein concerning the problem of constructing pure states in spin glass systems. We mainly discuss about what happens in finite dimensional, realistic spin glasses. Together with a detailed review of some of most important features, facts, data, phenomena, we present some new theoretical ideas and numerical results. We discuss among others the basic idea of the RSB theory, correlation functions, interfaces, overlaps, pure states, random field and the dynamical approach. We present new numerical results for the behavior of coupled replicas and about the numerical verification of sum rules, and we review some of the available numerical results that we consider of larger importance (for example the determination of the phase transition point, the correlation functions, the window overlaps, the dynamical behavior of the system). (author)

Rotationally resolved flurorescence as a probe of molecular photoionization dynamics

International Nuclear Information System (INIS)

Poliakoff, E.D.; Kakar, S.; Choi, H.C.

1993-01-01

We present rotationally resolved data for N 2 (2σ u -1 ) photoionization in the excitation energy range 19 ≤ hν ≤ 35 eV. These are the first rotationally resolved measurements on the photoion over an extended spectral range above the ionization threshold. The requisite resolution is obtained by measuring rotationally resolved fluorescence from electronically excited photoions created by synchrotron radiation. This technique is useful for studying dynamical features embedded deep in the ionization continua and should supplement laser-based methods that are limited to probing near-threshold phenomena. The present study shows that the outgoing photoelectron can alter the rotational motion of the more massive photoion by exchanging angular momentum and this partitioning of angular momentum depends on the ionization dynamics. Thus, our data directly probe electron-molecule interactions and are sensitive probes of scattering dynamics. We are currently investigating dynamical features such as shape resonances and Cooper minima with rotational resolution for deciphering microscopic aspects of molecular scattering and these efforts will be discussed

3D printed replicas for endodontic education.

Science.gov (United States)

Reymus, M; Fotiadou, C; Kessler, A; Heck, K; Hickel, R; Diegritz, C

2018-06-14

To assess the feasibility of producing artificial teeth for endodontic training using 3D printing technology, to analyse the accuracy of the printing process, and to evaluate the teeth by students when used during training. Sound extracted human teeth were selected, digitalized by cone beam computed tomography (CBCT) and appropriate software and finally reproduced by a stereolithographic printer. The printed teeth were scanned and compared with the original ones (trueness) and to one another (precision). Undergraduate dental students in the third and fourth years performed root canal treatment on printed molars and were subsequently asked to evaluate their experience with these compared to real teeth. The workflow was feasible for manufacturing 3D printed tooth replicas. The absolute deviation after printing (trueness) ranged from 50.9μm to 104.3μm. The values for precision ranged from 43.5μm to 68.2μm. Students reported great benefits in the use of the replicated teeth for training purposes. The presented workflow is feasible for any dental educational institution who has access to a CBCT unit and a stereolithographic printer. The accuracy of the printing process is suitable for the production of tooth replicas for endodontic training. Undergraduate students favoured the availability of these replicas and the fairness they ensured in training due to standardization. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Creating technical heritage object replicas in a virtual environment

Science.gov (United States)

Egorova, Olga; Shcherbinin, Dmitry

2016-03-01

The paper presents innovative informatics methods for creating virtual technical heritage replicas, which are of significant scientific and practical importance not only to researchers but to the public in general. By performing 3D modeling and animation of aircrafts, spaceships, architectural-engineering buildings, and other technical objects, the process of learning is achieved while promoting the preservation of the replicas for future generations. Modern approaches based on the wide usage of computer technologies attract a greater number of young people to explore the history of science and technology and renew their interest in the field of mechanical engineering.

An improved molecular dynamics algorithm to study thermodiffusion in binary hydrocarbon mixtures

Science.gov (United States)

Antoun, Sylvie; Saghir, M. Ziad; Srinivasan, Seshasai

2018-03-01

In multicomponent liquid mixtures, the diffusion flow of chemical species can be induced by temperature gradients, which leads to a separation of the constituent components. This cross effect between temperature and concentration is known as thermodiffusion or the Ludwig-Soret effect. The performance of boundary driven non-equilibrium molecular dynamics along with the enhanced heat exchange (eHEX) algorithm was studied by assessing the thermodiffusion process in n-pentane/n-decane (nC5-nC10) binary mixtures. The eHEX algorithm consists of an extended version of the HEX algorithm with an improved energy conservation property. In addition to this, the transferable potentials for phase equilibria-united atom force field were employed in all molecular dynamics (MD) simulations to precisely model the molecular interactions in the fluid. The Soret coefficients of the n-pentane/n-decane (nC5-nC10) mixture for three different compositions (at 300.15 K and 0.1 MPa) were calculated and compared with the experimental data and other MD results available in the literature. Results of our newly employed MD algorithm showed great agreement with experimental data and a better accuracy compared to other MD procedures.

Standard practice for production and evaluation of field metallographic replicas

CERN Document Server

American Society for Testing and Materials. Philadelphia

2001-01-01

1.1 This practice covers recognized methods for the preparation and evaluation of cellulose acetate or plastic film replicas which have been obtained from metallographically prepared surfaces. It is designed for the evaluation of replicas to ensure that all significant features of a metallographically prepared surface have been duplicated and preserved on the replica with sufficient detail to permit both LM and SEM examination with optimum resolution and sensitivity. 1.2 This practice may be used as a controlling document in commercial situations. 1.3 The values stated in SI units are to be regarded as the standard. Inch-pound units given in parentheses are for information only. 1.4 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use.

Are international fund flows related to exchange rate dynamics?

NARCIS (Netherlands)

Li, Suxiao; de Haan, Jakob; Scholtens, Bert

2018-01-01

Employing monthly data for 53 countries between 1996 and 2015, we investigate the relationship between international fund flows and exchange rate dynamics. We find strong co-movement between funds flows (as measured with the EPFR Global data base) and bilateral real exchange rates vis-à-vis the USD.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

Science.gov (United States)

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

On the hydration of subnanometric antifouling organosilane adlayers: a molecular dynamics simulation.

Science.gov (United States)

Sheikh, Sonia; Blaszykowski, Christophe; Nolan, Robert; Thompson, Damien; Thompson, Michael

2015-01-01

The connection between antifouling and surface hydration is a fascinating but daunting question to answer. Herein, we use molecular dynamics (MD) computer simulations to gain further insight into the role of surface functionalities in the molecular-level structuration of water (surface kosmotropicity)--within and atop subnanometric organosilane adlayers that were shown in previous experimental work to display varied antifouling behavior. Our simulations support the hypothesized intimate link between surface hydration and antifouling, in particular the importance of both internal and interfacial hydrophilicity and kosmotropicity. The antifouling mechanism is also discussed in terms of surface dehydration energy and water dynamicity (lability and mobility), notably the crucial requirement for clustered water molecules to remain tightly bound for extensive periods of time--i.e. exhibit slow exchange dynamics. A substrate effect on surface hydration, which would also participate in endowing antifouling adlayers with hydrogel-like characteristics, is also proposed. In contrast, the role of adlayer flexibility, if any, is assigned a secondary role in these ultrathin structures made of short building blocks. The conclusions from this work are well in line with those previously drawn in the literature. Copyright © 2014 Elsevier Inc. All rights reserved.

Neat and complete: Thiolate-ligand exchange on a silver molecular nanoparticle

KAUST Repository

AbdulHalim, Lina G.

2014-11-12

Atomically precise thiolate-protected noble metal molecular nanoparticles are a promising class of model nanomaterials for catalysis, optoelectronics, and the bottom-up assembly of true molecular crystals. However, these applications have not fully materialized due to a lack of ligand exchange strategies that add functionality, but preserve the properties of these remarkable particles. Here we present a method for the rapid (<30 s) and complete thiolate-for-thiolate exchange of the highly sought after silver molecular nanoparticle [Ag44(SR)30]-4. Only by using this method were we able to preserve the precise nature of the particles and simultaneously replace the native ligands with ligands containing a variety of functional groups. Crucially, as a result of our method we were able to process the particles into smooth thin films, paving the way for their integration into solution-processed devices.

Neat and complete: Thiolate-ligand exchange on a silver molecular nanoparticle

KAUST Repository

AbdulHalim, Lina G.; Kothalawala, Nuwan; Sinatra, Lutfan; Dass, Amala; Bakr, Osman

2014-01-01

Atomically precise thiolate-protected noble metal molecular nanoparticles are a promising class of model nanomaterials for catalysis, optoelectronics, and the bottom-up assembly of true molecular crystals. However, these applications have not fully materialized due to a lack of ligand exchange strategies that add functionality, but preserve the properties of these remarkable particles. Here we present a method for the rapid (<30 s) and complete thiolate-for-thiolate exchange of the highly sought after silver molecular nanoparticle [Ag44(SR)30]-4. Only by using this method were we able to preserve the precise nature of the particles and simultaneously replace the native ligands with ligands containing a variety of functional groups. Crucially, as a result of our method we were able to process the particles into smooth thin films, paving the way for their integration into solution-processed devices.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-01

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-06

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Molecular MRI using exogenous enzymatic sensors and endogenous chemical exchange contrast

OpenAIRE

Taylor, Alexander John

2016-01-01

Molecular magnetic resonance imaging (MRI) methods have the potential to provide detailed information regarding cellular and molecular processes at small scales within the human body. Nuclear signals from chemical samples can be probed using specialised MRI techniques, to highlight molecular contrast from particular enzymes or metabolites. The aim of the work described in this thesis is to investigate both exogenous and endogenous contrast mechanisms using fluorine MRI and chemical exchange s...

Replica-Based High-Performance Tuple Space Computing

DEFF Research Database (Denmark)

Andric, Marina; De Nicola, Rocco; Lluch Lafuente, Alberto

2015-01-01

of concurrency and data access. We investigate issues related to replica consistency, provide an operational semantics that guides the implementation of the language, and discuss the main synchronization mechanisms of our prototypical run-time framework. Finally, we provide a performance analysis, which includes...

A Novel General Chemistry Laboratory: Creation of Biomimetic Superhydrophobic Surfaces through Replica Molding

Science.gov (United States)

Verbanic, Samuel; Brady, Owen; Sanda, Ahmed; Gustafson, Carolina; Donhauser, Zachary J.

2014-01-01

Biomimetic replicas of superhydrophobic lotus and taro leaf surfaces can be made using polydimethylsiloxane. These replicas faithfully reproduce the microstructures of the leaves' surface and can be analyzed using contact angle goniometry, self-cleaning experiments, and optical microscopy. These simple and adaptable experiments were used to…

Automated magnification calibration in transmission electron microscopy using Fourier analysis of replica images

International Nuclear Information System (INIS)

Laak, Jeroen A.W.M. van der; Dijkman, Henry B.P.M.; Pahlplatz, Martin M.M.

2006-01-01

The magnification factor in transmission electron microscopy is not very precise, hampering for instance quantitative analysis of specimens. Calibration of the magnification is usually performed interactively using replica specimens, containing line or grating patterns with known spacing. In the present study, a procedure is described for automated magnification calibration using digital images of a line replica. This procedure is based on analysis of the power spectrum of Fourier transformed replica images, and is compared to interactive measurement in the same images. Images were used with magnification ranging from 1,000x to 200,000x. The automated procedure deviated on average 0.10% from interactive measurements. Especially for catalase replicas, the coefficient of variation of automated measurement was considerably smaller (average 0.28%) compared to that of interactive measurement (average 3.5%). In conclusion, calibration of the magnification in digital images from transmission electron microscopy may be performed automatically, using the procedure presented here, with high precision and accuracy

Polymer friction Molecular Dynamics

DEFF Research Database (Denmark)

Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

Double agents and secret agents: the emerging fields of exogenous chemical exchange saturation transfer and T2-exchange magnetic resonance imaging contrast agents for molecular imaging.

Science.gov (United States)

Daryaei, Iman; Pagel, Mark D

2015-01-01

Two relatively new types of exogenous magnetic resonance imaging contrast agents may provide greater impact for molecular imaging by providing greater specificity for detecting molecular imaging biomarkers. Exogenous chemical exchange saturation transfer (CEST) agents rely on the selective saturation of the magnetization of a proton on an agent, followed by chemical exchange of a proton from the agent to water. The selective detection of a biomarker-responsive CEST signal and an unresponsive CEST signal, followed by the ratiometric comparison of these signals, can improve biomarker specificity. We refer to this improvement as a "double-agent" approach to molecular imaging. Exogenous T 2 -exchange agents also rely on chemical exchange of protons between the agent and water, especially with an intermediate rate that lies between the slow exchange rates of CEST agents and the fast exchange rates of traditional T 1 and T 2 agents. Because of this intermediate exchange rate, these agents have been relatively unknown and have acted as "secret agents" in the contrast agent research field. This review exposes these secret agents and describes the merits of double agents through examples of exogenous agents that detect enzyme activity, nucleic acids and gene expression, metabolites, ions, redox state, temperature, and pH. Future directions are also provided for improving both types of contrast agents for improved molecular imaging and clinical translation. Therefore, this review provides an overview of two new types of exogenous contrast agents that are becoming useful tools within the armamentarium of molecular imaging.

Nanostructure and molecular mechanics of spider dragline silk protein assemblies

Science.gov (United States)

Keten, Sinan; Buehler, Markus J.

2010-01-01

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206

Real Exchange Rate Dynamics in a Small, Primary-Exporting Country

OpenAIRE

Mohsin S. Khan; Peter J. Montiel

1987-01-01

Although the nominal exchange rate is often used as a policy instrument in small, primary-commodity-exporting countries, the real exchange rate is an endogenous variable that responds to both exogenous and policyinduced shocks. This paper examines the dynamic effects on the real exchange rate of various shocks, such as devaluation, fiscal and trade policies, and changes in the terms of trade and foreign real interest rates. Because the path of the real exchange rate differs for different type...

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

Science.gov (United States)

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Synthesis and properties of ZnFe2O4 replica with biological hierarchical structure

International Nuclear Information System (INIS)

Liu, Hongyan; Guo, Yiping; Zhang, Yangyang; Wu, Fen; Liu, Yun; Zhang, Di

2013-01-01

Highlights: • ZFO replica with hierarchical structure was synthesized from butterfly wings. • Biotemplate has a significant impact on the properties of ZFO material. • Our method opens up new avenues for the synthesis of spinel ferrites. -- Abstract: ZnFe 2 O 4 replica with biological hierarchical structure was synthesized from Papilio paris by a sol–gel method followed by calcination. The crystallographic structure and morphology of the obtained samples were characterized by X-ray diffraction, field-emission scanning electron microscope, and transmittance electron microscope. The results showed that the hierarchical structures were retained in the ZFO replica of spinel structure. The magnetic behavior of such novel products was measured by a vibrating sample magnetometer. A superparamagnetism-like behavior was observed due to nanostructuration size effects. In addition, the ZFO replica with “quasi-honeycomb-like structure” showed a much higher specific capacitance of 279.4 F g −1 at 10 mV s −1 in comparison with ZFO powder of 137.3 F g −1 , attributing to the significantly increased surface area. These results demonstrated that ZFO replica is a promising candidate for novel magnetic devices and supercapacitors

A distance-aware replica adaptive data gathering protocol for Delay Tolerant Mobile Sensor Networks.

Science.gov (United States)

Feng, Yong; Gong, Haigang; Fan, Mingyu; Liu, Ming; Wang, Xiaomin

2011-01-01

In Delay Tolerant Mobile Sensor Networks (DTMSNs) that have the inherent features of intermitted connectivity and frequently changing network topology it is reasonable to utilize multi-replica schemes to improve the data gathering performance. However, most existing multi-replica approaches inject a large amount of message copies into the network to increase the probability of message delivery, which may drain each mobile node's limited battery supply faster and result in too much contention for the restricted resources of the DTMSN, so a proper data gathering scheme needs a trade off between the number of replica messages and network performance. In this paper, we propose a new data gathering protocol called DRADG (for Distance-aware Replica Adaptive Data Gathering protocol), which economizes network resource consumption through making use of a self-adapting algorithm to cut down the number of redundant replicas of messages, and achieves a good network performance by leveraging the delivery probabilities of the mobile sensors as main routing metrics. Simulation results have shown that the proposed DRADG protocol achieves comparable or higher message delivery ratios at the cost of the much lower transmission overhead than several current DTMSN data gathering schemes.

Quantum master equation method based on the broken-symmetry time-dependent density functional theory: application to dynamic polarizability of open-shell molecular systems.

Science.gov (United States)

Kishi, Ryohei; Nakano, Masayoshi

2011-04-21

A novel method for the calculation of the dynamic polarizability (α) of open-shell molecular systems is developed based on the quantum master equation combined with the broken-symmetry (BS) time-dependent density functional theory within the Tamm-Dancoff approximation, referred to as the BS-DFTQME method. We investigate the dynamic α density distribution obtained from BS-DFTQME calculations in order to analyze the spatial contributions of electrons to the field-induced polarization and clarify the contributions of the frontier orbital pair to α and its density. To demonstrate the performance of this method, we examine the real part of dynamic α of singlet 1,3-dipole systems having a variety of diradical characters (y). The frequency dispersion of α, in particular in the resonant region, is shown to strongly depend on the exchange-correlation functional as well as on the diradical character. Under sufficiently off-resonant condition, the dynamic α is found to decrease with increasing y and/or the fraction of Hartree-Fock exchange in the exchange-correlation functional, which enhances the spin polarization, due to the decrease in the delocalization effects of π-diradical electrons in the frontier orbital pair. The BS-DFTQME method with the BHandHLYP exchange-correlation functional also turns out to semiquantitatively reproduce the α spectra calculated by a strongly correlated ab initio molecular orbital method, i.e., the spin-unrestricted coupled-cluster singles and doubles.

Molecular exchange of n-hexane in zeolite sieves studied by diffusion-diffusion and T{sub 1}-diffusion nuclear magnetic resonance exchange spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Neudert, Oliver; Stapf, Siegfried; Mattea, Carlos, E-mail: carlos.mattea@tu-ilmenau.de [Fachgebiet Technische Physik II/Polymerphysik, Institute of Physics, Technische Universitaet Ilmenau, PO Box 100 565, 98684 Ilmenau (Germany)

2011-03-15

Molecular exchange properties and diffusion of n-hexane embedded in a bimodal pore structure with characteristic length scales in the order of nano and micrometres, respectively, formed by packing of zeolite particles, are studied. Two-dimensional (2D) nuclear magnetic resonance (NMR) diffusion correlation experiments together with relaxation-diffusion correlation experiments are performed at low magnetic field using a single-sided NMR scanner. The exchange time covers a range from 10{sup -3} to 10{sup -1} s. The molecular exchange properties are modulated by transport inside the zeolite particles. Different exchange regimes are observed for molecules starting from different positions inside the porous sample. The influence of the spin-lattice relaxation properties of the fluid molecules inside the zeolite particles on the signal intensity is also studied. A Monte Carlo simulation of the exchange process is performed and is used to support the analysis of the experimental data.

Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

International Nuclear Information System (INIS)

Imran, Muhammad; Hussain, Fayyaz; Ullah, Hafeez; Ahmad, Ejaz; Rashid, Muhammad; Ismail, Muhammad; Cai, Yongqing; Javid, M Arshad; Ahmad, S A

2016-01-01

Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results. (paper)

Next generation extended Lagrangian first principles molecular dynamics.

Science.gov (United States)

Niklasson, Anders M N

2017-08-07

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Ligand and proton exchange dynamics in recombinant human myoglobin mutants.

Science.gov (United States)

Lambright, D G; Balasubramanian, S; Boxer, S G

1989-05-05

Site-specific mutants of human myoglobin have been prepared in which lysine 45 is replaced by arginine (K45R) and aspartate 60 by glutamate (D60E), in order to examine the influence of these residues and their interaction on the dynamics of the protein. These proteins were studied by a variety of methods, including one and two-dimensional proton nuclear magnetic resonance spectroscopy, exchange kinetics for the distal and proximal histidine NH protons as a function of pH in the met cyano forms, flash photolysis of the CO forms, and ligand replacement kinetics. The electronic absorption and proton nuclear magnetic resonance spectra of the CO forms of these proteins are virtually identical, indicating that the structure of the heme pocket is unaltered by these mutations. There are, however, substantial changes in the dynamics of both CO binding and proton exchange for the mutant K45R, whereas the mutant D60E exhibits behavior indistinguishable from the reference human myoglobin. K45R has a faster CO bimolecular recombination rate and slower CO off-rate relative to the reference. The kinetics for CO binding are independent of pH (6.5 to 10) as well as ionic strength (0 to 1 M-NaCl). The exchange rate for the distal histidine NH is substantially lower for K45R than the reference, whereas the proximal histidine NH exchange rate is unaltered. The exchange behavior of the human proteins is similar to that reported for a comparison of the exchange rates for myoglobins having lysine at position 45 with sperm whale myoglobin, which has arginine at this position. This indicates that the differences in exchange rates reflects largely the Lys----Arg substitution. The lack of a simple correlation for the CO kinetics with this substitution means that these are sensitive to other factors as well. Specific kinetic models, whereby substitution of arginine for lysine at position 45 can affect ligand binding dynamics, are outlined. These experiments demonstrate that a relatively

Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

Directory of Open Access Journals (Sweden)

Lin Lin

2013-12-01

Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

A Molecular Dynamics Study of Lunasin | Singh | South African ...

African Journals Online (AJOL)

A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

Decay of surface nanostructures via long-time-scale dynamics

International Nuclear Information System (INIS)

Voter, A.F.; Stanciu, N.

1998-01-01

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have developed a new approach for extending the time scale of molecular dynamics simulations. For infrequent-event systems, the category that includes most diffusive events in the solid phase, this hyperdynamics method can extend the simulation time by a few orders of magnitude compared to direct molecular dynamics. The trajectory is run on a potential surface that has been biased to raise the energy in the potential basins without affecting the transition state region. The method is described and applied to surface and bulk diffusion processes, achieving microsecond and millisecond simulation times. The authors have also developed a new parallel computing method that is efficient for small system sizes. The combination of the hyperdynamics with this parallel replica dynamics looks promising as a general materials simulation tool

NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1†

Science.gov (United States)

Parkesh, Raman; Fountain, Matthew; Disney, Matthew D.

2011-01-01

The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single hydrogen bonded structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bonded structure is the most populated one but the UU pair interconverts between 0, 1, and 2 hydrogen bonded pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins. PMID:21204525

Spin-diffusions and diffusive molecular dynamics

Science.gov (United States)

Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon

2017-12-01

Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.

Replica analysis of partition-function zeros in spin-glass models

International Nuclear Information System (INIS)

Takahashi, Kazutaka

2011-01-01

We study the partition-function zeros in mean-field spin-glass models. We show that the replica method is useful to find the locations of zeros in a complex parameter plane. For the random energy model, we obtain the phase diagram in the plane and find that there are two types of distributions of zeros: two-dimensional distribution within a phase and one-dimensional one on a phase boundary. Phases with a two-dimensional distribution are characterized by a novel order parameter defined in the present replica analysis. We also discuss possible patterns of distributions by studying several systems.

The added value of the replica simulators in the exploitation of nuclear power plants

International Nuclear Information System (INIS)

Diaz Giron, P. a.; Ortega, F.; Rivero, N.

2011-01-01

Nuclear power plants full scope replica simulators were in the past solely designed following operational personnel training criteria. Nevertheless, these simulators not only feature a high replica control room but also provide an accurate process response. Control room replica simulators are presently based on complex technological platforms permitting highest physical and functional fidelity, allowing to be used as versatile and value added tools in diverse plants operation and maintenance activities. In recent years. Tecnatom has extended the use of such simulators to different engineering applications. this article intends to identify the simulators use in training and other applications beyond training. (Author)

Cardioplegia heat exchanger design modelling using computational fluid dynamics.

Science.gov (United States)

van Driel, M R

2000-11-01

A new cardioplegia heat exchanger has been developed by Sorin Biomedica. A three-dimensional computer-aided design (CAD) model was optimized using computational fluid dynamics (CFD) modelling. CFD optimization techniques have commonly been applied to velocity flow field analysis, but CFD analysis was also used in this study to predict the heat exchange performance of the design before prototype fabrication. The iterative results of the optimization and the actual heat exchange performance of the final configuration are presented in this paper. Based on the behaviour of this model, both the water and blood fluid flow paths of the heat exchanger were optimized. The simulation predicted superior heat exchange performance using an optimal amount of energy exchange surface area, reducing the total contact surface area, the device priming volume and the material costs. Experimental results confirm the empirical results predicted by the CFD analysis.

Stability of nanofluids: Molecular dynamic approach and experimental study

International Nuclear Information System (INIS)

Farzaneh, H.; Behzadmehr, A.; Yaghoubi, M.; Samimi, A.; Sarvari, S.M.H.

2016-01-01

Highlights: • Nanofluid stability is investigated and discussed. • A molecular dynamic approach, considering different forces on the nanoparticles, is adopted. • Stability diagrams are presented for different thermo-fluid conditions. • An experimental investigation is carried out to confirm the theoretical approach. - Abstract: Nanofluids as volumetric absorbent in solar energy conversion devices or as working fluid in different heat exchangers have been proposed by various researchers. However, dispersion stability of nanofluids is an important issue that must be well addressed before any industrial applications. Conditions such as severe temperature gradient, high temperature of heat transfer fluid, nanoparticle mean diameters and types of nanoparticles and base fluid are among the most effective parameters on the stability of nanofluid. A molecular dynamic approach, considering kinetic energy of nanoparticles and DLVO potential energy between nanoparticles, is adopted to study the nanofluid stability for different nanofluids at different working conditions. Different forces such as Brownian, thermophoresis, drag and DLVO are considered to introduce the stability diagrams. The latter presents the conditions for which a nanofluid can be stable. In addition an experimental investigation is carried out to find a stable nanofluid and to show the validity of the theoretical approach. There is a good agreement between the experimental and theoretical results that confirms the validity of our theoretical approach.

Molecular dynamics study on the structure I clathrate-hydrate of methane + ethane mixture

International Nuclear Information System (INIS)

Erfan-Niya, Hamid; Modarress, Hamid; Zaminpayma, Esmaeil

2011-01-01

Molecular dynamics (MD) simulations are used to study the structure I stability of methane + ethane clathrate-hydrates at temperatures 273, 275 and 277 K. NVT- and NPT-ensembles are utilized in MD simulation, and each consists of 3 x 3 x 3 replica unit cells containing 46 water molecules which are considered as the host molecules and up to eight methane + ethane molecules considered as the guest molecules. In MD simulations for host-host interactions, the potential model used was a type of simple point charge (SPC) model, and for guest-guest and host-guest interactions the potential used was Lennard-Jones model. In the process of MD simulation, achieving equilibrium of the studied system was recognized by stability in calculated pressure for NVT-ensemble and volume for NPT-ensemble. To understand the characteristic configurations of the structure I hydrate, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules as well as other properties including kinetic energy, potential energy and total energy were calculated. The results show that guest molecules interaction with host molecules cannot decompose the hydrate structure, and these results are consistent with most previous experimental and theoretical investigations that methane + ethane mixtures form structure I hydrates over the entire mixture composition range.

Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

Energy Technology Data Exchange (ETDEWEB)

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15

The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

Free-energy landscape of a hyperstable RNA tetraloop.

Science.gov (United States)

Miner, Jacob C; Chen, Alan A; García, Angel E

2016-06-14

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

Science.gov (United States)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Thermodynamics versus Kinetics Dichotomy in the Linear Self-Assembly of Mixed Nanoblocks.

Science.gov (United States)

Ruiz, L; Keten, S

2014-06-05

We report classical and replica exchange molecular dynamics simulations that establish the mechanisms underpinning the growth kinetics of a binary mix of nanorings that form striped nanotubes via self-assembly. A step-growth coalescence model captures the growth process of the nanotubes, which suggests that high aspect ratio nanostructures can grow by obeying the universal laws of self-similar coarsening, contrary to systems that grow through nucleation and elongation. Notably, striped patterns do not depend on specific growth mechanisms, but are governed by tempering conditions that control the likelihood of depropagation and fragmentation.

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

Science.gov (United States)

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).

DNA strand exchange catalyzed by molecular crowding in PEG solutions

KAUST Repository

Feng, Bobo; Frykholm, Karolin; Nordé n, Bengt; Westerlund, Fredrik

2010-01-01

DNA strand exchange is catalyzed by molecular crowding and hydrophobic interactions in concentrated aqueous solutions of polyethylene glycol, a discovery of relevance for understanding the function of recombination enzymes and with potential applications to DNA nanotechnology. © 2010 The Royal Society of Chemistry.

Zeolite-templated carbon replica: a Grand Canonical Monte-Carlo simulation study

International Nuclear Information System (INIS)

Thomas Roussel; Roland J M Pellenq; Christophe Bichara; Roger Gadiou; Antoine Didion; Cathie Vix Guterl; Fabrice Gaslain; Julien Parmentier; Valentin Valtchev; Joel Patarin

2005-01-01

Microporous carbon materials are interesting for several applications such as hydrogen storage, catalysis or electrical double layer capacitors. The development of the negative templating method to obtain carbon replicas from ordered templates, has lead to the synthesis of several new materials which have interesting textural properties, attractive for energy storage. Among the possible templates, zeolites can be used to obtain highly microporous carbon materials. Nevertheless, the phenomena involved in the replica synthesis are not fully understood, and the relationships between the structure of the template, the carbon precursor and the resulting carbon material need to be investigated. Experimental results for carbon zeolite-templated nano-structures can be found in a series of papers; see for instance ref. [1] in which Wang et al describe a route to ultra-small Single Wall Carbon Nano-tubes (SWNTs) using the porosity of zeolite AlPO 4 -5. After matrix removal, the resulting structure is a free-standing bundle of 4 Angstroms large nano-tubes. However, it is highly desirable to obtain an ordered porous carbon structure that forms a real 3D network to be used for instance in gas storage applications. Carbon replica of faujasite and EMT zeolites can have these properties since these zeolites have a 3D porous network made of 10 Angstroms cages connected to each other through 7 Angstroms large windows. The first step of this study was to generate a theoretical carbon replica structure of various zeolites (faujasite, EMT, AlPO 4 -5, silicalite). For this purpose, we used the Grand Canonical Monte-Carlo (GCMC) technique in which the carbon-carbon interactions were described within the frame of a newly developed Tight Binding approach and the carbon-zeolite interactions assumed to be characteristic of physi-sorption. The intrinsic stability of the subsequent carbon nano-structures was then investigated after mimicking the removal of the inorganic phase by switching

Utility of replica techniques for x-ray microanalysis of second phase particles

International Nuclear Information System (INIS)

Bentley, J.

1984-01-01

X-ray microanalysis of second phase particles in ion-milled or electropolished thin foils is often complicated by the presence of the matrix nearby. Extraction replica techniques provide a means to avoid many of the complications of thin-foil analyses. In this paper, three examples of the analysis of second phase particles are described and illustrate the improvement obtained by the use of extraction replicas for qualitative analysis, quantitative analysis, and analysis of radioactive specimens

Thermally driven molecular linear motors - A molecular dynamics study

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

2009-01-01

We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Directory of Open Access Journals (Sweden)

Mark James Abraham

2015-09-01

Full Text Available GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.

Pion double charge exchange and hadron dynamics

International Nuclear Information System (INIS)

Johnson, M.B.

1991-01-01

This paper will review theoretical results to show how pion double charge exchange is contributing to our understanding of hadron dynamics in nuclei. The exploitation of the nucleus as a filter is shown to be essential in facilitating the comparison between theory and experiment. 23 refs., 3 figs., 2 tabs

A role for the juxtamembrane cytoplasm in the molecular dynamics of focal adhesions.

Directory of Open Access Journals (Sweden)

Haguy Wolfenson

Full Text Available Focal adhesions (FAs are specialized membrane-associated multi-protein complexes that link the cell to the extracellular matrix and play crucial roles in cell-matrix sensing. Considerable information is available on the complex molecular composition of these sites, yet the regulation of FA dynamics is largely unknown. Based on a combination of FRAP studies in live cells, with in silico simulations and mathematical modeling, we show that the FA plaque proteins paxillin and vinculin exist in four dynamic states: an immobile FA-bound fraction, an FA-associated fraction undergoing exchange, a juxtamembrane fraction experiencing attenuated diffusion, and a fast-diffusing cytoplasmic pool. The juxtamembrane region surrounding FAs displays a gradient of FA plaque proteins with respect to both concentration and dynamics. Based on these findings, we propose a new model for the regulation of FA dynamics in which this juxtamembrane domain acts as an intermediary layer, enabling an efficient regulation of FA formation and reorganization.

Sorption of Molecular Oxygen by Metal-Ion Exchanger Nanocomposites

Science.gov (United States)

Krysanov, V. A.; Plotnikova, N. V.; Kravchenko, T. A.

2018-03-01

Kinetic features are studied of the chemisorption and reduction of molecular oxygen from water by metal-ion exchanger nanocomposites that differ in the nature of the dispersed metal and state of oxidation. In the Pd equilibrium sorption coefficient for oxygen dissolved in water ranges from 20 to 50, depending on the nature and oxidation state of the metal component.

The Efficacy of Epidemic Algorithms on Detecting Node Replicas in Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Narasimha Shashidhar

2015-12-01

Full Text Available A node replication attack against a wireless sensor network involves surreptitious efforts by an adversary to insert duplicate sensor nodes into the network while avoiding detection. Due to the lack of tamper-resistant hardware and the low cost of sensor nodes, launching replication attacks takes little effort to carry out. Naturally, detecting these replica nodes is a very important task and has been studied extensively. In this paper, we propose a novel distributed, randomized sensor duplicate detection algorithm called Discard to detect node replicas in group-deployed wireless sensor networks. Our protocol is an epidemic, self-organizing duplicate detection scheme, which exhibits emergent properties. Epidemic schemes have found diverse applications in distributed computing: load balancing, topology management, audio and video streaming, computing aggregate functions, failure detection, network and resource monitoring, to name a few. To the best of our knowledge, our algorithm is the first attempt at exploring the potential of this paradigm to detect replicas in a wireless sensor network. Through analysis and simulation, we show that our scheme achieves robust replica detection with substantially lower communication, computational and storage requirements than prior schemes in the literature.

A hybrid particle–field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes

International Nuclear Information System (INIS)

Milano, Giuseppe; De Nicola, Antonio; Kawakatsu, Toshihiro

2013-01-01

This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle–field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle–field models. This feature makes these models very promising ones in the exploration of several problems in biophysics. (paper)

Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

International Nuclear Information System (INIS)

Perez, Danny

2012-01-01

We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

Science.gov (United States)

Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

2016-08-23

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Surgery planning and navigation by laser lithography plastic replica. Features, clinical applications, and advantages

International Nuclear Information System (INIS)

Kihara, Tomohiko; Tanaka, Yuuko; Furuhata, Kentaro

1995-01-01

The use of three-dimensional replicas created using laserlithography has recently become popular for surgical planning and intraoperative navigation in plastic surgery and oral maxillofacial surgery. In this study, we investigated many clinical applications that we have been involved in regarding the production of three-dimensional replicas. We have also analyzed the features, application classes, and advantages of this method. As a result, clinical applications are categorized into three classes, which are 'three-dimensional shape recognition', 'simulated surgery', and 'template'. The distinct features of three-dimensional replicas are 'direct recognition', 'fast manipulation', and 'free availability'. Meeting the requirements of surgical planning and intraoperative navigation, they have produced satisfactory results in clinical applications. (author)

Current-driven dynamics in molecular-scale devices

International Nuclear Information System (INIS)

Seideman, Tamar

2003-01-01

We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

Molecular Dynamics Studies of Nanofluidic Devices

DEFF Research Database (Denmark)

Zambrano Rodriguez, Harvey Alexander

of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries

Directory of Open Access Journals (Sweden)

Sanna L. Diemer

2015-09-01

Full Text Available Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system.

Molecular dynamics in porous media studied by nuclear magnetic resonance techniques

International Nuclear Information System (INIS)

Mattea, C.

2006-01-01

Field cycling NMR relaxometry was used to study dynamics of fluids under confinement in different scenarios: fluids flowing through porous media, fluids partially filling porous media and polymer melts in nanoscopic pores. Diffusion in partially filled porous media was also studied with the aid of an NMR diffusometry technique. It is shown that hydrodynamic flow influences the spin-lattice relaxation rate of water confined in mesoscopic porous media under certain conditions. The effect is predicted by an analytical theory and Monte Carlo simulations, and confirmed experimentally by field-cycling NMR relaxometry. Field-cycling NMR relaxometry has been applied to polar and non polar adsorbates in partially filled silica porous glasses. The dependence of the spin-lattice relaxation rate on the filling degree shows that limits for slow and fast exchange between different phases can be distinguished and identified depending on the pore size and polarity of the solvents. Diffusion in the same unsaturated systems was studied with the aid of NMR diffusometry technique. The effective diffusion coefficient of solvents with different polarities displays opposite tendencies as a function of the liquid content. A two-phase fast exchange model including Knudsen and ordinary diffusion and different effective tortuosities is presented accounting for these phenomena. In the case of polymer melts confined in narrow artificial tubes of a porous solid matrix with variable diameter (9 to 57 nm), the characteristics of reptation were experimentally verified using proton field cycling NMR relaxometry technique. This observation is independent of the molecular mass and pore size. In bulk, the same polymer melts show either Rouse or renormalized Rouse dynamics, depending on the molecular mass. The polymers under confinement show features specific for reptation even with a pore diameter 15 times larger than the Flory radius while bulk melts of the same polymers do not. (orig.)

Dynamics of the cross flow heat exchanger for heating purposes

Energy Technology Data Exchange (ETDEWEB)

Mueller, K [Karlsruhe Univ. (TH) (Germany, F.R.). Inst. fuer Mess- und Regelungstechnik mit Maschinenlaboratorium

1980-09-01

A series of publications is available on the dynamic behaviour of heat exchangers (or heat transmitters, respectively), the subject of which is to deal with direct methods or with refined starting models for this general theme. The bridging between both these manners of advance remained as a problem. The author tried in his own investigation to solve the problem, and indeed by the selection of the correct starting model. He succeeded in this way, in that he removed conceptually a finned pipe from an arbitrary place of a heat exchanger and, furthermore, cut out from this particular pipe an arbitrary section. This section now does not stand alone for itself because the processes, which occur upstream of this section at the air-side and the water-side, are the input quantities of the section, which changes them due to its static and dynamic behaviour and emits them again as output quantities. The author, therefore, treats at first the dynamic behaviour of the section, which is represented in a signal flow diagram and which is used to derive approximate solutions from it. Furthermore, the author discusses the evident derivation of the total behaviour of heat exchangers.

Two-dimensional exchange and nutation exchange nuclear quadrupole resonance spectroscopy

International Nuclear Information System (INIS)

Mackowiak, M.; Sinyavsky, N.; Velikite, N.; Nikolaev, D.

2002-01-01

A theoretical treatment of the 2D exchange NQR pulse sequence is presented and applied to a quantitative study of exchange processes in molecular crystals. It takes into account the off-resonance irradiation, which critically influences the spin dynamics. The response to the three-pulse sequence of a system of spins I=3/2 in zero applied field, experiencing electric quadrupole couplings, is analysed. The mixing dynamics by exchange and the expected cross-peak intensities as a function of the frequency offset have been derived. The theory is illustrated by a study of the optimization procedure, which is of crucial importance for the detection of the cross- and diagonal-peaks in a 2D-exchange spectrum. The systems investigated are hexachloroethane and tetrachloroethylene. They show threefold and twofold reorientational jumps about the carbon-carbon axis, respectively. A new method of direct determination of rotational angles based on two-dimensional nutation exchange NQR spectroscopy is proposed. The method involves the detection of exchange processes through NQR nutation spectra recorded after the mixing interval. The response of a system of spins I=3/2 to the three-pulse sequence with increasing pulse widths is analyzed. It is shown that the 2D-nutation exchange NQR spectrum exhibits characteristic ridges, which manifest the motional mechanism in a model-independent fashion. The angles through which the molecule rotates can be read directly from elliptical ridges in the 2D spectrum, which are also sensitive to the asymmetry parameter of the electric field gradient tensor. (orig.)

Computer simulation study of in-zeolites templated carbon replicas: structural and adsorption properties for hydrogen storage application

International Nuclear Information System (INIS)

Roussel, T.

2007-05-01

Hydrogen storage is the key issue to envisage this gas for instance as an energy vector in the field of transportation. Porous carbons are materials that are considered as possible candidates. We have studied well-controlled microporous carbon nano-structures, carbonaceous replicas of meso-porous ordered silica materials and zeolites. We realized numerically (using Grand Canonical Monte Carlo Simulations, GCMC) the atomic nano-structures of the carbon replication of four zeolites: AlPO 4 -5, silicalite-1, and Faujasite (FAU and EMT). The faujasite replicas allow nano-casting of a new form of carbon crystalline solid made of tetrahedrally or hexagonally interconnected single wall nano-tubes. The pore size networks are nano-metric giving these materials optimized hydrogen molecular storage capacities (for pure carbon phases). However, we demonstrate that these new carbon forms are not interesting for room temperature efficient storage compared to the void space of a classical gas cylinder. We showed that doping with an alkaline element, such as lithium, one could store the same quantities at 350 bar compared to a classical tank at 700 bar. This result is a possible route to achieve interesting performances for on-board docking systems for instance. (author)

Synthesis and properties of ZnFe{sub 2}O{sub 4} replica with biological hierarchical structure

Energy Technology Data Exchange (ETDEWEB)

Liu, Hongyan; Guo, Yiping, E-mail: ypguo@sjtu.edu.cn; Zhang, Yangyang; Wu, Fen; Liu, Yun; Zhang, Di, E-mail: zhangdi@sjtu.edu.cn

2013-09-20

Highlights: • ZFO replica with hierarchical structure was synthesized from butterfly wings. • Biotemplate has a significant impact on the properties of ZFO material. • Our method opens up new avenues for the synthesis of spinel ferrites. -- Abstract: ZnFe{sub 2}O{sub 4} replica with biological hierarchical structure was synthesized from Papilio paris by a sol–gel method followed by calcination. The crystallographic structure and morphology of the obtained samples were characterized by X-ray diffraction, field-emission scanning electron microscope, and transmittance electron microscope. The results showed that the hierarchical structures were retained in the ZFO replica of spinel structure. The magnetic behavior of such novel products was measured by a vibrating sample magnetometer. A superparamagnetism-like behavior was observed due to nanostructuration size effects. In addition, the ZFO replica with “quasi-honeycomb-like structure” showed a much higher specific capacitance of 279.4 F g{sup −1} at 10 mV s{sup −1} in comparison with ZFO powder of 137.3 F g{sup −1}, attributing to the significantly increased surface area. These results demonstrated that ZFO replica is a promising candidate for novel magnetic devices and supercapacitors.

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

Energy Technology Data Exchange (ETDEWEB)

Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Fujimoto, K. [Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nakagawa, A. [Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan); Nomoto, A. [Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)

2014-10-28

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

International Nuclear Information System (INIS)

Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

2014-01-01

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10 6 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

Science.gov (United States)

Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

2014-10-01

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

Theoretical Concepts in Molecular Photodissociation Dynamics

DEFF Research Database (Denmark)

Henriksen, Niels Engholm

1995-01-01

This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

First principles molecular dynamics without self-consistent field optimization

International Nuclear Information System (INIS)

Souvatzis, Petros; Niklasson, Anders M. N.

2014-01-01

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

Insights into the folding and unfolding processes of wild-type and mutated SH3 domain by molecular dynamics and replica exchange molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Wen-Ting Chu

Full Text Available Src-homology regions 3 (SH3 domain is essential for the down-regulation of tyrosine kinase activity. Mutation A39V/N53P/V55L of SH3 is found to be relative to the urgent misfolding diseases. To gain insight, the human and gallus SH3 domains (PDB ID: 1NYG and 2LP5, including 58 amino acids in each protein, were selected for MD simulations (Amber11, ff99SB force field and cluster analysis to investigate the influence of mutations on the spatial structure of the SH3 domain. It is found that the large conformational change of mutations mainly exists in three areas in the vicinity of protein core: RT loop, N-src loop, distal β-hairpin to 310 helix. The C-terminus of the mutated gallus SH3 is disordered after simulation, which represents the intermediate state of aggregation. The disappeared strong Hbond net in the mutated human and gallus systems will make these mutated proteins looser than the wild-type proteins. Additionally, by performing the REMD simulations on the gallus SH3 domain, the mutated domain is found to have an obvious effect on the unfolding process. These studies will be helpful for further aggregation mechanisms investigations on SH3 family.

Methanol exchange dynamics between a temperate cropland soil and the atmosphere

Science.gov (United States)

Bachy, A.; Aubinet, M.; Amelynck, C.; Schoon, N.; Bodson, B.; Moureaux, C.; Delaplace, P.; De Ligne, A.; Heinesch, B.

2018-03-01

Soil methanol (CH3OH) exchange is often considered as several orders of magnitude smaller than plant methanol exchange. However, for some ecosystems, it is significant in regard with plant exchange and worth thus better consideration. Our study sought to gain a better understanding of soil exchange. Methanol flux was measured at the ecosystem scale on a bare agricultural soil over two contrasted periods using the disjunct eddy covariance by mass scanning technique. A proton-transfer-reaction mass spectrometer was used for the methanol ambient mixing ratio measurements. Bi-directional exchange dynamics were observed. Methanol emission occurred under dry and warm conditions and correlated best with soil surface temperature, whereas methanol uptake occurred under wet and mild conditions and correlated well with the methanol ambient concentration. After having tested a physical adsorption-desorption model and by confronting our data with the literature, we propose that the exchange was ruled by both a physical adsorption/desorption mechanism and by a methanol source, which still needs to be identified. The soil emission decreased when the vegetation developed. The reasons for the decrease still need to be determined. Overall, the dynamics observed at our site were similar to those reported by other studies for both cropland and forest ecosystems. The mechanism proposed in our work can thus be possibly applied to other sites or ecosystems. In addition, the methanol exchange rate was in the upper range of the exchange rates reported by other soil studies, suggesting that cropland soils are more important methanol exchangers than those in other ecosystems and should therefore be further investigated.

Gamma-ray dosimetry measurements of the Little Boy replica

International Nuclear Information System (INIS)

Plassmann, E.A.; Pederson, R.A.

1984-01-01

We present the current status of our gamma-ray dosimetry results for the Little Boy replica. Both Geiger-Mueller and thermoluminescent detectors were used in the measurements. Future work is needed to test assumptions made in data analysis

Molecular dynamics and diffusion a compilation

CERN Document Server

Fisher, David

2013-01-01

The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

Extended Lagrangian Excited State Molecular Dynamics.

Science.gov (United States)

Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

2018-02-13

An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

Advances in molecular vibrations and collision dynamics molecular clusters

CERN Document Server

Bacic, Zatko

1998-01-01

This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

Evaluation of creep damage development by the replica method; Utvaerdering av krypskadeutveckling med replikmetoden

Energy Technology Data Exchange (ETDEWEB)

Storesund, Jan [Det Norske Veritas AB, Stockholm (Sweden); Roennholm, Markku [Fortum (Sweden)

2002-04-01

Creep damage development in high temperature components can be monitored by the replica method. Damage is classified and an experience based time period for safe operation is recommended where a re-inspection should be conducted. Original recommendations are still commonly used but there are also developed ones are mostly less conservative. A data base of more than 6000 replicas, collected from welded components in Swedish and Finnish power plants, has been evaluated with respect to damage development in the present project. The results are in general in good agreement to the existing developed recommendations for re-inspections. Important factors that should be considered for use of the recommendations are highlighted: Service history, Material, welding and heat treatment, Measure of pressure and temperature, System stresses, Geometrical stress concentrations, stress distributions, Design of components and welds, Creep crack growth, Starts and stops, Extent and performance of the replica method. These factors have been analysed with respect to the evaluated data resulting in comments to the existing recommendations. In addition, recommendations and conditions for a high reliability of the replica method are described. The comments and recommendations can be read in separate sections in the end of the report.

Comparison of pulsed versus continuous oxygen delivery using realistic adult nasal airway replicas

Directory of Open Access Journals (Sweden)

Chen JZ

2017-08-01

Full Text Available John Z Chen,1 Ira M Katz,2 Marine Pichelin,2 Kaixian Zhu,3 Georges Caillibotte,2 Michelle L Noga,4 Warren H Finlay,1 Andrew R Martin1 1Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada; 2Medical R&D, Air Liquide Santé International, Centre de Recherche Paris-Saclay, Les Loges-en-Josas, 3Centre Explor!, Air Liquide Healthcare, Gentilly, France; 4Radiology and Diagnostic Imaging, University of Alberta, Edmonton, AB, Canada Background: Portable oxygen concentrators (POCs typically include pulse flow (PF modes to conserve oxygen. The primary aims of this study were to develop a predictive in vitro model for inhaled oxygen delivery using a set of realistic airway replicas, and to compare PF for a commercial POC with steady flow (SF from a compressed oxygen cylinder. Methods: Experiments were carried out using a stationary compressed oxygen cylinder, a POC, and 15 adult nasal airway replicas based on airway geometries derived from medical images. Oxygen delivery via nasal cannula was tested at PF settings of 2.0 and 6.0, and SF rates of 2.0 and 6.0 L/min. A test lung simulated three breathing patterns representative of a chronic obstructive pulmonary disease patient at rest, during exercise, and while asleep. Volume-averaged fraction of inhaled oxygen (FiO2 was calculated by analyzing oxygen concentrations sampled at the exit of each replica and inhalation flow rates over time. POC pulse volumes were also measured using a commercial O2 conserver test system to attempt to predict FiO2 for PF. Results: Relative volume-averaged FiO2 using PF ranged from 68% to 94% of SF values, increasing with breathing frequency and tidal volume. Three of 15 replicas failed to trigger the POC when used with the sleep breathing pattern at the 2.0 setting, and four of 15 replicas failed to trigger at the 6.0 setting. FiO2 values estimated from POC pulse characteristics followed similar trends but were lower than those derived from

Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

Indian Academy of Sciences (India)

Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

Spin and orbital exchange interactions from Dynamical Mean Field Theory

Energy Technology Data Exchange (ETDEWEB)

Secchi, A., E-mail: a.secchi@science.ru.nl [Radboud University, Institute for Molecules and Materials, 6525 AJ Nijmegen (Netherlands); Lichtenstein, A.I., E-mail: alichten@physnet.uni-hamburg.de [Universitat Hamburg, Institut für Theoretische Physik, Jungiusstraße 9, D-20355 Hamburg (Germany); Katsnelson, M.I., E-mail: m.katsnelson@science.ru.nl [Radboud University, Institute for Molecules and Materials, 6525 AJ Nijmegen (Netherlands)

2016-02-15

We derive a set of equations expressing the parameters of the magnetic interactions characterizing a strongly correlated electronic system in terms of single-electron Green's functions and self-energies. This allows to establish a mapping between the initial electronic system and a spin model including up to quadratic interactions between the effective spins, with a general interaction (exchange) tensor that accounts for anisotropic exchange, Dzyaloshinskii–Moriya interaction and other symmetric terms such as dipole–dipole interaction. We present the formulas in a format that can be used for computations via Dynamical Mean Field Theory algorithms. - Highlights: • We give formulas for the exchange interaction tensor in strongly correlated systems. • Interactions are written in terms of electronic Green's functions and self-energies. • The method is suitable for a Dynamical Mean Field Theory implementation. • No quenching of the orbital magnetic moments is assumed. • Spin and orbital contributions to magnetism can be computed separately.

Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

Czech Academy of Sciences Publication Activity Database

Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

2016-01-01

Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

NMR magnetization exchange dynamics for three spin-1/2 systems

International Nuclear Information System (INIS)

Demco, D.E.; Filip, X.; Filip, C.

1997-01-01

The magnetization exchange dynamics in one-dimensional NMR exchange experiments performed with static samples is analyzed for the relevant case of three spin systems. The magnetization decays recorded in the experiments performed with different chemical shift filters for the short mixing times are derived analytically. In this regime the decay rates depend on the dipolar coupling between the spins belonging to different functional groups. The predictions of the theoretical model are compared with the magnetization exchange data obtained for cross-linked poly(styrene-co-butadiene) samples. The residual dipolar coupling between the functional CH- and CH2-groups of butadiene are measured from the magnetization exchange experiments in the short mixing time regime. (authors)

Effect of cation nature of zeolite on carbon replicas and their electrochemical capacitance

International Nuclear Information System (INIS)

Zhou, Jin; Li, Wen; Zhang, Zhongshen; Wu, Xiaozhong; Xing, Wei; Zhuo, Shuping

2013-01-01

Graphical abstract: Cation nature of zeolite influences the porosity, surface chemical properties of carbon replicas of zeolite, resulting in different electrochemical capacitance. Highlights: ► The porosity of carbon replica strongly depends on zeolite's effective pore size. ► The surface chemical properties influence by the cation nature of zeolite. ► The N-doping introduces large pseudo-capacitance. ► The HYC800 carbon showed a high capacitance of up to 312 F g −1 in 1 M H 2 SO 4 . ► The prepared carbons show good durability of galvanostatic cycle. -- Abstract: N-doped carbon replicas of zeolite Y are prepared, and the effect of cation nature of zeolite (H + or Na + ) on the carbon replicas is studied. The morphology, structure and surface properties of the carbon materials are investigated by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), N 2 adsorption, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FT-IR). The pore regularity, pore parameter and surface chemical properties of the carbons may strongly depend on the cation nature of the zeolite Y. The carbon replicas of zeolite HY (H-form of zeolite Y) possesses higher pore regularity and much larger surface area than those of zeolite NaY (Na-form of zeolite Y), while the latter carbons seem to possess higher carbonization degrees. Electrochemical measurements show a large faradaic capacitance related to the N- or O-containing groups for the prepared carbons. Owing to the large specific surface area, high pore regularity and heteroatom-doping, the HYC800 sample derived from zeolite HY presents very high gravimetric capacitance, up to 312.4 F g −1 in H 2 SO 4 electrolyte, and this carbon can operate at 1.2 V with good retention ratio in the range of 0.25 to 10 A g −1

Quark exchange and nuclear dynamics

International Nuclear Information System (INIS)

Moniz, E.J.

1985-01-01

This paper gives a qualitative understanding of hadronic phenomena in terms of quark degrees of freedom. The basic model which incorporates saturating confining interactions and the study of hadron-hadron scattering has been carried through in collaboration with F. Lenz, J.T. Londergan, R. Rosenfelder, M. Stingl and K. Yazaki. It is shown that minimal confining dynamics together with exchange symmetry indeed leads to a remarkable range of phenomena at both the nuclear and particle energy scales. Most observables are well described by an effective hadron theory, the quark momentum distribution being the major exception. These features emerge even in the simplest model, namely, U(1) color and hadrons composed of two quarks (anti qq or qq). The author concentrates here on this model. In the concluding section, he remarks on the SU(N) results, particularly on the extent to which the color-hidden dynamics are constrained by examining the systematics of nuclear and hadronic phenomena. (Auth.)

Visualizing Energy on Target: Molecular Dynamics Simulations

Science.gov (United States)

2017-12-01

ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

Molecular simulations of hydrated proton exchange membranes. The structure

Energy Technology Data Exchange (ETDEWEB)

Marcharnd, Gabriel [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie; Bordeaux Univ., Talence (France). Dept. of Chemistry; Bopp, Philippe A. [Bordeaux Univ., Talence (France). Dept. of Chemistry; Spohr, Eckhard [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie

2013-01-15

The structure of two hydrated proton exchange membranes for fuel cells (PEMFC), Nafion {sup registered} (Dupont) and Hyflon {sup registered} (Solvay), is studied by all-atom molecular dynamics (MD) computer simulations. Since the characteristic times of these systems are long compared to the times for which they can be simulated, several different, but equivalent, initial configurations with a large degree of randomness are generated for different water contents and then equilibrated and simulated in parallel. A more constrained structure, analog to the newest model proposed in the literature based on scattering experiments, is investigated in the same way. One might speculate that a limited degree of entanglement of the polymer chains is a key feature of the structures showing the best agreement with experiment. Nevertheless, the overall conclusion remains that the scattering experiments cannot distinguish between the several, in our view equally plausible, structural models. We thus find that the characteristic features of experimental scattering curves are, after equilibration, fairly well reproduced by all systems prepared with our method. We thus study in more detail some structural details. We attempt to characterize the spatial and size distribution of the water rich domains, which is where the proton diffusion mostly takes place, using several clustering algorithms. (orig.)

Nonadiabatic electron wavepacket dynamics behind molecular autoionization

Science.gov (United States)

Matsuoka, Takahide; Takatsuka, Kazuo

2018-01-01

A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

Ultrafast molecular dynamics illuminated with synchrotron radiation

International Nuclear Information System (INIS)

Bozek, John D.; Miron, Catalin

2015-01-01

Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

Rheology via nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1982-10-01

The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference

Dynamical implications of bi-directional resource exchange within a meta-ecosystem.

Science.gov (United States)

Rodriguez, Marisabel Rodriguez; Kopp, Darin; Allen, Daniel; Kang, Yun

2018-05-05

The exchange of resources across ecosystem boundaries can have large impacts on ecosystem structures and functions at local and regional scales. In this article, we develop a simple model to investigate dynamical implications of bi-directional resource exchanges between two local ecosystems in a meta-ecosystem framework. In our model, we assume that (1) Each local ecosystem acts as both a resource donor and recipient, such that one ecosystem donating resources to another results in a cost to the donating system and a benefit to the recipient; and (2) The costs and benefits of the bi-directional resource exchange between two ecosystems are correlated in a nonlinear fashion. Our model could apply to the resource interactions between terrestrial and aquatic ecosystems that are supported by the literature. Our theoretical results show that bi-directional resource exchange between two ecosystems can indeed generate complicated dynamical outcomes, including the coupled ecosystems having amensalistic, antagonistic, competitive, or mutualistic interactions, with multiple alternative stable states depending on the relative costs and benefits. In addition, if the relative cost for resource exchange for an ecosystem is decreased or the relative benefit for resource exchange for an ecosystem is increased, the production of that ecosystem would increase; however, depending on the local environment, the production of the other ecosystem may increase or decrease. We expect that our work, by evaluating the potential outcomes of resource exchange theoretically, can facilitate empirical evaluations and advance the understanding of spatial ecosystem ecology where resource exchanges occur in varied ecosystems through a complicated network. Copyright © 2018. Published by Elsevier Inc.

First-principles molecular dynamics for metals

International Nuclear Information System (INIS)

Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

1989-01-01

A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization.

Directory of Open Access Journals (Sweden)

Gianvito Grasso

Full Text Available The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine.

MOLECULAR DESCRIPTION OF ELECTROLYTE SOLUTION IN A CARBON AEROGEL ELECTRODE

Directory of Open Access Journals (Sweden)

A.Kovalenko

2003-01-01

Full Text Available We develop a molecular theory of aqueous electrolyte solution sorbed in a nanoporous carbon aerogel electrode, based on the replica reference interaction site model (replica RISM for realistic molecular quenched-annealed systems. We also briefly review applications of carbon aerogels for supercapacitor and electrochemical separation devices, as well as theoretical and computer modelling of disordered porous materials. The replica RISM integral equation theory yields the microscopic properties of the electrochemical double layer formed at the surface of carbon aerogel nanopores, with due account of chemical specificities of both sorbed electrolyte and carbon aerogel material. The theory allows for spatial disorder of aerogel pores in the range from micro- to macroscopic size scale. We considered ambient aqueous solution of 1 M sodium chloride sorbed in two model nanoporous carbon aerogels with carbon nanoparticles either arranged into branched chains or randomly distributed. The long-range correlations of the carbon aerogel nanostructure substantially affect the properties of the electrochemical double layer formed by the solution sorbed in nanopores.

File-based replica management

CERN Document Server

Kunszt, Peter Z; Stockinger, Heinz; Stockinger, Kurt

2005-01-01

Data replication is one of the best known strategies to achieve high levels of availability and fault tolerance, as well as minimal access times for large, distributed user communities using a world-wide Data Grid. In certain scientific application domains, the data volume can reach the order of several petabytes; in these domains, data replication and access optimization play an important role in the manageability and usability of the Grid. In this paper, we present the design and implementation of a replica management Grid middleware that was developed within the EDG project left bracket European Data Grid Project (EDG), http://www.eu-egee.org right bracket and is designed to be extensible so that user communities can adjust its detailed behavior according to their QoS requirements.

How Dynamic Visualization Technology Can Support Molecular Reasoning

Science.gov (United States)

Levy, Dalit

2013-01-01

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

A Replica Detection Scheme Based on the Deviation in Distance Traveled Sliding Window for Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Alekha Kumar Mishra

2017-01-01

Full Text Available Node replication attack possesses a high level of threat in wireless sensor networks (WSNs and it is severe when the sensors are mobile. A limited number of replica detection schemes in mobile WSNs (MWSNs have been reported till date, where most of them are centralized in nature. The centralized detection schemes use time-location claims and the base station (BS is solely responsible for detecting replica. Therefore, these schemes are prone to single point of failure. There is also additional communication overhead associated with sending time-location claims to the BS. A distributed detection mechanism is always a preferred solution to the above kind of problems due to significantly lower communication overhead than their counterparts. In this paper, we propose a distributed replica detection scheme for MWSNs. In this scheme, the deviation in the distance traveled by a node and its replica is recorded by the observer nodes. Every node is an observer node for some nodes in the network. Observers are responsible for maintaining a sliding window of recent time-distance broadcast of the nodes. A replica is detected by an observer based on the degree of violation computed from the deviations recorded using the time-distance sliding window. The analysis and simulation results show that the proposed scheme is able to achieve higher detection probability compared to distributed replica detection schemes such as Efficient Distributed Detection (EDD and Multi-Time-Location Storage and Diffusion (MTLSD.

Applied research for profilometric testing of the state of interior surfaces in heat exchanger tubes

International Nuclear Information System (INIS)

Gyongyosi, Tiberiu; Panaitescu, Valeriu Nicolae

2009-01-01

Generally, the surface flaws identified at heat exchangers tubing are characteristic for the heat secondary systems, located on the external surfaces of the heat exchanger tubes and are mostly the results of the ageing phenomena in systems operation. The tests performed, with the impressing replicating device confirmed the applicability of the technique, functionality of the device and resulted in replicas on metal support, these being the hard copy of the negative of the test tube surface, allowing the profile measurement. The visual inspection of the replicas on the metallic support gives information about the surface geometry replicated, pointing out the marks, which belong to the same area under observation. The minimum and maximum values for the depth of the channel worked out in the inner test tube wall have been determined by profile graphic measurement on the replicas. The paper presents the structural and functional description of the experimental devices. The first results and some conclusions are also included. Two patent applications were submitted at State Office for Inventions and Trademarks (OSIM) covering the original data to protect royalty: 'The local pit flaws, scratches, incipient micro-cracks replicating device on inner cylindrical surfaces', under no. A/00299/17.04.2008 and 'The annular local flaw, incipient micro-cracks replicating device on inner cylindrical surface' under no. A/00300/17.04.2008

Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors

Energy Technology Data Exchange (ETDEWEB)

Malaby, Andrew W.; Das, Sanchaita; Chakravarthy, Srinivas; Irving, Thomas C.; Bilsel, Osman; Lambright, David G.

2018-01-01

Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization and conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site.

Atomistic model of the spider silk nanostructure

Science.gov (United States)

Keten, Sinan; Buehler, Markus J.

2010-04-01

Spider silk is an ultrastrong and extensible self-assembling biopolymer that outperforms the mechanical characteristics of many synthetic materials including steel. Here we report atomic-level structures that represent aggregates of MaSp1 proteins from the N. Clavipes silk sequence based on a bottom-up computational approach using replica exchange molecular dynamics. We discover that poly-alanine regions predominantly form distinct and orderly beta-sheet crystal domains while disorderly structures are formed by poly-glycine repeats, resembling 31-helices. These could be the molecular source of the large semicrystalline fraction observed in silks, and also form the basis of the so-called "prestretched" molecular configuration. Our structures are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content.

Physical adsorption and molecular dynamics

International Nuclear Information System (INIS)

Cohan, N.V.

1981-01-01

Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

The mean-size dependence of the exchange narrowing in molecular J-aggregates

International Nuclear Information System (INIS)

Chen Yulu; Zhao Jijun

2011-01-01

The effect of segment-size fluctuations on exchange narrowing in a molecular J-aggregate of site-energy disordered distributions is studied using a one-dimensional Frenkel-exciton model. It is found that the segment-size disorder leads to the width of the absorption spectra deviating from the scaling law, σ 4/3 of the site-energy disordered standard deviation σ, being suitable for the system only with the site-energy disorder. In larger σ, the segment-size disorder has little influence on the linear absorption spectra. With increasing segment mean-length, the absorption line width monotonically increases, and then approaches a saturated value. By comparing a system of larger mean-length segment with a smaller one, both with the same segment-size disorder, it is found that the absorption line width of the former is broadened, and the exchange narrowing effect is reduced. The present result shows that the correlation effect can be partially maintained for the system with larger mean-length segment. -- Research Highlights: → Segment fluctuations affect the exchange narrowing of molecular J-aggregates. → The width of the absorption spectra is found to deviate from the scaling law. → Increase in segment size causes increase in the width and then saturates. → Exchange narrowing is reduced for larger mean-size segment. → Correlation can be kept partly in the larger size segment.

Implementation and performance analysis of the LHCb LFC replica using Oracle streams technology

CERN Document Server

Düllmann, D; Martelli, B; Peco, G; Bonifazzi, F; Da Fonte Perez, E; Baranowski, Z; Vagnoni, V

2007-01-01

The presentation will describe the architecture and the deployment of the LHCb read-only File Catalogue for the LHC Computing Grid (LFC) replica implemented at the Italian INFN National Centre for Telematics and Informatics (CNAF), and evaluate a series of tests on the LFC with replica. The LHCb computing model foresees the replication of the central LFC database in every Tier-1, in order to assure more scalability and fault tolerance to LHCb applications Scientific data intensive applications use a large collection of files for storing data. In particular, as regards the HEP community, data generated by large detectors will be managed and stored using databases. The intensive access to information stored in databases by the Grid computing applications requires a distributed database replication in order to guarantee the scalability and, in case of failure, redundancy. Besides the results of the tests will be an important reference for all the Grid users This talk will describe the replica implementation of L...

Thomas-Fermi molecular dynamics

International Nuclear Information System (INIS)

Clerouin, J.; Pollock, E.L.; Zerah, G.

1992-01-01

A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

Molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

2012-01-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

Molecular dynamics for dense matter

Science.gov (United States)

Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

2012-08-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

Science.gov (United States)

2017-01-01

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.

Directory of Open Access Journals (Sweden)

M Olivia Kim

2015-10-01

Full Text Available BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer's disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

Science.gov (United States)

2014-01-01

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

Combined Steady-State and Dynamic Heat Exchanger Experiment

Science.gov (United States)

Luyben, William L.; Tuzla, Kemal; Bader, Paul N.

2009-01-01

This paper describes a heat-transfer experiment that combines steady-state analysis and dynamic control. A process-water stream is circulated through two tube-in-shell heat exchangers in series. In the first, the process water is heated by steam. In the second, it is cooled by cooling water. The equipment is pilot-plant size: heat-transfer areas…

Replica Node Detection Using Enhanced Single Hop Detection with Clonal Selection Algorithm in Mobile Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

L. S. Sindhuja

2016-01-01

Full Text Available Security of Mobile Wireless Sensor Networks is a vital challenge as the sensor nodes are deployed in unattended environment and they are prone to various attacks. One among them is the node replication attack. In this, the physically insecure nodes are acquired by the adversary to clone them by having the same identity of the captured node, and the adversary deploys an unpredictable number of replicas throughout the network. Hence replica node detection is an important challenge in Mobile Wireless Sensor Networks. Various replica node detection techniques have been proposed to detect these replica nodes. These methods incur control overheads and the detection accuracy is low when the replica is selected as a witness node. This paper proposes to solve these issues by enhancing the Single Hop Detection (SHD method using the Clonal Selection algorithm to detect the clones by selecting the appropriate witness nodes. The advantages of the proposed method include (i increase in the detection ratio, (ii decrease in the control overhead, and (iii increase in throughput. The performance of the proposed work is measured using detection ratio, false detection ratio, packet delivery ratio, average delay, control overheads, and throughput. The implementation is done using ns-2 to exhibit the actuality of the proposed work.

Vibrational properties of the amide group in acetanilide: A molecular-dynamics study

Science.gov (United States)

Campa, Alessandro; Giansanti, Andrea; Tenenbaum, Alexander

1987-09-01

A simplified classical model of acetanilide crystal is built in order to study the mechanisms of vibrational energy transduction in a hydrogen-bonded solid. The intermolecular hydrogen bond is modeled by an electrostatic interaction between neighboring excess charges on hydrogen and oxygen atoms. The intramolecular interaction in the peptide group is provided by a dipole-charge interaction. Forces are calculated up to second-order terms in the atomic displacements from equilibrium positions; the model is thus a chain of nonlinear coupled oscillators. Numerical molecular-dynamics experiments are performed on chain segments of five molecules. The dynamics is ordered, at all temperatures. Energy is widely exchanged between the stretching and the bending of the N-H bond, with characteristic times of the order of 0.2 ps. Energy transduction through the H bond is somewhat slower and of smaller amplitude, and is strongly reduced when the energies of the two bound molecules are very different: This could reduce the dissipation of localized energy fluctuations.

Zeolite-templated carbon replica: a grand canonical Monte-Carlo simulation study

International Nuclear Information System (INIS)

Roussel, Th.; Pellenq, R.J.M.; Bichara, Ch.; Gadiou, R.; Didion, A.; Vix-Guterl, C.; Gaslain, F.; Parmentier, J.; Valtchev, V.; Patarin, J.

2005-01-01

Microporous carbon materials are interesting for several applications such as hydrogen storage, catalysis or electrical double layer capacitors. The development of the negative templating method to obtain carbon replicas from ordered templates, has lead to the synthesis of several new materials which have interesting textural properties, attractive for energy storage. Among the possible templates, zeolites can be used to obtain highly microporous carbon materials. Nevertheless, the phenomena involved in the replica synthesis are not fully understood, and the relationships between the structure of the template, the carbon precursor and the resulting carbon material need to be investigated. Experimental results for carbon zeolite-templated nano-structures can be found in a series of papers; see for instance ref. [1] in which Wang et al describe a route to ultra-small Single Wall Carbon Nano-tubes (SWNTs) using the porosity of zeolite AlPO 4 -5. After matrix removal, the resulting structure is a free-standing bundle of 4 Angstroms large nano-tubes. However, it is highly desirable to obtain an ordered porous carbon structure that forms a real 3D network to be used for instance in gas storage applications. Carbon replica of faujasite and EMT zeolites can have these properties since these zeolites have a 3D porous network made of 10 Angstroms cages connected to each other through 7 Angstroms large windows. The first step of this study was to generate a theoretical carbon replica structure of various zeolites (faujasite, EMT, AlPO 4 -5, silicalite). For this purpose, we used the Grand Canonical Monte-Carlo (GCMC) technique in which the carbon-carbon interactions were described within the frame of a newly developed Tight Binding approach and the carbon-zeolite interactions assumed to be characteristic of physisorption. The intrinsic stability of the subsequent carbon nano-structures was then investigated after mimicking the removal of the inorganic phase by switching

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

Energy Technology Data Exchange (ETDEWEB)

Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn; Zhu, Weiliang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); Shi, Jiye, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [UCB Pharma, 216 Bath Road, Slough SL1 4EN (United Kingdom)

2015-03-28

The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much less computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.

Sampling the Denatured State of Polypeptides in Water, Urea, and Guanidine Chloride to Strict Equilibrium Conditions with the Help of Massively Parallel Computers.

Science.gov (United States)

Meloni, Roberto; Camilloni, Carlo; Tiana, Guido

2014-02-11

The denatured state of polypeptides and proteins, stabilized by chemical denaturants like urea and guanidine chloride, displays residual secondary structure when studied by nuclear-magnetic-resonance spectroscopy. However, these experimental techniques are weakly sensitive, and thus molecular-dynamics simulations can be useful to complement the experimental findings. To sample the denatured state, we made use of massively-parallel computers and of a variant of the replica exchange algorithm, in which the different branches, connected with unbiased replicas, favor the formation and disruption of local secondary structure. The algorithm is applied to the second hairpin of GB1 in water, in urea, and in guanidine chloride. We show with the help of different criteria that the simulations converge to equilibrium. It results that urea and guanidine chloride, besides inducing some polyproline-II structure, have different effect on the hairpin. Urea disrupts completely the native region and stabilizes a state which resembles a random coil, while guanidine chloride has a milder effect.

Molecular dynamics with deterministic and stochastic numerical methods

CERN Document Server

Leimkuhler, Ben

2015-01-01

This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications.  Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...

Neutron and gamma-ray dose-rates from the Little Boy replica

International Nuclear Information System (INIS)

Plassmann, E.A.; Pederson, R.A.

1984-01-01

We report dose-rate information obtained at many locations in the near vicinity of, and at distances out to 0.64 km from, the Little Boy replica while it was operated as a critical assembly. The measurements were made with modified conventional dosimetry instruments that used an Anderson-Braun detector for neutrons and a Geiger-Mueller tube for gamma rays with suitable electronic modules to count particle-induced pulses. Thermoluminescent dosimetry methods provide corroborative data. Our analysis gives estimates of both neutron and gamma-ray relaxation lengths in air for comparison with earlier calculations. We also show the neutron-to-gamma-ray dose ratio as a function of distance from the replica. Current experiments and further data analysis will refine these results. 7 references, 8 figures

Molecular ions, Rydberg spectroscopy and dynamics

International Nuclear Information System (INIS)

Jungen, Ch.

2015-01-01

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

Molecular ions, Rydberg spectroscopy and dynamics

Energy Technology Data Exchange (ETDEWEB)

Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

2015-01-22

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

X(3872) and other possible heavy molecular states

International Nuclear Information System (INIS)

Liu, Xiang; Luo, Zhi-Gang; Zhu, Shi-Lin; Liu, Yan-Rui

2009-01-01

We perform a systematic study of the possible molecular states composed of a pair of heavy mesons such as D anti D,D * anti D,D * anti D * in the framework of the meson exchange model. The exchanged mesons include the pseudoscalar, scalar and vector mesons. Through our investigation, we find the following results. (1) The structure X(3764) is not a molecular state. (2) There exists strong attraction in the range r * anti D * system with J=0,1. If future experiments confirm Z + (4051) as a loosely bound molecular state, its quantum number is probably J P =0 + . Its partner state Φ **0 may be searched for in the π 0 χ c1 channel. (3) Vector meson exchange provides strong attraction in the D * anti D channel together with pion exchange. A bound state solution may exist with a reasonable cutoff parameter Λ∝1.4 GeV. X(3872) may be accommodated as a molecular state dynamically although drawing a very definite conclusion needs further investigation. (4) The B * anti B molecular state may exist. (orig.)

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

Directory of Open Access Journals (Sweden)

Renata De Paris

2015-01-01

Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

Preliminary results of statistical dynamic experiments on a heat exchanger

International Nuclear Information System (INIS)

Corran, E.R.; Cummins, J.D.

1962-10-01

The inherent noise signals present in a heat exchanger have been recorded and analysed in order to determine some of the statistical dynamic characteristics of the heat exchanger. These preliminary results show that the primary side temperature frequency response may be determined by analysing the inherent noise. The secondary side temperature frequency response and cross coupled temperature frequency responses between primary and secondary are poorly determined because of the presence of a non-stationary noise source in the secondary circuit of this heat exchanger. This may be overcome by correlating the dependent variables with an externally applied noise signal. Some preliminary experiments with an externally applied random telegraph type of signal are reported. (author)

Development of the atomic and molecular data markup language for internet data exchange

International Nuclear Information System (INIS)

Ralchenko, Yuri; Clark Robert E.H.; Humbert, Denis; Schultz, David R.; Kato, Takako; Rhee, Yong Joo

2006-01-01

Accelerated development of the Internet technologies, including those relevant to the atomic and molecular physics, poses new requirements for the proper communication between computers, users and applications. To this end, a new standard for atomic and molecular data exchange that would reflect the recent achievements in this field becomes a necessity. We report here on development of the Atomic and Molecular Data Markup Language (AMDML) that is based on eXtensible Markup Language (XML). The present version of the AMDML Schema covers atomic spectroscopic data as well as the electron-impact collisions. (author)

Biosynthesis of cathodoluminescent zinc oxide replicas using butterfly (Papilio paris) wing scales as templates

International Nuclear Information System (INIS)

Zhang Wang; Zhang Di; Fan Tongxiang; Ding Jian; Gu Jiajun; Guo Qixin; Ogawa, Hiroshi

2009-01-01

Papilio paris butterflies have an iridescent blue color patch on their hind wings which is visible over a wide viewing angle. Optical and scanning electron microscopy observations of scales from the wings show that the blue color scales have very different microstructure to the matt black ones which also populate the wings. Scanning electron micrographs of the blue scales show that their surfaces comprise a regular two-dimensional array of concavities. By contrast the matt black scales have fine, sponge-like structure, between the ridges and the cross ribs in the scales. Using both types of scale as bio-templates, we obtain zinc oxide (ZnO) replicas of the microstructures of the original scales. Room temperature (T = 300 K) cathodoluminescence spectra of these ZnO replicas have also been studied. Both spectra show a similar sharp near-band-edge emission, but have different green emission, which we associate with the different microstructures of the ZnO replicas

Biosynthesis of cathodoluminescent zinc oxide replicas using butterfly (Papilio paris) wing scales as templates

Energy Technology Data Exchange (ETDEWEB)

Zhang Wang [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China); Zhang Di [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China)], E-mail: zhangdi@sjtu.edu.cn; Fan Tongxiang; Ding Jian; Gu Jiajun [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China); Guo Qixin; Ogawa, Hiroshi [Department of Electrical and Electronic Engineering, Saga University, Saga 840-8502 (Japan)

2009-01-01

Papilio paris butterflies have an iridescent blue color patch on their hind wings which is visible over a wide viewing angle. Optical and scanning electron microscopy observations of scales from the wings show that the blue color scales have very different microstructure to the matt black ones which also populate the wings. Scanning electron micrographs of the blue scales show that their surfaces comprise a regular two-dimensional array of concavities. By contrast the matt black scales have fine, sponge-like structure, between the ridges and the cross ribs in the scales. Using both types of scale as bio-templates, we obtain zinc oxide (ZnO) replicas of the microstructures of the original scales. Room temperature (T = 300 K) cathodoluminescence spectra of these ZnO replicas have also been studied. Both spectra show a similar sharp near-band-edge emission, but have different green emission, which we associate with the different microstructures of the ZnO replicas.

Molecular dynamics study of the coordination sphere of trivalent lanthanum in a highly concentrated LiCl aqueous solution: A combined classical and ab initio approach

International Nuclear Information System (INIS)

Vuilleumier, R.; Petit, L.; Maldivi, P.; Adamo, C.

2008-01-01

The first coordination sphere of trivalent lanthanum in a highly concentrated (14 M) lithium chloride solution is studied with a combination of classical molecular dynamics and density functional theory based first principle molecular dynamics. This method enables us to obtain a solvation shell of La 3+ containing 2 chloride ions and 6 water molecules. After refinement using first principle molecular dynamics, the resulting cation-water and cation-anion distances are in very good agreement with experiment. The 2 Cl - and the 6 water molecules arrange in a square anti-prism around La 3+ . Exchange of water molecules was also observed in the first-principle simulation, with an intermediate structure comprising 7 water molecules stable for 2.5 ps. Finally, evaluation of dipole moments using maximally localized Wannier functions shows a substantial polarization of the chloride anions and the water molecules in the first solvation shell of trivalent lanthanum. (authors)

Quantitative chemical exchange saturation transfer with hyperpolarized nuclei (qHyper-CEST): sensing xenon-host exchange dynamics and binding affinities by NMR.

Science.gov (United States)

Kunth, M; Witte, C; Schröder, L

2014-11-21

The reversible binding of xenon to host molecules has found numerous applications in nuclear magnetic resonance studies. Quantitative characterization of the Xe exchange dynamics is important to understand and optimize the physico-chemical behavior of such Xe hosts, but is often challenging to achieve at low host concentrations. We have investigated a sensitive quantification technique based on chemical exchange saturation transfer with hyperpolarized nuclei, qHyper-CEST. Using simulated signals we demonstrated that qHyper-CEST yielded accurate and precise results and was robust in the presence of large amounts of noise (10%). This is of particular importance for samples with completely unknown exchange rates. Using these findings we experimentally determined the following exchange parameters for the Xe host cryptophane-A monoacid in dimethyl sulfoxide in one type of experiment: the ratio of bound and free Xe, the Xe exchange rate, the resonance frequencies of free and bound Xe, the Xe host occupancy, and the Xe binding constant. Taken together, qHyper-CEST facilitates sensitive quantification of the Xe exchange dynamics and binding to hydrophobic cavities and has the potential to analyze many different host systems or binding sites. This makes qHyper-CEST an indispensable tool for the efficient design of highly specific biosensors.

Structural characterization of amorphous materials applied to low-k organosilicate materials

Energy Technology Data Exchange (ETDEWEB)

Raymunt, Alexandra Cooper, E-mail: amc442@cornell.edu; Clancy, Paulette

2014-07-01

We present a methodology to create computational atomistic-level models of porous amorphous materials, in particular, an organosilicate structure for ultra-low dielectric constant (ULK) materials known as “SiCOH.” The method combines the ability to satisfy geometric and chemical constraints with subsequent molecular dynamics (MD) techniques as a way to capture the complexities of the porous and amorphous nature of these materials. The motivation for studying ULK materials arises from a desire to understand the origin of the material's weak mechanical properties. The first step towards understanding how these materials might behave under processing conditions that are intended to improve their mechanical properties is to develop a suitable computational model of the material and hence is the focus of this paper. We define the atomic-scale topology of ULK materials that have been produced by chemical vapor deposition-like experimental techniques. Specifically, we have developed a method of defining the initial atom configurations and interactions, as well as a method to rearrange these starting configurations into relaxed structures. The main advantage of our described approach is the ability of our structure generation method to maintain a random distribution of relevant structural motifs throughout the structure, without relying on large unit cells and periodic boundaries to approximate the behavior of this complex material. The minimization of the different models was accomplished using replica exchange molecular dynamics (REMD). Following the generation of the ‘equilibrium’ configurations that result from REMD for a ULK material of a pre-specified composition, we demonstrate that its structural properties, including bonding topology, porosity and pore size distribution are similar to experimentally used ULK materials. - Highlights: • Method for creating a model of a low dielectric constant organosilicate material • Method of defining porosity in

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer.

Science.gov (United States)

Donnini, Serena; Ullmann, R Thomas; Groenhof, Gerrit; Grubmüller, Helmut

2016-03-08

In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its charge to fluctuate. To keep the total charge of the system constant, the uptake and release of protons by the buffer are coupled to the titration of the biomolecule with a constraint. We find that, because the fluctuation of the total charge (number of protons) of a typical biomolecule is much smaller than the number of titratable sites of the biomolecule, the number of buffer sites required to maintain overall charge neutrality without compromising the charge fluctuations of the biomolecule, is typically much smaller than the number of titratable sites, implying markedly enhanced simulation and sampling efficiency.

A fermionic molecular dynamics technique to model nuclear matter

International Nuclear Information System (INIS)

Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

2009-01-01

Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

Dynamical photo-induced electronic properties of molecular junctions

Science.gov (United States)

Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

2018-03-01

Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

Dynamical processes in atomic and molecular physics

CERN Document Server

Ogurtsov, Gennadi

2012-01-01

Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

Theory and application of quantum molecular dynamics

CERN Document Server

Zeng Hui Zhang, John

1999-01-01

This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

Dynamics of hadronic molecule in one-boson exchange approach and possible heavy flavor molecules

International Nuclear Information System (INIS)

Ding Guijun; Liu Jiafeng; Yan Mulin

2009-01-01

We extend the one pion exchange model at quark level to include the short distance contributions coming from η, σ, ρ and ω exchange. This formalism is applied to discuss the possible molecular states of DD*/DD*, BB*/BB*, DD*, BB*, the pseudoscalar-vector systems with C=B=1 and C=-B=1 respectively. The ''δ function'' term contribution and the S-D mixing effects have been taken into account. We find the conclusions reached after including the heavier mesons exchange are qualitatively the same as those in the one pion exchange model. The previous suggestion that 1 ++ BB*/BB* molecule should exist, is confirmed in the one-boson exchange model, whereas DD* bound state should not exist. The DD*/DD* system can accommodate a 1 ++ molecule close to the threshold, the mixing between the molecule and the conventional charmonium has to be considered to identify this state with X(3872). For the BB* system, the pseudoscalar-vector systems with C=B=1 and C=-B=1, near threshold molecular states may exist. These bound states should be rather narrow, isospin is violated and the I=0 component is dominant. Experimental search channels for these states are suggested.

Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

2014-01-01

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

Topological phase transition in the two-dimensional anisotropic Heisenberg model: A study using the Replica Exchange Wang-Landau sampling

Science.gov (United States)

Figueiredo, T. P.; Rocha, J. C. S.; Costa, B. V.

2017-12-01

Although the topological Berezinskii-Kosterlitz-Thouless transition was for the first time described by 40 years ago, it is still a matter of discussion. It has been used to explain several experiments in the most diverse physical systems. In contrast with the ordinary continuous phase transitions the BKT-transition does not break any symmetry. However, in some contexts it can easily be confused with other continuous transitions, in general due to an insufficient data analysis. The two-dimensional XY (or sometimes called planar rotator) spin model is the fruit fly model describing the BKT transition. As demonstrated by Bramwell and Holdsworth (1993) the finite-size effects are more important in two-dimensions than in others due to the logarithmic system size dependence of the properties of the system. Closely related is the anisotropic two dimensional Heisenberg model (AH). Although they have the same Hamiltonian the spin variable in the former has only two degrees of freedom while the AH has three. Many works treat the AH model as undergoing a transition in the same universality class as the XY model. However, its characterization as being in the BKT class of universality deserve some investigation. This paper has two goals. First, we describe an analytical evidence showing that the AH model is in the BKT class of universality. Second, we make an extensive simulation, using the numerical Replica Exchange Wang-Landau method that corroborate our analytical calculations. From our simulation we obtain the BKT transition temperature as TBKT = 0 . 6980(10) by monitoring the susceptibility, the two point correlation function and the helicity modulus. We discuss the misuse of the fourth order Binder's cumulant to locate the transition temperature. The specific heat is shown to have a non-critical behavior as expected in the BKT transition. An analysis of the two point correlation function at low temperature, C(r) ∝r - η(T), shows that the exponent, η, is consistent

Dynamic signature of molecular association in methanol

International Nuclear Information System (INIS)

Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.

2016-01-01

Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

Molecular dynamics for fermions

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

2000-02-01

The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

Pattern recognition in molecular dynamics. [FORTRAN

Energy Technology Data Exchange (ETDEWEB)

Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

1977-07-01

An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

Coupling fast water exchange to slow molecular tumbling in Gd3+ chelates: why faster is not always better.

Science.gov (United States)

Avedano, Stefano; Botta, Mauro; Haigh, Julian S; Longo, Dario L; Woods, Mark

2013-08-05

The influence of dynamics on solution state structure is a widely overlooked consideration in chemistry. Variations in Gd(3+) chelate hydration with changing coordination geometry and dissociative water exchange kinetics substantially impact the effectiveness (or relaxivity) of monohydrated Gd(3+) chelates as T1-shortening contrast agents for MRI. Theory shows that relaxivity is highly dependent upon the Gd(3+)-water proton distance (rGdH), and yet this distance is almost never considered as a variable in assessing the relaxivity of a Gd(3+) chelate as a potential contrast agent. The consequence of this omission can be seen when considering the relaxivity of isomeric Gd(3+) chelates that exhibit different dissociative water exchange kinetics. The results described herein show that the relaxivity of a chelate with "optimal" dissociative water exchange kinetics is actually lower than that of an isomeric chelate with "suboptimal" dissociative water exchange. When the rate of molecular tumbling of these chelates is slowed, an approach that has long been understood to increase relaxivity, the observed difference in relaxivity is increased with the more rapidly exchanging ("optimal") chelate exhibiting lower relaxivity than the "suboptimally" exchanging isomer. The difference between the chelates arises from a non-field-dependent parameter: either the hydration number (q) or rGdH. For solution state Gd(3+) chelates, changes in the values of q and rGdH are indistinguishable. These parametric expressions simply describe the hydration state of the chelate--i.e., the number and position of closely associating water molecules. The hydration state (q/rGdH(6)) of a chelate is intrinsically linked to its dissociative water exchange rate kex, and the interrelation of these parameters must be considered when examining the relaxivity of Gd(3+) chelates. The data presented herein indicate that the changes in the hydration parameter (q/rGdH(6)) associated with changing dissociative

Mesoporous titanium phosphate molecular sieves with ion-exchange capacity.

Science.gov (United States)

Bhaumik, A; Inagaki, S

2001-01-31

Novel open framework molecular sieves, titanium(IV) phosphates named, i.e., TCM-7 and -8 (Toyota Composite Materials, numbers 7 and 8), with new mesoporous cationic framework topologies obtained by using both cationic and anionic surfactants are reported. The (31)P MAS NMR, UV-visible absorption, and XANES data suggest the tetrahedral state of P and Ti, and stabilization of the tetrahedral state of Ti in TCM-7/8 is due to the incorporation of phosphorus (at Ti/P = 1:1) vis-à-vis the most stable octahedral state of Ti in the pure mesoporous TiO(2). Mesoporous TCM-7 and -8 show anion exchange capacity due to the framework phosphonium cation and cation exchange capacity due to defective P-OH groups. The high catalytic activity in the liquid-phase partial oxidation of cyclohexene with a dilute H(2)O(2) oxidant supports the tetrahedral coordination of Ti in these materials.

Physical replicas and the Bose glass in cold atomic gases

International Nuclear Information System (INIS)

Morrison, S; Kantian, A; Daley, A J; Zoller, P; Katzgraber, H G; Lewenstein, M; Buechler, H P

2008-01-01

We study cold atomic gases in a disorder potential and analyse the correlations between different systems subjected to the same disorder landscape. Such independent copies with the same disorder landscape are known as replicas. While, in general, these are not accessible experimentally in condensed matter systems, they can be realized using standard tools for controlling cold atomic gases in an optical lattice. Of special interest is the overlap function which represents a natural order parameter for disordered systems and is a correlation function between the atoms of two independent replicas with the same disorder. We demonstrate an efficient measurement scheme for the determination of this disorder-induced correlation function. As an application, we focus on the disordered Bose-Hubbard model and determine the overlap function within the perturbation theory and a numerical analysis. We find that the measurement of the overlap function allows for the identification of the Bose-glass phase in certain parameter regimes

Physical replicas and the Bose glass in cold atomic gases

Energy Technology Data Exchange (ETDEWEB)

Morrison, S; Kantian, A; Daley, A J; Zoller, P [Institute for Theoretical Physics, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck (Austria); Katzgraber, H G [Theoretische Physik, ETH Zurich, CH-8093 Zuerich (Switzerland); Lewenstein, M [ICAO-Institut de Ciencies Fotoniques, Parc Mediterrani de la Tecnologia, E-08860 Castelldefels, Barcelona (Spain); Buechler, H P [Institute for Theoretical Physics III, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany)], E-mail: sarah.morrison@uibk.ac.at

2008-07-15

We study cold atomic gases in a disorder potential and analyse the correlations between different systems subjected to the same disorder landscape. Such independent copies with the same disorder landscape are known as replicas. While, in general, these are not accessible experimentally in condensed matter systems, they can be realized using standard tools for controlling cold atomic gases in an optical lattice. Of special interest is the overlap function which represents a natural order parameter for disordered systems and is a correlation function between the atoms of two independent replicas with the same disorder. We demonstrate an efficient measurement scheme for the determination of this disorder-induced correlation function. As an application, we focus on the disordered Bose-Hubbard model and determine the overlap function within the perturbation theory and a numerical analysis. We find that the measurement of the overlap function allows for the identification of the Bose-glass phase in certain parameter regimes.

Platinum replica electron microscopy: Imaging the cytoskeleton globally and locally.

Science.gov (United States)

Svitkina, Tatyana M

2017-05-01

Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the "comfort zones" of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. Copyright © 2017 Elsevier Ltd. All rights reserved.

Coupled acoustic-gravity field for dynamic evaluation of ion exchange with a single resin bead.

Science.gov (United States)

Kanazaki, Takahiro; Hirawa, Shungo; Harada, Makoto; Okada, Tetsuo

2010-06-01

A coupled acoustic-gravity field is efficient for entrapping a particle at the position determined by its acoustic properties rather than its size. This field has been applied to the dynamic observation of ion-exchange reactions occurring in a single resin bead. The replacement of counterions in an ion-exchange resin induces changes in its acoustic properties, such as density and compressibility. Therefore, we can visually trace the advancement of an ion-exchange reaction as a time change in the levitation position of a resin bead entrapped in the field. Cation-exchange reactions occurring in resin beads with diameters of 40-120 microm are typically completed within 100-200 s. Ion-exchange equilibrium or kinetics is often evaluated with off-line chemical analyses, which require a batch amount of ion exchangers. Measurements with a single resin particle allow us to evaluate ion-exchange dynamics and kinetics of ions including those that are difficult to measure by usual off-line analyses. The diffusion properties of ions in resins have been successfully evaluated from the time change in the levitation positions of resin beads.

Characterization of Nb SRF cavity materials by white light interferometry and replica techniques

Energy Technology Data Exchange (ETDEWEB)

Xu, Chen [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); The Applied Science Department, The College of William and Mary, Williamsburg, VA 23185 (United States); Reece, Charles [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); Kelley, Michael, E-mail: mkelley@jlab.org [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); The Applied Science Department, The College of William and Mary, Williamsburg, VA 23185 (United States)

2013-06-01

Much work has shown that the topography of the interior surface is an important contributor to the performance of Nb superconducting radiofrequency (SRF) accelerator cavities. Micron-scale topography is implicated in non-linear loss mechanisms that limit the useful accelerating gradient range and impact cryogenic cost. Aggressive final chemical treatments in cavity production seek to reliably obtain “smoothest” surfaces with superior performance. Process development suffers because the cavity interior surface cannot be viewed directly without cutting out pieces, rendering the cavities unavailable for further study. Here we explore replica techniques as an alternative, providing imprints of cavity internal surface that can be readily examined. A second matter is the topography measurement technique used. Atomic force microscopy (AFM) has proven successful, but too time intensive for routine use in this application. We therefore introduce white light interferometry (WLI) as an alternative approach. We examined real surfaces and their replicas, using AFM and WLI. We find that the replica/WLI is promising to provide the large majority of the desired information, recognizing that a trade-off is being made between best lateral resolution (AFM) and the opportunity to examine much more surface area (WLI).

Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

Institute of Scientific and Technical Information of China (English)

Chengzhen Sun; Bofeng Bai

2017-01-01

Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

Classical and quantum molecular dynamics in NMR spectra

CERN Document Server

Szymański, Sławomir

2018-01-01

The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

Multiscale equation-free algorithms for molecular dynamics

Science.gov (United States)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Scalable Molecular Dynamics for Large Biomolecular Systems

Directory of Open Access Journals (Sweden)

Robert K. Brunner

2000-01-01

Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

Exact time-dependent exchange-correlation potentials for strong-field electron dynamics

International Nuclear Information System (INIS)

Lein, Manfred; Kuemmel, Stephan

2005-01-01

By solving the time-dependent Schroedinger equation and inverting the time-dependent Kohn-Sham scheme we obtain the exact time-dependent exchange-correlation potential of density-functional theory for the strong-field dynamics of a correlated system. We demonstrate that essential features of the exact exchange-correlation potential can be related to derivative discontinuities in stationary density-functional theory. Incorporating the discontinuity in a time-dependent density-functional calculation greatly improves the description of the ionization process

Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

Science.gov (United States)

Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

2015-05-01

Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

Molecular dinamics of tetrahedral clelate compounds of Cd(2) in solutions

International Nuclear Information System (INIS)

Nivorozhkin, L.E.; Minkin, V.I.; Borisenko, N.I.; Konstantinovskij, L.E.; Korobov, M.S.; Olekhnovich, R.Ya.

1981-01-01

Interconversion kinetics of enantiomers of tetrahedral intracomplex compounds of metals (ICM) on the base of unsymmetric ligands in solu-- tions is studied for several series of compounds according to the temperature dependence of the shape of line of prochiral substituents using the methods of the dynamic NMR (DNMR). The use of tetracoordinated ICM in the solutions of synthesized compounds of Cd(2) with the inclusion of magnetic isotope 111 Cd(S=1/2) to study molecular dynamics and the application of the corresponding methods of calculation of the DNMR signal forms permitted to clearly separate the mechanisms of digonal twist and degenerated ligand exchange. In ICM solutions the low-barrier transformations, connected with intramolecular digonal twist, take place as well as high-barrier processes of degenerated ligand exchange. The technique suggested can be applied to the studies of ICM molecular dynamics with other magnetic isotopes of metals ( 207 Pb, 199 Hg, etc.) and rapid non-degenerated ligand exchanges [ru

Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy.

Science.gov (United States)

Fayer, M D

2009-01-01

A wide variety of molecular systems undergo fast structural changes under thermal equilibrium conditions. Such transformations are involved in a vast array of chemical problems. Experimentally measuring equilibrium dynamics is a challenging problem that is at the forefront of chemical research. This review describes ultrafast 2D IR vibrational echo chemical exchange experiments and applies them to several types of molecular systems. The formation and dissociation of organic solute-solvent complexes are directly observed. The dissociation times of 13 complexes, ranging from 4 ps to 140 ps, are shown to obey a relationship that depends on the complex's formation enthalpy. The rate of rotational gauche-trans isomerization around a carbon-carbon single bond is determined for a substituted ethane at room temperature in a low viscosity solvent. The results are used to obtain an approximate isomerization rate for ethane. Finally, the time dependence of a well-defined single structural transformation of a protein is measured.

Application of carbon extraction replicas in grain-size measurements of high-strength steels using TEM

International Nuclear Information System (INIS)

Poorhaydari, Kioumars; Ivey, Douglas G.

2007-01-01

In this paper, the application of carbon extraction replicas in grain-size measurements is introduced and discussed. Modern high-strength microalloyed steels, used as structural or pipeline materials, have very small grains with substructures. Replicas used in transmission electron microscopes can resolve the grain boundaries and can be used for systematic measurement of grain size in cases where the small size of the grains pushes the resolution of conventional optical microscopes. The grain-size variations obtained from replicas are compared with those obtained from optical and scanning electron microscopy. An emphasis is placed on the importance of using the correct technique for imaging and the optimal magnification. Grain-size measurements are used for estimation of grain-boundary strengthening contribution to yield strength. The variation in grain size is also correlated with hardness in the base metal of several microalloyed steels, as well as the fine-grained heat-affected zone of a weld structure with several heat inputs

Molecular quantum dynamics. From theory to applications

International Nuclear Information System (INIS)

Gatti, Fabien

2014-01-01

An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

Molecular quantum dynamics. From theory to applications

Energy Technology Data Exchange (ETDEWEB)

Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

2014-09-01

An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

Multiple Reserve Requirements, Exchange Rates, Sudden Stops and Equilibrium Dynamics in a Small Open Economy

OpenAIRE

Paula Hernandez-Verme; Wen-Yao Wang

2009-01-01

We model a typical Asian-crisis-economy using dynamic general equilibrium tech-niques. Exchange rates obtain from nontrivial fiat-currencies demands. Sudden stops/bank-panics are possible, and key for evaluating the merits of alternative ex-change rate regimes. Strategic complementarities contribute to the severe indetermi-nacy of the continuum of equilibria. The scope for existence and indeterminacy of equilibria and dynamic properties are associated with the underlying policy regime. Bindin...

Excited-state molecular photoionization dynamics

International Nuclear Information System (INIS)

Pratt, S.T.

1995-01-01

This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

Symmetry of quantum molecular dynamics

International Nuclear Information System (INIS)

Burenin, A.V.

2002-01-01

The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru

Molecular dynamics modeling of polymer flammability

International Nuclear Information System (INIS)

Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

1992-01-01

Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals.

Science.gov (United States)

Kroonblawd, Matthew P; Sewell, Thomas D; Maillet, Jean-Bernard

2016-02-14

In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.

Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals

International Nuclear Information System (INIS)

Kroonblawd, Matthew P.; Sewell, Thomas D.; Maillet, Jean-Bernard

2016-01-01

In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock

Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals

Science.gov (United States)

Kroonblawd, Matthew P.; Sewell, Thomas D.; Maillet, Jean-Bernard

2016-02-01

In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.

Electron-nuclear dynamics of molecular systems

International Nuclear Information System (INIS)

Diz, A.; Oehrn, Y.

1994-01-01

The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

Dynamics of anion exchange of lanthanides in aqueous-organic complexing media

International Nuclear Information System (INIS)

Sheveleva, I.V.; Bogatyrev, I.O.

1987-01-01

Effect of organic solvents (ethanol, acetone, acetonitrile) on change in kinetic parameters of the anion exchange process (anion-exchange column chromatography) of r.e.e. (europium and gadolinium) in complexing nitric acid media has been studied. It is established that complex LnA 4 anion is the only sorbing form of europium and gadolinium on anionite. When the organic component content of the solution being the same, the dynamic parameters of lanthanide exchange have higher values in aqueous-acetonitrile and aqueous-acetone media in comparison with aqueous-enthanol solutions of nitric acid. Lesser mobility of complex lanthanide anions in aqueous-alcoholic solutions can be explained by stronger solvation in the presence of solvents with higher acceptor properties

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

2015-04-21

Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

Dynamics of molecular superrotors in an external magnetic field

Science.gov (United States)

Korobenko, Aleksey; Milner, Valery

2015-08-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

A dynamic model for helium core heat exchangers

International Nuclear Information System (INIS)

Schiesser, W.E.; Shih, H.J.; Hartozog, D.G.; Herron, D.M.; Nahmias, D.; Stuber, W.G.; Hindmarsh, A.C.

1990-04-01

To meet the helium (He) requirements of the superconducting supercollider (SSC), the cryogenic plants must be able to respond to time-varying loads. Thus the design and simulation of the cryogenic plants requires dynamic models of their principal components, and in particular, the core heat exchangers. In this paper, we detail the derivation and computer implementation of a model for core heat exchangers consisting of three partial differential equations (PDES) for each fluid stream (the continuity, energy and momentum balances for the He), and one PDE for each parting sheet (the energy balance for the parting sheet metal); the PDEs have time and axial position along the exchanger as independent variables. The computer code can accommodate any number of fluid streams and parting sheets in an adiabatic group. Features of the code include: rigorous or approximate thermodynamic properties for He, upwind and downwind approximation of the PDE spatial derivatives, and sparse matrix time integration. The outputs from the code include the time-dependent axial profiles of the fluid He mass flux, density, pressure, temperature, internal energy and enthalpy. The code is written in transportable Fortran 77, and can therefore be executed on essentially any computer

A dynamic model for helium core heat exchangers

International Nuclear Information System (INIS)

Schiesser, W.E.; Shih, H.J.; Hartzog, D.G.; Herron, D.M.; Nahmias, D.; Stuber, W.G.; Hindmarsh, A.C.

1990-01-01

To meet the helium (He) requirements of the superconducting supercollider (SSC), the cryogenic plants must be able to respond to time-varying loads. Thus the design and simulation of the cryogenic plants requires dynamic models of their principal components, and in particular, the core heat exchangers. In this paper, we detail the derivation and computer implementation of a model for core heat exchangers consisting of three partial differential equations (PDEs) for each fluid stream (the continuity, energy and momentum balances for the He), and one PDE for each parting sheet (the energy balance for the parting sheet metal); the PDEs have time and axial position along the exchanger as independent variables. The computer code can accommodate any number of fluid streams and parting sheets in an adiabatic group. Features of the code include: rigorous or approximate thermodynamic properties for He, upwind and downwind approximation of the PDE spatial derivatives, and sparse matrix time integration. The outputs from the code include the time-dependent axial profiles of the fluid He mass flux, density, pressure, temperature, internal energy and enthalpy. The code is written in transportable Fortran 77, and can therefore be executed on essentially any computer. 10 refs., 10 figs

Comparison and validation of dynamic characteristic analytical method for tubular heat exchanger

International Nuclear Information System (INIS)

Huang Qing; Xu Dinggeng; Chen Meng; Shen Rui

2013-01-01

In this study, the natural frequencies of Normal Residual Heat Removal Heat Exchangers are evaluated based on the beam and shell-beam finite element models. The corresponding results are compared and some discrepancies are observed. These discrepancies are analyzed in terms of the analysis of a cylindrical shell and the unreasonable treatment of boundary conditions is accordingly pointed out. The experimental data of the natural frequencies of heat exchangers used for Qinshan Phase Ⅰ Nuclear Power Plant are compared with the computational results from the shell-beam models for corresponding heat exchangers of C-2 program. The experimental and numerical results agree quite well, which implies that the shell-beam finite element simplification is applicable to the heat exchangers. The results indicate that the procedures introduced in this article apply to the dynamic analysis of other similar heat exchangers. (authors)

Femtochemistry and femtobiology ultrafast dynamics in molecular science

CERN Document Server

Douhal, Abderrazzak

2002-01-01

This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

Effect of roughness and material strength on the mechanical properties of fracture replicas

International Nuclear Information System (INIS)

Wibowo, J.; Amadei, B.; Sture, S.

1995-08-01

This report presents the results of 11 rotary shear tests conducted on replicas of three hollow cylinders of natural fractures with JRC values of 7.7, 9.4 and 12.0. The JRC values were determined from the results of laser profilometer measurements. The replicas were created from gypsum cement. By varying the water-to-gypsum cement ratio from 30 to 45%, fracture replicas with different values of compressive strength (JCS) were created. The rotary shear experiments were performed under constant normal (nominal) stresses ranging between 0.2 and 1.6 MPa. In this report, the shear test results are compared with predictions using Barton's empirical peak shear strength equation. observations during the experiments indicate that only certain parts of the fracture profiles influence fracture shear strength and dilatancy. Under relatively low applied normal stresses, the JCS does not seem to have a significant effect on shear behavior. As an alternative, a new procedure for predicting the shear behavior of fractures was developed. The approach is based on basic fracture properties such as fracture surface profile data and the compressive strength, modulus of elasticity, and Poisson's ratio of the fracture walls. Comparison between predictions and actual shear test results shows that the alternative procedure is a reliable method

Why the long hours? Job demands and social exchange dynamics.

Science.gov (United States)

Genin, Emilie; Haines, Victor Y; Pelletier, David; Rousseau, Vincent; Marchand, Alain

2016-11-22

This study investigates the determinants of long working hours from the perspectives of the demand-control model [Karasek, 1979] and social exchange theory [Blau, 1964; Goulder, 1960]. These two theoretical perspectives are tested to understand why individuals work longer (or shorter) hours. The hypotheses are tested with a representative sample of 1,604 employed Canadians. In line with Karasek's model, the results support that high job demands are positively associated with longer work hours. The social exchange perspective would predict a positive association between skill discretion and work hours. This hypothesis was supported for individuals with a higher education degree. Finally, the results support a positive association between active jobs and longer work hours. Our research suggests that job demands and social exchange dynamics need to be considered together in the explanation of longer (or shorter) work hours.

Replica field theory for a polymer in random media

International Nuclear Information System (INIS)

Goldschmidt, Yadin Y.

2000-01-01

In this paper we revisit the problem of a (non-self-avoiding) polymer chain in a random medium which was previously investigated by Edwards and Muthukumar (EM) [J. Chem. Phys. 89, 2435 (1988)]. As noticed by Cates and Ball (CB) [J. Phys. (France) 49, 2009 (1988)] there is a discrepancy between the predictions of the replica calculation of EM and the expectation that in an infinite medium the quenched and annealed results should coincide (for a chain that is free to move) and a long polymer should always collapse. CB argued that only in a finite volume one might see a ''localization transition'' (or crossover) from a stretched to a collapsed chain in three spatial dimensions. Here we carry out the replica calculation in the presence of an additional confining harmonic potential that mimics the effect of a finite volume. Using a variational scheme with five variational parameters we derive analytically for d -1/(4-d) ∼(g ln V) -1/(4-d) , where R is the radius of gyration, g is the strength of the disorder, μ is the spring constant associated with the confining potential, and V is the associated effective volume of the system. Thus the EM result is recovered with their constant replaced by ln V as argued by CB. We see that in the strict infinite volume limit the polymer always collapses, but for finite volume a transition from a stretched to a collapsed form might be observed as a function of the strength of the disorder. For d V ' ∼exp(g 2/(2-d) L (4-d)/(2-d) ) the annealed results are recovered and R∼(Lg) 1/(d-2) , where L is the length of the polymer. Hence the polymer also collapses in the large L limit. The one-step replica symmetry breaking solution is crucial for obtaining the above results. (c) 2000 The American Physical Society

Molecular dynamics simulation of ribosome jam

KAUST Repository

Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

2011-01-01

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.

Science.gov (United States)

Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E; Zhao, Jianhua; Schulten, Klaus

2016-07-07

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

2010-01-01

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...

Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

Science.gov (United States)

Stella, L.; Lorenz, C. D.; Kantorovich, L.

2014-04-01

The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

Isovector meson-exchange currents in the light-front dynamics

International Nuclear Information System (INIS)

Desplanques, B.; Karmanov, V.A.; Mathiot, J.F.

1994-09-01

In the light-front dynamics, there is no pair term that plays the role of the dominant isovector pion exchange current. This current gives rise to the large and experimentally observed contribution to the deuteron electrodisintegration cross-section near threshold for pseudo-scalar πNN coupling. It is analytically shown that in leading 1/m order the amplitude in the light-front dynamics coincides, however, with the one given by the pair term. At high Q 2 , it consists of two equal parts. One comes from extra components of the deuteron and final state relativistic wave functions. The other results from the contact NNπγ interaction which appears in the light-front dynamics. This provides a transparent link between relativistic and non-relativistic approaches. (author). 16 refs., 4 figs

Ejection dynamics of hydrogen molecular ions from methanol in intense laser fields

International Nuclear Information System (INIS)

Okino, T; Furukawa, Y; Liu, P; Ichikawa, T; Itakura, R; Hoshina, K; Yamanouchi, K; Nakano, H

2006-01-01

The ejection of hydrogen molecular ions from two-body Coulomb explosion processes of methanol (CH 3 OH, CD 3 OH and CH 3 OD) in an intense laser field (800 nm, 60 fs, 0.2 PW cm -2 ) is investigated by a coincidence momentum imaging method. From the coincidence momentum maps, the ejection processes of hydrogen molecular ions, CH 3 OH 2+ → H m + + CH (3-m) OH + (m = 2, 3), CD 3 OH 2+ → D m + + CH (3-m) OH + (m = 2, 3) and CH 3 OD 2+ → H m + + CH (3-m) OD + (m = 2, 3), are identified. Based on the results obtained with isotopically substituted methanol, the isotope effect on the ejection process of hydrogen molecular ions is discussed. Furthermore, the ejection of H/D exchanged hydrogen molecular ions (HD + , HD 2 + and H 2 D + ) is identified, and the timescales for the H/D exchanging processes are estimated from the extent of anisotropy in the ejection directions

“Invisible” Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations

Science.gov (United States)

Fizil, Ádám; Gáspári, Zoltán; Barna, Terézia; Marx, Florentine; Batta, Gyula

2015-01-01

Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20–40 % at 298 K in a disulfide-rich protein. In addition, sensitive 15N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR “dark matter”. Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction. PMID:25676351

Dynamics of molecular superrotors in an external magnetic field

International Nuclear Information System (INIS)

Korobenko, Aleksey; Milner, Valery

2015-01-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

Science.gov (United States)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

DEFF Research Database (Denmark)

Papaleo, Elena

2015-01-01

that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

AceCloud: Molecular Dynamics Simulations in the Cloud.

Science.gov (United States)

Harvey, M J; De Fabritiis, G

2015-05-26

We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

Stability and replica symmetry in the ising spin glass: a toy model

International Nuclear Information System (INIS)

De Dominicis, C.; Mottishaw, P.

1986-01-01

Searching for possible replica symmetric solutions in an Ising spin glass (in the tree approximation) we investigate a toy model whose bond distribution has two non vanishing cumulants (instead of one only as in a gaussian distribution)

Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

Science.gov (United States)

Radford, Isolde H; Fersht, Alan R; Settanni, Giovanni

2011-06-09

Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry

Science.gov (United States)

Huang, Richard Y.-C.; Iacob, Roxana E.; Sankaranarayanan, Sethu; Yang, Ling; Ahlijanian, Michael; Tao, Li; Tymiak, Adrienne A.; Chen, Guodong

2018-01-01

Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. [Figure not available: see fulltext.

Molecular dynamics simulations of RNA motifs

Czech Academy of Sciences Publication Activity Database

Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

2002-01-01

Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

Tunable hydrodynamic characteristics in microchannels with biomimetic superhydrophobic (lotus leaf replica) walls.

Science.gov (United States)

Dey, Ranabir; Raj M, Kiran; Bhandaru, Nandini; Mukherjee, Rabibrata; Chakraborty, Suman

2014-05-21

The present work comprehensively addresses the hydrodynamic characteristics through microchannels with lotus leaf replica (exhibiting low adhesion and superhydrophobic properties) walls. The lotus leaf replica is fabricated following an efficient, two-step, soft-molding process and is then integrated with rectangular microchannels. The inherent biomimetic, superhydrophobic surface-liquid interfacial hydrodynamics, and the consequential bulk flow characteristics, are critically analyzed by the micro-particle image velocimetry technique. It is observed that the lotus leaf replica mediated microscale hydrodynamics comprise of two distinct flow regimes even within the low Reynolds number paradigm, unlike the commonly perceived solely apparent slip-stick dominated flows over superhydrophobic surfaces. While the first flow regime is characterized by an apparent slip-stick flow culminating in an enhanced bulk throughput rate, the second flow regime exhibits a complete breakdown of the aforementioned laminar and uni-axial flow model, leading to a predominantly no-slip flow. Interestingly, the critical flow condition dictating the transition between the two hydrodynamic regimes is intrinsically dependent on the micro-confinement effect. In this regard, an energetically consistent theoretical model is also proposed to predict the alterations in the critical flow condition with varying microchannel configurations, by addressing the underlying biomimetic surface-liquid interfacial conditions. Hence, the present research endeavour provides a new design-guiding paradigm for developing multi-functional microfluidic devices involving biomimetic, superhydrophobic surfaces, by judicious exploitation of the tunable hydrodynamic characteristics in the two regimes.

Monte Carlo-molecular dynamics simulations for two-dimensional magnets

International Nuclear Information System (INIS)

Kawabata, C.; takeuchi, M.; Bishop, A.R.

1985-01-01

A combined Monte Carlo-molecular dynamics simulation technique is used to study the dynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians

Localization-Free Detection of Replica Node Attacks in Wireless Sensor Networks Using Similarity Estimation with Group Deployment Knowledge

Directory of Open Access Journals (Sweden)

Chao Ding

2017-01-01

Full Text Available Due to the unattended nature and poor security guarantee of the wireless sensor networks (WSNs, adversaries can easily make replicas of compromised nodes, and place them throughout the network to launch various types of attacks. Such an attack is dangerous because it enables the adversaries to control large numbers of nodes and extend the damage of attacks to most of the network with quite limited cost. To stop the node replica attack, we propose a location similarity-based detection scheme using deployment knowledge. Compared with prior solutions, our scheme provides extra functionalities that prevent replicas from generating false location claims without deploying resource-consuming localization techniques on the resource-constraint sensor nodes. We evaluate the security performance of our proposal under different attack strategies through heuristic analysis, and show that our scheme achieves secure and robust replica detection by increasing the cost of node replication. Additionally, we evaluate the impact of network environment on the proposed scheme through theoretic analysis and simulation experiments, and indicate that our scheme achieves effectiveness and efficiency with substantially lower communication, computational, and storage overhead than prior works under different situations and attack strategies.

Molecular dynamics and Monte Carlo calculations in statistical mechanics

International Nuclear Information System (INIS)

Wood, W.W.; Erpenbeck, J.J.

1976-01-01

Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

Evaluation of generalized degrees of freedom for sparse estimation by replica method

Science.gov (United States)

Sakata, A.

2016-12-01

We develop a method to evaluate the generalized degrees of freedom (GDF) for linear regression with sparse regularization. The GDF is a key factor in model selection, and thus its evaluation is useful in many modelling applications. An analytical expression for the GDF is derived using the replica method in the large-system-size limit with random Gaussian predictors. The resulting formula has a universal form that is independent of the type of regularization, providing us with a simple interpretation. Within the framework of replica symmetric (RS) analysis, GDF has a physical meaning as the effective fraction of non-zero components. The validity of our method in the RS phase is supported by the consistency of our results with previous mathematical results. The analytical results in the RS phase are calculated numerically using the belief propagation algorithm.

Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

Czech Academy of Sciences Publication Activity Database

Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

2015-01-01

Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf

Nanotribology investigations with classical molecular dynamics

NARCIS (Netherlands)

Solhjoo, Soheil

2017-01-01

This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

Science.gov (United States)

Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

2009-03-01

Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Barry J Grant

2009-03-01

Full Text Available Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75 intermediate between GTP and GDP states, or distinct loop3 (46-49, loop7 (105-110, and alpha5 C-terminus (159-166 conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74 with alpha3-loop7 (93-110, loop2 (26-37 with loop10 (145-151, and loop3 (46-49 with alpha5 (152-167. The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD simulations, is a low-frequency motion intrinsic to the structure.

Environmental variation, vegetation distribution, carbon dynamics and water/energy exchange at high latitudes

Science.gov (United States)

McGuire, A.D.; Wirth, C.; Apps, M.; Beringer, J.; Clein, J.; Epstein, H.; Kicklighter, D.W.; Bhatti, J.; Chapin, F. S.; De Groot, B.; Efremov, D.; Eugster, W.; Fukuda, M.; Gower, T.; Hinzman, L.; Huntley, B.; Jia, G.J.; Kasischke, E.; Melillo, J.; Romanovsky, V.; Shvidenko, A.; Vaganov, E.; Walker, D.

2002-01-01

The responses of high latitude ecosystems to global change involve complex interactions among environmental variables, vegetation distribution, carbon dynamics, and water and energy exchange. These responses may have important consequences for the earth system. In this study, we evaluated how vegetation distribution, carbon stocks and turnover, and water and energy exchange are related to environmental variation spanned by the network of the IGBP high latitude transects. While the most notable feature of the high latitude transects is that they generally span temperature gradients from southern to northern latitudes, there are substantial differences in temperature among the transects. Also, along each transect temperature co-varies with precipitation and photosynthetically active radiation, which are also variable among the transects. Both climate and disturbance interact to influence latitudinal patterns of vegetation and soil carbon storage among the transects, and vegetation distribution appears to interact with climate to determine exchanges of heat and moisture in high latitudes. Despite limitations imposed by the data we assembled, the analyses in this study have taken an important step toward clarifying the complexity of interactions among environmental variables, vegetation distribution, carbon stocks and turnover, and water and energy exchange in high latitude regions. This study reveals the need to conduct coordinated global change studies in high latitudes to further elucidate how interactions among climate, disturbance, and vegetation distribution influence carbon dynamics and water and energy exchange in high latitudes.

Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu, H.G.; Muckerman, J.T.

2010-06-01

The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Directory of Open Access Journals (Sweden)

Mingyuan Xu

2018-05-01

Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Molecular Structure and Dynamics in Thin Water Films at the Silica and Graphite Surfaces

Energy Technology Data Exchange (ETDEWEB)

Argyris, Dr. Dimitrios [University of Oklahoma; Tummala, Dr. Naga Rajesh [University of Oklahoma; StrioloDr., A [Vanderbilt University; Cole, David R [ORNL

2008-01-01

The structure and dynamic properties of interfacial water at the graphite and silica solid surfaces were investigated using molecular dynamics simulations. The effect of surface properties on the characteristics of interfacial water was quantified by computing density profiles, radial distribution functions, surface density distributions, orientation order parameters, and residence and reorientation correlation functions. In brief, our results show that the surface roughness, chemical heterogeneity, and surface heterogeneous charge distribution affect the structural and dynamic properties of the interfacial water molecules, as well as their rate of exchange with bulk water. Most importantly, our results indicate the formation of two distinct water layers at the SiO2 surface covered by a large density of hydroxyl groups. Further analysis of the data suggests a highly confined first layer where the water molecules assume preferential hydrogen-down orientation and a second layer whose behavior and characteristics are highly dependent on those of the first layer through a well-organized hydrogen bond network. The results suggest that water-water interactions, in particular hydrogen bonds, may be largely responsible for macroscopic interfacial properties such as adsorption and contact angle.

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

Molecular dynamics simulation of defect formation during energetic Cu deposition

International Nuclear Information System (INIS)

Gilmore, Charles M.; Sprague, James A.

2002-01-01

The deposition of energetic Cu atoms from 5 to 80 eV onto (0 0 1) Cu was simulated with molecular dynamics. The Cu-Cu interaction potential was a spline of the embedded atom potential developed from equilibrium data, and the universal scattering potential. Incident Cu atoms substituted for first layer substrate atoms by an exchange process at energies as low as 5 eV. Incident Cu atoms of 20 eV penetrated to the second substrate layer, and 20 eV was sufficient energy to produce interstitial defects. Incident atoms of 80 eV penetrated to the third atomic layer, produced interstitials 12 atomic layers into the substrate by focused replacement collision sequences, and produced sputtered atoms with a 16% yield. Interstitial clusters of up to 7 atoms were observed. The observed mechanisms of film growth included: the direct deposition of atoms into film equilibrium atom positions, the exchange of substrate atoms to equilibrium film atoms positions, and the migration of interstitials to equilibrium film atom positions. The relative frequency of each process was a function of incident energy. Since all observed growth mechanisms resulted in film atoms in equilibrium atomic positions, these simulations suggest that stresses in homoepitaxial Cu thin films are due to point defects. Vacancies would produce tensile strain and interstitial atoms would produce compressive strain in the films. It is proposed that immobile interstitial clusters could be responsible for retaining interstitial atoms and clusters in growing metal thin films

An Event-Driven Hybrid Molecular Dynamics and Direct Simulation Monte Carlo Algorithm

Energy Technology Data Exchange (ETDEWEB)

Donev, A; Garcia, A L; Alder, B J

2007-07-30

A novel algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with the solvent particles with hard core potentials. The algorithm uses event-driven molecular dynamics (MD) for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in event-driven algorithms, rather, the momentum and energy exchange in the solvent is determined stochastically using the Direct Simulation Monte Carlo (DSMC) method. The coupling between the solvent and the solute is consistently represented at the particle level, however, unlike full MD simulations of both the solvent and the solute, the spatial structure of the solvent is ignored. The algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard wall subjected to uniform shear. The algorithm closely reproduces full MD simulations with two orders of magnitude greater efficiency. Results do not confirm the existence of periodic (cycling) motion of the polymer chain.

Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

Science.gov (United States)

Cheng, Mary Hongying; Coalson, Rob D.

2012-01-01

Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferred through comparative molecular dynamics simulations with protonated and deprotonated GLUex in the presence/absence of external potentials. Adaptive biasing force calculations are employed to estimate the potential of mean force profiles associated with transport of a Cl– ion from Sext to Sint, depending on the Cl– occupancy of other sites. Our simulations demonstrate that protonation of GLUex is essential for Cl– transport from Sext to Scen. The Scen site may be occupied by two Cl– ions simultaneously due to a high energy barrier (∼8 Kcal/mol) for a single Cl– ion to translocate from Scen to Sint. Binding two Cl– ions to Scen induces a continuous water wire from Scen to the extracellular solution through the side chain of the GLUex gate. This may initiate deprotonation of GLUex, which then drives the two Cl– ions out of Scen toward the intracellular side via two putative Cl– transport paths. Finally, a conformational cycle is proposed that would account for the exchange stoichiometry. PMID:22455919

Modeling ramp compression experiments using large-scale molecular dynamics simulation.

Energy Technology Data Exchange (ETDEWEB)

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

Neutron and gamma dose and spectra measurements on the Little Boy replica

International Nuclear Information System (INIS)

Hoots, S.; Wadsworth, D.

1984-01-01

The radiation-measurement team of the Weapons Engineering Division at Lawrence Livermore National Laboratory (LLNL) measured neutron and gamma dose and spectra on the Little Boy replica at Los Alamos National Laboratory (LANL) in April 1983. This assembly is a replica of the gun-type atomic bomb exploded over Hiroshima in 1945. These measurements support the National Academy of Sciences Program to reassess the radiation doses due to atomic bomb explosions in Japan. Specifically, the following types of information were important: neutron spectra as a function of geometry, gamma to neutron dose ratios out to 1.5 km, and neutron attenuation in the atmosphere. We measured neutron and gamma dose/fission from close-in to a kilometer out, and neutron and gamma spectra at 90 and 30 0 close-in. This paper describes these measurements and the results. 12 references, 13 figures, 5 tables

A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

KAUST Repository

Neumann, Philipp; Tchipev, Nikola

2012-01-01

We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

KAUST Repository

Yoon, Seyoon; Monteiro, Paulo J.M.

2013-01-01

The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current

Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

DEFF Research Database (Denmark)

Toxvaerd, Søren

2001-01-01

Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

molecular dynamics simulations and quantum chemical calculations

African Journals Online (AJOL)

ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

Invariant molecular-dynamics approach to structural phase transitions

International Nuclear Information System (INIS)

Wentzcovitch, R.M.

1991-01-01

Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

International Nuclear Information System (INIS)

Aradi, Balint; Frauenheim, Thomas

2015-01-01

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology

Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

Science.gov (United States)

Dizkirici, Ayten; Tekpinar, Mustafa

2015-03-01

GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

Science.gov (United States)

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

NMR investigations of molecular dynamics

Science.gov (United States)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

Excitation dynamics and relaxation in a molecular heterodimer

International Nuclear Information System (INIS)

Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

2012-01-01

Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

The nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1992-03-01

MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

Reaction dynamics of molecular hydrogen on silicon surfaces

DEFF Research Database (Denmark)

Bratu, P.; Brenig, W.; Gross, A.

1996-01-01

of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

Número de replicações de inquéritos dietéticos para estimativa da ingestão de nutrientes em gestantes brasileiras

Directory of Open Access Journals (Sweden)

Daniela Saes Sartorelli

2014-12-01

Full Text Available Objetivos: determinar o número de replicações de inquéritos dietéticos necessários para estimar a ingestão usual de nutrientes e em categorias de consumo de gestantes no Brasil. Métodos: estudo prospectivo conduzido entre 82 gestantes, no qual as informações sobre energia e 18 nutrientes foram obtidas em três inquéritos recordatórios de 24 horas, sendo um em cada trimestre gestacional. Empregaram-se diferentes fórmulas para o cálculo do número de replicações do método necessárias para classificar as gestantes em categorias de ingestão, que considera a razão das variâncias intrapessoal/interpessoal, e para a estimativa da ingestão usual, baseado na variância intrapessoal. Resultados: para classificar as gestantes em categorias são necessárias entre 11 e 51 replicações do método, considerando-se coeficiente de correlação de 0,9. Admitindo coeficiente de correlação de 0,7, o número de replicações do método variou entre quatro e 19. Para a estimativa da ingestão usual são necessárias entre duas e 33 replicações, admitindo-se um erro de 10%. Considerando-se um erro de 20%, são necessárias entre uma e sete replicações de inquéritos dietéticos. Conclusões: é necessário um elevado número de replicações de inquéritos dietéticos na estimativa da ingestão de nutrientes na gestação e o emprego de um número reduzido de replicações poderá atenuar as associações entre a dieta e desfechos de saúde maternos e fetais.

State-to-state dynamics of molecular energy transfer

Energy Technology Data Exchange (ETDEWEB)

Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

1993-12-01

The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

Line-shape theory and molecular dynamics in collision-induced light scattering

International Nuclear Information System (INIS)

Balucani, U.; Tognetti, V.; Vallauri, R.

1979-01-01

Molecular-dynamics studies in argon at 148 amagats are presented for gaining information on the dynamical properties responsible for the depolarized light scattering from simple fluids. The total and pair-correlation functions are computed within the simple dipole--induced-dipole model of polarizability anisotropy. The pair spectral shape is derived. These results are compared with a theoretical analysis based on a continued-fraction approach. The necessary frequency moments are calculated both in the low-density limit and taking into account first-order density corrections, and compared with the molecular-dynamics data. The agreement between the theoretical spectra and molecular-dynamics data shows the validity of the memory-function approach. The comparison with the real experimental results allows one to test the relevant physical contributions to the polarizability anisotropy

Energy exchange analysis in droplet dynamics via the Navier-Stokes-Cahn-Hilliard model

Science.gov (United States)

Espath, L. F. R.; Sarmiento, A. F.; Vignal, P.; Varga, B. O. N.; Cortes, A. M. A.; Dalcin, L.; Calo, V. M.

2016-06-01

We develop the energy budget equation of the coupled Navier-Stokes-Cahn-Hilliard (NSCH) system. We use the NSCH equations to model the dynamics of liquid droplets in a liquid continuum. Buoyancy effects are accounted for through the Boussinesq assumption. We physically interpret each quantity involved in the energy exchange to further insight into the model. Highly resolved simulations involving density-driven flows and merging of droplets allow us to analyze these energy budgets. In particular, we focus on the energy exchanges when droplets merge, and describe flow features relevant to this phenomenon. By comparing our numerical simulations to analytical predictions and experimental results available in the literature, we conclude that modeling droplet dynamics within the framework of NSCH equations is a sensible approach worth further research.

IAEA technical meeting on 'Technical aspects of atomic and molecular data processing and exchange'. Summary report

International Nuclear Information System (INIS)

Humbert, Denis

2004-03-01

The proceedings of the IAEA Advisory Group Meeting on 'Technical Aspects of Atomic and Molecular Data Processing and Exchange' (17th Meeting of A+M Data Centres and ALADDIN Network), held on 6-7 October, 2003 in Vienna, Austria are briefly described. The meeting conclusions and recommendations on the priorities in A+M data compilation and evaluation, and on the technical aspects of data processing, exchange, and distribution are also presented. (author)

Temporal Dynamics of Social Exchange and the Development of Solidarity: "Testing the Waters" versus "Taking a Leap of Faith"

Science.gov (United States)

Kuwabara, Ko; Sheldon, Oliver

2012-01-01

In their concerted efforts to unpack the microprocesses that transform repeated exchanges into an exchange relation, exchange theorists have paid little attention to how actors perceive changes and dynamics in exchanges over time. We help fill this gap by studying how temporal patterns of exchange affect the development of cohesion. Some exchange…

Coulomb interactions via local dynamics: a molecular-dynamics algorithm

International Nuclear Information System (INIS)

Pasichnyk, Igor; Duenweg, Burkhard

2004-01-01

We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

DEFF Research Database (Denmark)

Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

2012-01-01

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

Science.gov (United States)

Hu, Hao; Liu, Haiyan

2013-05-30

Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

Structual Dynamics and Function of the Na+/H+ Exchanger 1

DEFF Research Database (Denmark)

Hendus-Altenburger, Ruth

Na+/H+ Exchangers (SLC9As) are of pivotal importance in several physiological processes, and their dysfunction is linked to the pathogenesis of several diseases. The Na+/H+ Exchanger 1 (NHE1) is ubiquitously expressed at the plasma membrane. It contains two domains, the transmembrane ion...... translocation domain and a large cytoplasmic regulatory domain. Despite its physiological and pathophysiological importance, high resolution structural data of NHE1 is missing, and even though several binding partners and phosphorylation sites of the NHE1 regulatory domain are known and many more suggested......, the molecular structures and mechanisms underlying NHE1 regulation and function are still incompletely understood. In this work, in silico analysis revealed two structured and two intrinsically disordered regions in the regulatory domain. A divide-and-conquer approach was used to identify subdomains...

Communication: Multiple atomistic force fields in a single enhanced sampling simulation

Energy Technology Data Exchange (ETDEWEB)

Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

2015-07-14

The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

Proactive replica checking to assure reliability of data in cloud storage with minimum replication

Science.gov (United States)

Murarka, Damini; Maheswari, G. Uma

2017-11-01

The two major issues for cloud storage systems are data reliability and storage costs. For data reliability protection, multi-replica replication strategy which is used mostly in current clouds acquires huge storage consumption, leading to a large storage cost for applications within the loud specifically. This paper presents a cost-efficient data reliability mechanism named PRCR to cut back the cloud storage consumption. PRCR ensures data reliability of large cloud information with the replication that might conjointly function as a price effective benchmark for replication. The duplication shows that when resembled to the standard three-replica approach, PRCR will scale back to consume only a simple fraction of the cloud storage from one-third of the storage, thence considerably minimizing the cloud storage price.

Macroeconomic Effects of Nominal Exchange Rate Regimes: New Insights into the Role of Price Dynamics

OpenAIRE

Kollmann, Robert

2004-01-01

This Paper analyses the effects of pegged and floating exchange rates using a two-country dynamic general equilibrium model that is calibrated to the US and a European aggregate. The model assumes shocks to money, productivity and the interest parity condition. It captures the fact that the sharp increase in nominal exchange rate volatility after the abandonment of the Bretton Woods (BW) system was accompanied by a commensurate rise in real exchange rate volatility, but had no pronounced effe...

Ab initio molecular dynamics in a finite homogeneous electric field.

Science.gov (United States)

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

X-ray and neutron diffraction and molecular dynamics simulation of molten lithium and rubidium nitrates

International Nuclear Information System (INIS)

Yamaguchi, Toshio; Okada, Isao; Ohtaki, Hitoshi; Mikami, Masuhiro; Kawamura, Kazutaka

1986-01-01

Molecular dynamics simulations have been performed for lithium and rubidium nitrate melts at 550 and 600K, respectively, together with X-ray and neutron diffraction experiments. Simple Coulomb pair potentials with Born-type repulsions have been adopted in the simulations with a rigid body model for the nitrate ion. Structure functions derived from the X-ray and neutron experiments are well reproduced by the simulations, from which the three-dimensional cation distribution around the nitrate ion has been revealed. The self-diffusion coefficients, the velocity autocorrelation functions and the self-exchange velocities of lithium, rubidium and nitrate ions have been calculated. Anisotropic motion of nitrate ions has been found and is discussed on the basis of the structure of the melts. (author)

Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Bresme, F.; Armstrong, J.

2014-01-01

We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation

Dynamics of solutions and fluid mixtures by NMR

International Nuclear Information System (INIS)

Delpuech, J.J.

1994-01-01

After a short introduction to NMR spectroscopy, with a special emphasis on dynamical aspects, an overview on two fundamental aspects of molecular dynamics, NMR relaxation and its relationship with molecular reorientation, and magnetization transfer phenomena induced by molecular rate processes (dynamic NMR) is presented, followed by specific mechanisms of relaxation encountered in paramagnetic systems or with quadrupolar nuclei. Application fields are then reviewed: solvent exchange on metal ions with a variable pressure NMR approach, applications of field gradients in NMR, aggregation phenomena and micro-heterogeneity in surfactant solutions, polymers and biopolymers in the liquid state, liquid-like molecules in rigid matrices and in soft matter (swollen polymers and gels, fluids in and on inorganic materials, food)

Dynamic adsorption of CO2/N2 on cation-exchanged chabazite SSZ-13: A breakthrough analysis

Energy Technology Data Exchange (ETDEWEB)

Bower, Jamey K.; Barpaga, Dushyant; Prodinger, Sebastian; Krishna, Rajamani; Schaef, Herbert T.; McGrail, Bernard P.; Derewinski, Miroslaw A.; Motkuri, Radha K.

2018-04-17

Alkali exchanged SSZ-13 adsorbents were investigated for their applicability in separating N2 from CO2 in flue gas streams using a dynamic breakthrough method. In contrast to IAST calculations based on equilibrium isotherms, K+ exchanged SSZ-13 was found to yield the best N2 productivity under dynamic conditions where diffusion properties play a significant role. This was attributed to the selective, partial blockage of access to the CHA cavities enhancing the separation potential in a 15/85 CO2/N2 binary gas mixture.

Fermionic molecular dynamics for colliding and decaying nuclei

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

1993-11-01

Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)

Optical spectra and lattice dynamics of molecular crystals

CERN Document Server

Zhizhin, GN

1995-01-01

The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

Energy exchange analysis in droplet dynamics via the Navier–Stokes–Cahn–Hilliard model

KAUST Repository

Espath, L. F. R.

2016-05-23

We develop the energy budget equation of the coupled Navier-Stokes-Cahn-Hilliard (NSCH) system. We use the NSCH equations to model the dynamics of liquid droplets in a liquid continuum. Buoyancy effects are accounted for through the Boussinesq assumption. We physically interpret each quantity involved in the energy exchange to gain further insight into the model. Highly resolved simulations involving density-driven flows and the merging of droplets allow us to analyse these energy budgets. In particular, we focus on the energy exchanges when droplets merge, and describe flow features relevant to this phenomenon. By comparing our numerical simulations to analytical predictions and experimental results available in the literature, we conclude that modelling droplet dynamics within the framework of NSCH equations is a sensible approach worthy of further research. © 2016 Cambridge University Press.

Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

International Nuclear Information System (INIS)

De Leeuw, S.W.; Brakkee, M.J.D.

1990-01-01

Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

Energy Technology Data Exchange (ETDEWEB)

Lambert, F

2007-08-15

The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

Orthonormal Wavelet Bases for Quantum Molecular Dynamics

International Nuclear Information System (INIS)

Tymczak, C.; Wang, X.

1997-01-01

We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories.

Science.gov (United States)

Morishita, Tetsuya; Yonezawa, Yasushige; Ito, Atsushi M

2017-07-11

Efficient and reliable estimation of the mean force (MF), the derivatives of the free energy with respect to a set of collective variables (CVs), has been a challenging problem because free energy differences are often computed by integrating the MF. Among various methods for computing free energy differences, logarithmic mean-force dynamics (LogMFD) [ Morishita et al., Phys. Rev. E 2012 , 85 , 066702 ] invokes the conservation law in classical mechanics to integrate the MF, which allows us to estimate the free energy profile along the CVs on-the-fly. Here, we present a method called parallel dynamics, which improves the estimation of the MF by employing multiple replicas of the system and is straightforwardly incorporated in LogMFD or a related method. In the parallel dynamics, the MF is evaluated by a nonequilibrium path-ensemble using the multiple replicas based on the Crooks-Jarzynski nonequilibrium work relation. Thanks to the Crooks relation, realizing full-equilibrium states is no longer mandatory for estimating the MF. Additionally, sampling in the hidden subspace orthogonal to the CV space is highly improved with appropriate weights for each metastable state (if any), which is hardly achievable by typical free energy computational methods. We illustrate how to implement parallel dynamics by combining it with LogMFD, which we call logarithmic parallel dynamics (LogPD). Biosystems of alanine dipeptide and adenylate kinase in explicit water are employed as benchmark systems to which LogPD is applied to demonstrate the effect of multiple replicas on the accuracy and efficiency in estimating the free energy profiles using parallel dynamics.

Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

Energy Technology Data Exchange (ETDEWEB)

Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

2017-04-04

The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.

Replica Approach for Minimal Investment Risk with Cost

Science.gov (United States)

Shinzato, Takashi

2018-06-01

In the present work, the optimal portfolio minimizing the investment risk with cost is discussed analytically, where an objective function is constructed in terms of two negative aspects of investment, the risk and cost. We note the mathematical similarity between the Hamiltonian in the mean-variance model and the Hamiltonians in the Hopfield model and the Sherrington-Kirkpatrick model, show that we can analyze this portfolio optimization problem by using replica analysis, and derive the minimal investment risk with cost and the investment concentration of the optimal portfolio. Furthermore, we validate our proposed method through numerical simulations.

Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes

NARCIS (Netherlands)

Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

2007-01-01

This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the

Molecular dynamics for reactions of heterogeneous catalysis

NARCIS (Netherlands)

Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

1991-01-01

An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

Propensity of bond exchange as a window into the mechanical properties of metallic glasses

Energy Technology Data Exchange (ETDEWEB)

Jiao, W.; Wang, X. L., E-mail: xlwang@um.cityu.edu.hk; Lan, S. [Department of Physics and Materials Science, City University of Hong Kong, Hong Kong (China); Pan, S. P. [College of Materials Science and Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Lu, Z. P. [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China)

2015-02-09

We investigated the mechanical properties of Zr-Cu-Al bulk metallic glasses, by compression experiment and molecular dynamics simulations. From the simulation, we found that the large, solvent atom, Zr, has high propensity of bond exchange compared to those of the smaller solute atoms. The difference in bond exchange is consistent with the observed disparity in mechanical behaviors: Zr-rich metallic glass exhibits low elastic modulus and large plastic strain. X-ray photoelectron spectroscopy measurements suggest that the increased propensity in bond exchange is related to the softening of Zr bonds with increasing Zr content.

Nuclear research emulsion neutron spectrometry at the Little-Boy replica

International Nuclear Information System (INIS)

Gold, R.; Roberts, J.H.; Preston, C.C.

1985-10-01

Nuclear research emulsions (NRE) have been used to characterize the neutron spectrum emitted by the Little-Boy replica. NRE were irradiated at the Little-Boy surface as well as approximately 2 m from the center of the Little-Boy replica using polar angles of 0 0 , 30 0 , 60 0 and 90 0 . For the NRE exposed at 2 m, neutron background was determined using shadow shields of borated polyethylene. Emulsion scanning to date has concentrated exclusively on the 2-m, 0 0 and 2-m, 90 0 locations. Approximately 5000 proton-recoil tracks have been measured in NRE irradiated at each of these locations. Neutron spectra obtained from these NRE proton-recoil spectra are compared with both liquid scintillator neutron spectrometry and Monte Carlo calculations. NRE and liquid scintillator neutron spectra generally agree within experimental uncertainties at the 2-m, 90 0 location. However, at the 2-m, 0 0 location, the neutron spectra derived from these two independent experimental methods differ significantly. NRE spectra and Monte Carlo calculations exhibit general agreement with regard to both intensity as well as energy dependence. Better agreement is attained between theory and experiment at the 2-m, 90 0 location, where the neutron intensity is considerably higher. 14 refs., 18 figs., 11 tabs

Molecular dynamics simulations on PGLa using NMR orientational constraints

Energy Technology Data Exchange (ETDEWEB)

Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

2015-11-15

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

The consideration of dynamics and control in the design of heat exchanger networks

International Nuclear Information System (INIS)

Reimann, K.A.

1986-03-01

The heat exchanger network method is a way of abstracting the enthalpy and heat flows from the blueprints of a planned or existing processing plant. It enables a systematic design of a plant-wide heat recovery system which is optimal with regard to energy costs, capital costs and operational requirements. A heat exchanger network is a representation of all heat transfer relations between hot process streams and cold process streams within a plant. During the past ten years, the optimal design of heat exchanger networks (i.e. the optimal arrangement of heat transfer relations within a plant) has developed into a field of research of its own. Both, static methods ('interaction analysis') and dynamic methods ('process reaction curve analysis') from control theory have been used to explore the new field of heat exchanger network dynamics. As a major tool, an interactive, portable computer program for network simulation and controllability assessment has been developed (it is available as a design tool within the frame of the International Energy Agency). Based on the well-understood global parameters: effectiveness and NTU, which follow from the network design, some straightforward methods covering the following topics are presented: - 'paths' for control and disturbance signal transfer across the network, - locations of control bypasses around heat exchangers, and their capacity of emitting control signals or absorbing disturbances, - influence of the equipment besides the heat exchangers (which can be regarded as 'surrounding' the network, thus forming an 'associated' network). It has been found that networks which are designed according to the 'pinch-based' method have a potential for good controllability. It is shown how, using the freedoms given in the 'pinch-based' design and the above-mentioned methods, that potential is put into effect. (author)

Molecular dynamics simulations

International Nuclear Information System (INIS)

Alder, B.J.

1985-07-01

The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow

NARCIS (Netherlands)

Hunt, T.A.; Hunt, Thomas A.; Bernardi, Stefano; Todd, B.D.

2010-01-01

In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

NARCIS (Netherlands)

van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

NARCIS (Netherlands)

van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

Molecular states of HeH+. Energies and dynamical couplings

International Nuclear Information System (INIS)

Macias, A.; Riera, A.; Yanez, M.

1983-01-01

We complete the molecular results reported in a previous paper by presenting additional energies (for /sup 1,3/μ states) and radial couplings (between 'μ states) of the HeH + system. These results are needed to treat elastic and inelastic charge-exchange processes when full account is taken of momentum-transfer problems. We also present a formalism to calculate radial couplings between wave functions computed with the use of different variational methods and basis sets. The detailed form of the radial couplings is discussed and related to the Barat-Lichten correlation diagram. The effect of using finite basis sets in calculatig degenerate molecular energies is also discussed

Reaction dynamics in polyatomic molecular systems

Energy Technology Data Exchange (ETDEWEB)

Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

Energy conservation in molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

2012-01-01

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.

Science.gov (United States)

Lehn, Jean-Marie

2012-01-01

Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation.The merging of the features: -information and programmability, -dynamics and reversibility, -constitution and structural diversity, points to the emergence of adaptive and evolutive chemistry, towards a chemistry of complex matter.

Implementation of surface hopping molecular dynamics using semiempirical methods

International Nuclear Information System (INIS)

Fabiano, E.; Keal, T.W.; Thiel, W.

2008-01-01

A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained

Ab Initio molecular dynamics with excited electrons

NARCIS (Netherlands)

Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

1994-01-01

A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

Direct and quantitative characterization of dynamic ligand exchange between coordination-driven self-assembled supramolecular polygons.

Science.gov (United States)

Zheng, Yao-Rong; Stang, Peter J

2009-03-18

The direct observation of dynamic ligand exchange between Pt-N coordination-driven self-assembled supramolecular polygons (triangles and rectangles) has been achieved using stable (1)H/(2)D isotope labeling of the pyridyl donors and electrospray ionization mass spectrometry combined with NMR spectroscopy. Both the thermodynamic and kinetic aspects of such exchange processes have been established on the basis of quantitative mass spectral results. Further investigation has shown that the exchange is highly dependent on experimental conditions such as temperature, solvent, and the counteranions.

Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.

Science.gov (United States)

Dissanayake, Thakshila; Swails, Jason M; Harris, Michael E; Roitberg, Adrian E; York, Darrin M

2015-02-17

The measurement of reaction rate as a function of pH provides essential information about mechanism. These rates are sensitive to the pK(a) values of amino acids directly involved in catalysis that are often shifted by the enzyme active site environment. Experimentally observed pH-rate profiles are usually interpreted using simple kinetic models that allow estimation of "apparent pK(a)" values of presumed general acid and base catalysts. One of the underlying assumptions in these models is that the protonation states are uncorrelated. In this work, we introduce the use of constant pH molecular dynamics simulations in explicit solvent (CpHMD) with replica exchange in the pH-dimension (pH-REMD) as a tool to aid in the interpretation of pH-activity data of enzymes and to test the validity of different kinetic models. We apply the methods to RNase A, a prototype acid-base catalyst, to predict the macroscopic and microscopic pK(a) values, as well as the shape of the pH-rate profile. Results for apo and cCMP-bound RNase A agree well with available experimental data and suggest that deprotonation of the general acid and protonation of the general base are not strongly coupled in transphosphorylation and hydrolysis steps. Stronger coupling, however, is predicted for the Lys41 and His119 protonation states in apo RNase A, leading to the requirement for a microscopic kinetic model. This type of analysis may be important for other catalytic systems where the active forms of the implicated general acid and base are oppositely charged and more highly correlated. These results suggest a new way for CpHMD/pH-REMD simulations to bridge the gap with experiments to provide a molecular-level interpretation of pH-activity data in studies of enzyme mechanisms.

Molecular dynamics coupled with a virtual system for effective conformational sampling.

Science.gov (United States)

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

DEFF Research Database (Denmark)

Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

2007-01-01

The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

Science.gov (United States)

Shekhar, Adarsh

Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu H. G.; Muckerman, J.T.

2012-05-29

The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

Molecular dynamics simulation of self-diffusion coefficients for liquid metals

International Nuclear Information System (INIS)

Ju Yuan-Yuan; Zhang Qing-Ming; Gong Zi-Zheng; Ji Guang-Fu

2013-01-01

The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. (atomic and molecular physics)

Catalysis and communication in dynamic molecular networks

NARCIS (Netherlands)

Fanlo Virgos, Hugo

2015-01-01

The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity

Molecular dynamics study of atomic displacements in disordered solid alloys

Science.gov (United States)

Puzyrev, Yevgeniy S.

The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein

Science.gov (United States)

Day, Ryan; Paschek, Dietmar; Garcia, Angel E.

2012-01-01

We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent, using the Amberff99SB force field. Replica-exchange molecular dynamics (REMD) simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states, and at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs per replica timescale. The total simulation time employed in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P,T), over the whole region of temperature and pressures sampled in the simulations. The ΔG(P,T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (Tf = 321 K), free energy and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semi-empirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. PMID:20408169

Fabrication of micropillar substrates using replicas of alpha-particle irradiated and chemically etched PADC films

International Nuclear Information System (INIS)

Ng, C.K.M.; Chong, E.Y.W.; Roy, V.A.L.; Cheung, K.M.C.; Yeung, K.W.K.; Yu, K.N.

2012-01-01

We proposed a simple method to fabricate micropillar substrates. Polyallyldiglycol carbonate (PADC) films were irradiated by alpha particles and then chemically etched to form a cast with micron-scale spherical pores. A polydimethylsiloxane (PDMS) replica of this PADC film gave a micropillar substrate with micron-scale spherical pillars. HeLa cells cultured on such a micropillar substrate had significantly larger percentage of cells entering S-phase, attached cell numbers and cell spreading areas. - Highlights: ► We proposed a simple method to fabricate micropillar substrates. ► Polyallyldiglycol carbonate films were irradiated and etched to form casts. ► Polydimethylsiloxane replica then formed the micropillar substrates. ► Attachment and proliferation of HeLa cells were enhanced on these substrates.

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review

Science.gov (United States)

Miao, Yinglong; McCammon, J. Andrew

2016-01-01

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations. PMID:27453631

Bridging the gap between molecular dynamics simulations and phase-field modelling: dynamics of a [NixZr1-x]liquid-Zrcrystal solidification front

International Nuclear Information System (INIS)

Danilov, Denis; Nestler, Britta; Guerdane, Mohammed; Teichler, Helmar

2009-01-01

Results are presented from phase-field modelling and molecular dynamics simulations concerning the relaxation dynamics in a finite-temperature two-phase crystal-liquid sample subjected to an abrupt temperature drop. Relaxation takes place by propagation of the solidification front under formation of a spatially varying concentration profile in the melt. The molecular dynamics simulations are carried out with an interatomic model appropriate for the NiZr alloy system and provide the thermophysical data required for setting up the phase-field simulations. Regarding the concentration profile and velocity of the solidification front, best agreement between the phase-field model and molecular dynamics simulation is obtained when increasing the apparent diffusion coefficients in the phase-field treatment by a factor of four against their molecular dynamics estimates.

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Laser Controlled Molecular Orientation Dynamics

International Nuclear Information System (INIS)

Atabek, O.

2004-01-01

Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

Molecular potentials and relaxation dynamics

International Nuclear Information System (INIS)

Karo, A.M.

1981-01-01

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

Axial displacement of abutments into implants and implant replicas, with the tapered cone-screw internal connection, as a function of tightening torque.

Science.gov (United States)

Dailey, Bruno; Jordan, Laurence; Blind, Olivier; Tavernier, Bruno

2009-01-01

The passive fit of a superstructure on implant abutments is essential to success. One source of error when using a tapered cone-screw internal connection may be the difference between the tightening torque level applied to the abutments by the laboratory technician compared to that applied by the treating clinician. The purpose of this study was to measure the axial displacement of tapered cone-screw abutments into implants and their replicas as a function of the tightening torque level. Twenty tapered cone-screw abutments were selected. Two groups were created: 10 abutments were secured into 10 implants, and 10 abutments were secured into 10 corresponding implant replicas. Each abutment was tightened in increasing increments of 5 Ncm, from 0 Ncm to 45 Ncm, with a torque controller. The length of each sample was measured repeatedly with an Electronic Digital Micrometer. The mean axial displacement for the implant group and the replica group was calculated. The data were analyzed by the Mann-Whitney and Spearman tests. For both groups, there was always an axial displacement of the abutment upon each incremental application of torque. The mean axial displacement values varied between 7 and 12 microm for the implant group and between 6 and 21 microm for the replica group at each 5-Ncm increment. From 0 to 45 Ncm, the total mean axial displacement values were 89 microm for the implant group and 122 microm for the replica group. There was a continuous axial displacement of the abutments into implants and implant replicas when the applied torque was raised from 0 to 45 Ncm. Torque applied above the level recommended by the manufacturer increased the difference in displacement between the two groups.

The 2011 Dynamics of Molecular Collisions Conference

Energy Technology Data Exchange (ETDEWEB)

Nesbitt, David J. [JILA, NIST

2011-07-11

The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

A Dual-Channel Acquisition Method Based on Extended Replica Folding Algorithm for Long Pseudo-Noise Code in Inter-Satellite Links.

Science.gov (United States)

Zhao, Hongbo; Chen, Yuying; Feng, Wenquan; Zhuang, Chen

2018-05-25

Inter-satellite links are an important component of the new generation of satellite navigation systems, characterized by low signal-to-noise ratio (SNR), complex electromagnetic interference and the short time slot of each satellite, which brings difficulties to the acquisition stage. The inter-satellite link in both Global Positioning System (GPS) and BeiDou Navigation Satellite System (BDS) adopt the long code spread spectrum system. However, long code acquisition is a difficult and time-consuming task due to the long code period. Traditional folding methods such as extended replica folding acquisition search technique (XFAST) and direct average are largely restricted because of code Doppler and additional SNR loss caused by replica folding. The dual folding method (DF-XFAST) and dual-channel method have been proposed to achieve long code acquisition in low SNR and high dynamic situations, respectively, but the former is easily affected by code Doppler and the latter is not fast enough. Considering the environment of inter-satellite links and the problems of existing algorithms, this paper proposes a new long code acquisition algorithm named dual-channel acquisition method based on the extended replica folding algorithm (DC-XFAST). This method employs dual channels for verification. Each channel contains an incoming signal block. Local code samples are folded and zero-padded to the length of the incoming signal block. After a circular FFT operation, the correlation results contain two peaks of the same magnitude and specified relative position. The detection process is eased through finding the two largest values. The verification takes all the full and partial peaks into account. Numerical results reveal that the DC-XFAST method can improve acquisition performance while acquisition speed is guaranteed. The method has a significantly higher acquisition probability than folding methods XFAST and DF-XFAST. Moreover, with the advantage of higher detection

A Dual-Channel Acquisition Method Based on Extended Replica Folding Algorithm for Long Pseudo-Noise Code in Inter-Satellite Links

Directory of Open Access Journals (Sweden)

Hongbo Zhao

2018-05-01

Full Text Available Inter-satellite links are an important component of the new generation of satellite navigation systems, characterized by low signal-to-noise ratio (SNR, complex electromagnetic interference and the short time slot of each satellite, which brings difficulties to the acquisition stage. The inter-satellite link in both Global Positioning System (GPS and BeiDou Navigation Satellite System (BDS adopt the long code spread spectrum system. However, long code acquisition is a difficult and time-consuming task due to the long code period. Traditional folding methods such as extended replica folding acquisition search technique (XFAST and direct average are largely restricted because of code Doppler and additional SNR loss caused by replica folding. The dual folding method (DF-XFAST and dual-channel method have been proposed to achieve long code acquisition in low SNR and high dynamic situations, respectively, but the former is easily affected by code Doppler and the latter is not fast enough. Considering the environment of inter-satellite links and the problems of existing algorithms, this paper proposes a new long code acquisition algorithm named dual-channel acquisition method based on the extended replica folding algorithm (DC-XFAST. This method employs dual channels for verification. Each channel contains an incoming signal block. Local code samples are folded and zero-padded to the length of the incoming signal block. After a circular FFT operation, the correlation results contain two peaks of the same magnitude and specified relative position. The detection process is eased through finding the two largest values. The verification takes all the full and partial peaks into account. Numerical results reveal that the DC-XFAST method can improve acquisition performance while acquisition speed is guaranteed. The method has a significantly higher acquisition probability than folding methods XFAST and DF-XFAST. Moreover, with the advantage of higher