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.
Lightweight computational steering of very large scale molecular dynamics simulations
International Nuclear Information System (INIS)
Beazley, D.M.
1996-01-01
We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages
Computational challenges of large-scale, long-time, first-principles molecular dynamics
International Nuclear Information System (INIS)
Kent, P R C
2008-01-01
Plane wave density functional calculations have traditionally been able to use the largest available supercomputing resources. We analyze the scalability of modern projector-augmented wave implementations to identify the challenges in performing molecular dynamics calculations of large systems containing many thousands of electrons. Benchmark calculations on the Cray XT4 demonstrate that global linear-algebra operations are the primary reason for limited parallel scalability. Plane-wave related operations can be made sufficiently scalable. Improving parallel linear-algebra performance is an essential step to reaching longer timescales in future large-scale molecular dynamics calculations
Molecular dynamics based enhanced sampling of collective variables with very large time steps
Chen, Pei-Yang; Tuckerman, Mark E.
2018-01-01
Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.
Molecular dynamics simulations of sputtering of organic overlayers by slow, large clusters
International Nuclear Information System (INIS)
Rzeznik, L.; Czerwinski, B.; Garrison, B.J.; Winograd, N.; Postawa, Z.
2008-01-01
The ion-stimulated desorption of organic molecules by impact of large and slow clusters is examined using molecular dynamics (MDs) computer simulations. The investigated system, represented by a monolayer of benzene deposited on Ag{1 1 1}, is irradiated with projectiles composed of thousands of noble gas atoms having a kinetic energy of 0.1-20 eV/atom. The sputtering yield of molecular species and the kinetic energy distributions are analyzed and compared to the results obtain for PS4 overlayer. The simulations demonstrate quite clearly that the physics of ejection by large and slow clusters is distinct from the ejection events stimulated by the popular SIMS clusters, like C 60 , Au 3 and SF 5 at tens of keV energies.
International Nuclear Information System (INIS)
Gray, S.K.; Noid, D.W.; Sumpter, B.G.
1994-01-01
We test the suitability of a variety of explicit symplectic integrators for molecular dynamics calculations on Hamiltonian systems. These integrators are extremely simple algorithms with low memory requirements, and appear to be well suited for large scale simulations. We first apply all the methods to a simple test case using the ideas of Berendsen and van Gunsteren. We then use the integrators to generate long time trajectories of a 1000 unit polyethylene chain. Calculations are also performed with two popular but nonsymplectic integrators. The most efficient integrators of the set investigated are deduced. We also discuss certain variations on the basic symplectic integration technique
Crystallisation of a Lennard-Jones fluid by large scale molecular dynamics simulation
International Nuclear Information System (INIS)
Snook, I.
1998-01-01
Full text: The evolution of the structure of a large system of atoms interacting via a Lennard-Jones pair potential was simulated by the use of the Molecular Dynamics computer simulation technique. The system was initially equilibrated in the one phase region of the phase diagram at a temperature above critical then a temperature quench was performed which placed the system in a region were the single fluid phase was unstable. Quenches to below the triple point temperature gave rise to crystallisation The mechanism and final morphology is shown to depend strongly on the starting conditions e.g. the starting density
Dednam, W.; Botha, A. E.
2015-01-01
Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution
International Nuclear Information System (INIS)
Dednam, W; Botha, A E
2015-01-01
Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution
Directory of Open Access Journals (Sweden)
César Augusto F de Oliveira
2011-10-01
Full Text Available Chagas' disease, caused by the protozoan parasite Trypanosoma cruzi (T. cruzi, is a life-threatening illness affecting 11-18 million people. Currently available treatments are limited, with unacceptable efficacy and safety profiles. Recent studies have revealed an essential T. cruzi proline racemase enzyme (TcPR as an attractive candidate for improved chemotherapeutic intervention. Conformational changes associated with substrate binding to TcPR are believed to expose critical residues that elicit a host mitogenic B-cell response, a process contributing to parasite persistence and immune system evasion. Characterization of the conformational states of TcPR requires access to long-time-scale motions that are currently inaccessible by standard molecular dynamics simulations. Here we describe advanced accelerated molecular dynamics that extend the effective simulation time and capture large-scale motions of functional relevance. Conservation and fragment mapping analyses identified potential conformational epitopes located in the vicinity of newly identified transient binding pockets. The newly identified open TcPR conformations revealed by this study along with knowledge of the closed to open interconversion mechanism advances our understanding of TcPR function. The results and the strategy adopted in this work constitute an important step toward the rationalization of the molecular basis behind the mitogenic B-cell response of TcPR and provide new insights for future structure-based drug discovery.
Properties of liquid clusters in large-scale molecular dynamics nucleation simulations
International Nuclear Information System (INIS)
Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K.; Tanaka, Hidekazu
2014-01-01
We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 10 9 atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys. 139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ΔkT = 0.1ε for clusters with size i = 100. We find that the clusters deviate remarkably from spherical—with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%−30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates
Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Kunaseth, Manaschai; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Ohmura, Satoshi; Rajak, Pankaj; Shimamura, Kohei; Vashishta, Priya
2014-05-01
We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 106-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques
International Nuclear Information System (INIS)
Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya; Kunaseth, Manaschai; Ohmura, Satoshi; Shimamura, Kohei
2014-01-01
We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10 6 -atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of
A large-scale molecular dynamics study of the divacancy defect in graphene
International Nuclear Information System (INIS)
Leyssale, Jean-Marc; Vignoles, Gerard L.
2014-01-01
We report on the dynamical behavior of single divacancy defects in large graphene sheets as studied by extensive classical molecular dynamics (MD) simulations at high temperatures and static calculations. In the first part of the paper, the ability of the used interatomic potential to properly render the stability and dynamics (energy barriers) of such defects is validated against electronic structure calculations from the literature. Then, results from MD simulations are presented. In agreement with recent TEM studies, some mobility is observed through a series of Stone-Wales-like bond rotations involving the 5-8-5, 555-777, and 5555-6-7777 reconstructions. Although these three structures are by far the most probable structures of the DV defect, not less than 18 other full reconstructions, including the experimentally observed 55-66-77 defect, were occasionally observed in the ∼1.5 μs of MD trajectories analyzed in this work. Most of these additional reconstructions have moderate formation energies and can be formed by a bond rotation mechanism from one of the aforementioned structures, with a lower activation energy than the one required to form a Stone-Wales defect in graphene. Therefore their future experimental observation is highly probable. The results presented here also suggest that the barrier to a conventional Stone-Wales transformation (the formation of two pentagon/heptagon pairs from four hexagons) can be significantly reduced in the vicinity of an existing defect, strengthening a recently proposed melting mechanism for graphene based on the aggregation of Stone-Wales defects. From a structural point of view, in addition to pentagons, heptagons, and octagons, these new DV reconstructions can also contain four- and nine-member rings and show a particularly large spatial extent of up to 13 rings (42 atoms) against three (14 atoms) for the original 5-8-5 defect. (authors)
Homogeneous SPC/E water nucleation in large molecular dynamics simulations.
Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K; Tanaka, Hidekazu
2015-08-14
We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to ∼ 4 ⋅ 10(6) molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to ∼ 10(19) cm(-3) s(-1), helping close the gap between experimentally measured rates ∼ 10(17) cm(-3) s(-1). We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run average temperature. Also, we observe that post-critical clusters have densities very slightly higher, ∼ 5%, than bulk liquid. We re-calibrate a Hale-type J vs. S scaling relation using both experimental and simulation data, finding remarkable consistency in over 30 orders of magnitude in the nucleation rate range and 180 K in the temperature range.
Reinforced dynamics for enhanced sampling in large atomic and molecular systems
Zhang, Linfeng; Wang, Han; E, Weinan
2018-03-01
A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function. Parameterization using neural networks makes it feasible to handle cases with a large set of collective variables. This has the potential advantage that selecting precisely the right set of collective variables has now become less critical for capturing the structural transformations of the system. The method is illustrated by studying the full-atom explicit solvent models of alanine dipeptide and tripeptide, as well as the system of a polyalanine-10 molecule with 20 collective variables.
Large-scale molecular dynamics simulations of self-assembling systems.
Klein, Michael L; Shinoda, Wataru
2008-08-08
Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.
The consistency of large concerted motions in proteins in molecular dynamics simulations
de Groot, B.L.; van Aalten, D.M.F.; Amadei, A; Berendsen, H.J.C.
1996-01-01
A detailed investigation is presented into the effect of limited sampling time and small changes in the force field on molecular dynamics simulations of a protein. Thirteen independent simulations of the B1 IgG-binding domain of streptococcal protein G were performed, with small changes in the
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.
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.
International Nuclear Information System (INIS)
Mendez-Villuendas, E; Baoukina, S; Tieleman, D P
2012-01-01
Molecular dynamics simulations have rapidly grown in size and complexity, as computers have become more powerful and molecular dynamics software more efficient. Using coarse-grained models like MARTINI system sizes of the order of 50 nm × 50 nm × 50 nm can be simulated on commodity clusters on microsecond time scales. For simulations of biological membranes and monolayers mimicking lung surfactant this enables large-scale transformation and complex mixtures of lipids and proteins. Here we use a simulation of a monolayer with three phospholipid components, cholesterol, lung surfactant proteins, water, and ions on a ten microsecond time scale to illustrate some current challenges in analysis. In the simulation, phase separation occurs followed by formation of a bilayer fold in which lipids and lung surfactant protein form a highly curved structure in the aqueous phase. We use Voronoi analysis to obtain detailed physical properties of the different components and phases, and calculate local mean and Gaussian curvatures of the bilayer fold.
Directory of Open Access Journals (Sweden)
Carles Calero
2016-04-01
Full Text Available Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs. We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii to the higher probability of water–lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.
Tian, Jiting; Zhou, Wei; Feng, Qijie; Zheng, Jian
2018-03-01
An unsolved problem in research of sputtering from metals induced by energetic large cluster ions is that molecular dynamics (MD) simulations often produce sputtering yields much higher than experimental results. Different from the previous simulations considering only elastic atomic interactions (nuclear stopping), here we incorporate inelastic electrons-atoms interactions (electronic stopping, ES) into MD simulations using a friction model. In this way we have simulated continuous 45° impacts of 10-20 keV C60 on a Ag(111) surface, and found that the calculated sputtering yields can be very close to the experimental results when the model parameter is appropriately assigned. Conversely, when we ignore the effect of ES, the yields are much higher, just like the previous studies. We further expand our research to the sputtering of Au induced by continuous keV C60 or Ar100 bombardments, and obtain quite similar results. Our study indicates that the gap between the experimental and the simulated sputtering yields is probably induced by the ignorance of ES in the simulations, and that a careful treatment of this issue is important for simulations of cluster-ion-induced sputtering, especially for those aiming to compare with experiments.
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....
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.)
Energy Technology Data Exchange (ETDEWEB)
Fijany, A. [Jet Propulsion Lab., Pasadena, CA (United States); Coley, T.R. [Virtual Chemistry, Inc., San Diego, CA (United States); Cagin, T.; Goddard, W.A. III [California Institute of Technology, Pasadena, CA (United States)
1997-12-31
Successful molecular dynamics (MD) simulation of large systems (> million atoms) for long times (> nanoseconds) requires the integration of constrained equations of motion (CEOM). Constraints are used to eliminate high frequency degrees of freedom (DOF) and to allow the use of rigid bodies. Solving the CEOM allows for larger integration time-steps and helps focus the simulation on the important collective dynamics of chemical, biological, and materials systems. We explore advances in multibody dynamics which have resulted in O(N) algorithms for propagating the CEOM. However, because of their strictly sequential nature, the computational time required by these algorithms does not scale down with increased numbers of processors. We then present the new constraint force algorithm for solving the CEOM and show that this algorithm is fully parallelizable, leading to a computational cost of O(N/P+IogP) for N DOF on P processors.
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
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
Molecular dynamics of bacteriorhodopsin.
Lupo, J A; Pachter, R
1997-02-01
A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.
Molecular photoionization dynamics
International Nuclear Information System (INIS)
Dehmer, J.L.
1982-01-01
This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed
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
Stability of large-area molecular junctions
Akkerman, Hylke B.; Kronemeijer, Auke J.; Harkema, Jan; van Hal, Paul A.; Smits, Edsger C. P.; de Leeuw, Dago M.; Blom, Paul W. M.
The stability of molecular junctions is crucial for any application of molecular electronics. Degradation of molecular junctions when exposed to ambient conditions is regularly observed. In this report the stability of large-area molecular junctions under ambient conditions for more than two years
Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F; Harger, Matthew; Torabifard, Hedieh; Cisneros, G Andrés; Schnieders, Michael J; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y; Ponder, Jay W; Piquemal, Jean-Philip
2018-01-28
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over
Molecular dynamics simulations and quantum chemical calculations ...
African Journals Online (AJOL)
Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...
International Nuclear Information System (INIS)
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-01-01
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wave packet calculations that provide insights into energy flow between the vibrational modes of the molecule
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
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
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
Computational approach to large quantum dynamical problems
International Nuclear Information System (INIS)
Friesner, R.A.; Brunet, J.P.; Wyatt, R.E.; Leforestier, C.; Binkley, S.
1987-01-01
The organizational structure is described for a new program that permits computations on a variety of quantum mechanical problems in chemical dynamics and spectroscopy. Particular attention is devoted to developing and using algorithms that exploit the capabilities of current vector supercomputers. A key component in this procedure is the recursive transformation of the large sparse Hamiltonian matrix into a much smaller tridiagonal matrix. An application to time-dependent laser molecule energy transfer is presented. Rate of energy deposition in the multimode molecule for systematic variations in the molecular intermode coupling parameters is emphasized
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
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.
NMR investigations of molecular dynamics
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.
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.
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
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
Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad
2015-02-15
The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported. © 2014 Wiley Periodicals, Inc.
Towards the molecular bases of polymerase dynamics
International Nuclear Information System (INIS)
Chela Flores, J.
1991-03-01
One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs
Molecular dynamics study of silver
International Nuclear Information System (INIS)
Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.
1995-03-01
We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs
Approximation of quantum observables by molecular dynamics simulations
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
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.
Grid computing in large pharmaceutical molecular modeling.
Claus, Brian L; Johnson, Stephen R
2008-07-01
Most major pharmaceutical companies have employed grid computing to expand their compute resources with the intention of minimizing additional financial expenditure. Historically, one of the issues restricting widespread utilization of the grid resources in molecular modeling is the limited set of suitable applications amenable to coarse-grained parallelization. Recent advances in grid infrastructure technology coupled with advances in application research and redesign will enable fine-grained parallel problems, such as quantum mechanics and molecular dynamics, which were previously inaccessible to the grid environment. This will enable new science as well as increase resource flexibility to load balance and schedule existing workloads.
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
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
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)
Zhou, Tingting; Lou, Jianfeng; Zhang, Yangeng; Song, Huajie; Huang, Fenglei
2016-07-14
We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives.
Toofanny, Rudesh D; Simms, Andrew M; Beck, David A C; Daggett, Valerie
2011-08-10
Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation
Directory of Open Access Journals (Sweden)
Toofanny Rudesh D
2011-08-01
Full Text Available Abstract Background Molecular dynamics (MD simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Results Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster. For a 'full' simulation trajectory (51 ns spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster. Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36% was achieved using page level compression on both the data and indexes. Conclusions The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery
Molecular dynamics of liquid crystals
Sarman, Sten
1997-02-01
We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.
Molecular quantum dynamics. From theory to applications
International Nuclear Information System (INIS)
Gatti, Fabien
2014-01-01
calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.
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
introduction. Although the calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.
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...
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...
Fujita, Takatoshi; Mochizuki, Yuji
2018-04-19
We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems; in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.
Molecular Dynamics: New Frontier in Personalized Medicine.
Sneha, P; Doss, C George Priya
2016-01-01
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.
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...
Molecular dynamics in high electric fields
International Nuclear Information System (INIS)
Apostol, M.; Cune, L.C.
2016-01-01
Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.
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 ...
Chirality in molecular collision dynamics
Lombardi, Andrea; Palazzetti, Federico
2018-02-01
Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.
Large scale molecular simulations of nanotoxicity.
Jimenez-Cruz, Camilo A; Kang, Seung-gu; Zhou, Ruhong
2014-01-01
The widespread use of nanomaterials in biomedical applications has been accompanied by an increasing interest in understanding their interactions with tissues, cells, and biomolecules, and in particular, on how they might affect the integrity of cell membranes and proteins. In this mini-review, we present a summary of some of the recent studies on this important subject, especially from the point of view of large scale molecular simulations. The carbon-based nanomaterials and noble metal nanoparticles are the main focus, with additional discussions on quantum dots and other nanoparticles as well. The driving forces for adsorption of fullerenes, carbon nanotubes, and graphene nanosheets onto proteins or cell membranes are found to be mainly hydrophobic interactions and the so-called π-π stacking (between aromatic rings), while for the noble metal nanoparticles the long-range electrostatic interactions play a bigger role. More interestingly, there are also growing evidences showing that nanotoxicity can have implications in de novo design of nanomedicine. For example, the endohedral metallofullerenol Gd@C₈₂(OH)₂₂ is shown to inhibit tumor growth and metastasis by inhibiting enzyme MMP-9, and graphene is illustrated to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using the cytotoxicity of nanoparticles against cancer or bacteria cells. © 2014 Wiley Periodicals, Inc.
Molecular dynamics for reactions of heterogeneous catalysis
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.
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.
Molecular dynamics simulation of ribosome jam
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
Dynamical processes in atomic and molecular physics
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
Ab initio molecular dynamics in a finite homogeneous electric field.
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.
Visualizing Energy on Target: Molecular Dynamics Simulations
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 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
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.
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.
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)
Wavelet Analysis for Molecular Dynamics
2015-06-01
Our method takes as input the topology and sparsity of the bonding structure of a molecular system, and returns a hierarchical set of system-specific...problems, such as modeling crack initiation and propagation, or interfacial phenomena. In the present work, we introduce a wavelet-based approach to extend...Several functional forms are common for angle poten- tials complicating not only implementation but also choice of approximation. In all cases, the
Accelerating convergence of molecular dynamics-based structural relaxation
DEFF Research Database (Denmark)
Christensen, Asbjørn
2005-01-01
We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...
Molecular dynamics simulations of ballistic He penetration into W fuzz
Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.
2016-01-01
Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers
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...
Dynamic large eddy simulation: Stability via realizability
Mokhtarpoor, Reza; Heinz, Stefan
2017-10-01
The concept of dynamic large eddy simulation (LES) is highly attractive: such methods can dynamically adjust to changing flow conditions, which is known to be highly beneficial. For example, this avoids the use of empirical, case dependent approximations (like damping functions). Ideally, dynamic LES should be local in physical space (without involving artificial clipping parameters), and it should be stable for a wide range of simulation time steps, Reynolds numbers, and numerical schemes. These properties are not trivial, but dynamic LES suffers from such problems over decades. We address these questions by performing dynamic LES of periodic hill flow including separation at a high Reynolds number Re = 37 000. For the case considered, the main result of our studies is that it is possible to design LES that has the desired properties. It requires physical consistency: a PDF-realizable and stress-realizable LES model, which requires the inclusion of the turbulent kinetic energy in the LES calculation. LES models that do not honor such physical consistency can become unstable. We do not find support for the previous assumption that long-term correlations of negative dynamic model parameters are responsible for instability. Instead, we concluded that instability is caused by the stable spatial organization of significant unphysical states, which are represented by wall-type gradient streaks of the standard deviation of the dynamic model parameter. The applicability of our realizability stabilization to other dynamic models (including the dynamic Smagorinsky model) is discussed.
Advances in molecular vibrations and collision dynamics molecular clusters
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...
National Research Council Canada - National Science Library
Kalia, Rajiv
1997-01-01
Large-scale molecular-dynamics (MD) simulations were performed to investigate: (1) sintering process, structural correlations, and mechanical behavior including dynamic fracture in microporous and nanophase Si3N4...
Molecular dynamics and diffusion a compilation
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 ...
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...
AceCloud: Molecular Dynamics Simulations in the Cloud.
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.
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)
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
Theory and application of quantum molecular dynamics
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
Nonadiabatic electron wavepacket dynamics behind molecular autoionization
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.
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.
Investigating Ebola virus pathogenicity using molecular dynamics.
Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N
2017-08-11
Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.
Trust dynamics in a large system implementation
DEFF Research Database (Denmark)
Schlichter, Bjarne Rerup; Rose, Jeremy
2013-01-01
outcomes, but largely ignored the dynamics of trust relations. Giddens, as part of his study of modernity, theorises trust dynamics in relation to abstract social systems, though without focusing on information systems. We use Giddens’ concepts to investigate evolving trust relationships in a longitudinal......A large information systems implementation (such as Enterprise Resource Planning systems) relies on the trust of its stakeholders to succeed. Such projects impact diverse groups of stakeholders, each with their legitimate interests and expectations. Levels of stakeholder trust can be expected...... case analysis of a large Integrated Hospital System implementation for the Faroe Islands. Trust relationships suffered a serious breakdown, but the project was able to recover and meet its goals. We develop six theoretical propositions theorising the relationship between trust and project outcomes...
Molecular dynamics simulation of impact test
International Nuclear Information System (INIS)
Akahoshi, Y.; Schmauder, S.; Ludwig, M.
1998-01-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Ab Initio molecular dynamics with excited electrons
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.
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
Molecular dynamics simulation of impact test
Energy Technology Data Exchange (ETDEWEB)
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular dynamics simulation of a phospholipid membrane
Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.
We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in
Nanotribology investigations with classical molecular dynamics
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:
Catalysis and communication in dynamic molecular networks
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
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.
Folding very short peptides using molecular dynamics.
Directory of Open Access Journals (Sweden)
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.
Black hole dynamics at large D
CERN. Geneva
2016-01-01
We demonstrate that the classical dynamics of black holes can be reformulated as a dynamical problem of a codimension one membrane moving in flat space. This membrane - roughly the black hole event horizon - carries a conserved charge current and stress tensor which source radiation. This `membrane paradigm' may be viewed as a simplification of the equations of general relativity at large D, and suggests the possibility of using 1/D as a useful expansion parameter in the analysis of complicated four dimensional solutions of general relativity, for instance the collision between two black holes.
Kinetics from Replica Exchange Molecular Dynamics Simulations.
Stelzl, Lukas S; Hummer, Gerhard
2017-08-08
Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.
Towards molecular electronics with large-area molecular junctions
Akkerman, HB; Blom, PWM; de Leeuw, DM; de Boer, B
2006-01-01
Electronic transport through single molecules has been studied extensively by academic(1-8) and industrial(9,10) research groups. Discrete tunnel junctions, or molecular diodes, have been reported using scanning probes(11,12), break junctions(13,14), metallic crossbars(6) and nanopores(8,15). For
Dynamical quenching of tunneling in molecular magnets
Energy Technology Data Exchange (ETDEWEB)
José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)
2015-12-15
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.
Dynamical quenching of tunneling in molecular magnets
International Nuclear Information System (INIS)
José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.
2015-01-01
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation
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
Large Deformation Dynamic Bending of Composite Beams
Derian, E. J.; Hyer, M. W.
1986-01-01
Studies were conducted on the large deformation response of composite beams subjected to a dynamic axial load. The beams were loaded with a moderate eccentricity to promote bending. The study was primarily experimental but some finite element results were obtained. Both the deformation and the failure of the beams were of interest. The static response of the beams was also studied to determine potential differences between the static and dynamic failure. Twelve different laminate types were tested. The beams were loaded dynamically with a gravity driven impactor traveling at 19.6 ft/sec and quasi-static tests were conducted on identical beams in a displacement controlled manner. For laminates of practical interest, the failure modes under static and dynamic loadings were identical. Failure in most of the laminate types occurred in a single event involving 40% to 50% of the plies. However, failure in laminates with 30 deg or 15 deg off-axis plies occured in several events. All laminates exhibited bimodular elastic properties. Using empirically determined flexural properties, a finite element analysis was reasonably accurate in predicting the static and dynamic deformation response.
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
Coulomb explosion of large penetrating molecular clusters
International Nuclear Information System (INIS)
Wegner, H.E.; Thieberger, P.
1981-01-01
The main purpose of these Coulomb explosion measurements is to determine what kind of structure these and other complex molecules may have and also to determine what other special phenomena may come into play as these complex molecules pass through matter. Although the first preliminary measurements involving the Coulomb explosion of these molecules was reported at this workshop last year, the results are briefly summarized before going on to the more recent measurements obtained with a completely new kind of detector system. This new image intensifier detector system, coupled with a microcomputer, has proven to be a valuable tool in the study of the Coulomb explosion of complex molecules that penetrate matter. In the future, with some additional improvements in the system, and much better statistics for most of the molecules studied to date, it is expected that much new information will be gained about the structure of many kinds of complex molecular ions including the special effects that may be encountered when these fast molecular ions penetrate matter
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)
Frank, Martin
2015-01-01
Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).
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
Ultrafast dissociation: An unexpected tool for probing molecular dynamics
International Nuclear Information System (INIS)
Morin, Paul; Miron, Catalin
2012-01-01
Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.
Molecular Dynamics with Helical Periodic Boundary Conditions
Czech Academy of Sciences Publication Activity Database
Kessler, Jiří; Bouř, Petr
2014-01-01
Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014
Molecular dynamics simulation of a chemical reaction
International Nuclear Information System (INIS)
Gorecki, J.; Gryko, J.
1988-06-01
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
Modeling shockwave deformation via molecular dynamics
International Nuclear Information System (INIS)
Holian, B.L.
1987-01-01
Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too
Nonequilibrium molecular dynamics theory, algorithms and applications
Todd, Billy D
2017-01-01
Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...
Extended Lagrangian Excited State Molecular Dynamics.
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).
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.
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
Molecular dynamics studies of superionic conductors
International Nuclear Information System (INIS)
Rahman, A.; Vashishta, P.
1983-01-01
Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables
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.
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
International Nuclear Information System (INIS)
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-01-01
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
The temperature of large dust grains in molecular clouds
Clark, F. O.; Laureijs, R. J.; Prusti, T.
1991-01-01
The temperature of the large dust grains is calculated from three molecular clouds ranging in visual extinction from 2.5 to 8 mag, by comparing maps of either extinction derived from star counts or gas column density derived from molecular observations to I(100). Both techniques show the dust temperature declining into clouds. The two techniques do not agree in absolute scale.
Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen
1999-06-01
Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.
Optical spectra and lattice dynamics of molecular crystals
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.
Parallelization of quantum molecular dynamics simulation code
International Nuclear Information System (INIS)
Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu
1998-02-01
A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)
Lipid Configurations from Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek
2018-01-01
of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...
Molecular dynamics studies of actinide nitrides
International Nuclear Information System (INIS)
Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo
2004-01-01
The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)
Viscosity calculations at molecular dynamics simulations
International Nuclear Information System (INIS)
Kirova, E M; Norman, G E
2015-01-01
Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
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 estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
Molecular dynamics of surfactant protein C
DEFF Research Database (Denmark)
Ramírez, Eunice; Santana, Alberto; Cruz, Anthony
2006-01-01
Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...
Dynamics of large reflectors - Aerospatiale concepts
Flechais, A.; Picard, P.; Dauviau, C.; Truchi, C.
1992-08-01
An overview is presented of studies performed under an ESTEC contract and aimed at the identification of critical development areas of unfurlable reflectors and at the analysis of the dynamic interactions between reflectors and hosting spacecraft, in particular with respect to the design of the AOCS and antenna pointing mechanism (APM). Research and development performed by Aerospatiale since 1983 in the field of unfurlable mesh reflectors and supported by CNES are summarized. An analysis covering both the deployment phase and the deployed configuration is presented. The capabilities of classical AOCS and APM control laws for large reflectors are evaluated via simulations. It is shown that the baseline reflector under consideration is compatible with the PSDE mission and classical AOCS and APM control law designs.
Classical molecular dynamics simulation of nuclear fuels
International Nuclear Information System (INIS)
Devanathan, R.; Krack, M.; Bertolus, M.
2015-01-01
Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)
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
Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.
2017-03-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.
Molecular structures and intramolecular dynamics of pentahalides
Ischenko, A. A.
2017-03-01
This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.
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.
Dynamic analysis of the large deployable reflector
Calleson, Robert E.; Scott, A. Don
1987-01-01
The Large Deployable Reflector (LDR) is to be an astronomical observatory orbiting above Earth's obscuring atmosphere and operating in the spectral range between 30 microns and 1000 microns wavelength. The LDR will be used to study such astronomical phenomena as stellar and galactic formation, cosmology, and planetary atmospheres. The LDR will be the first observatory to be erected and assembled in space. This distinction brings with it several major technological challenges such as the development of ultra-lightweight deployable mirrors, advanced mirror fabrication techniques, advanced structures, and control of vibrations due to various sources of excitation. The purpose of this analysis is to provide an assessment of the vibrational response due to secondary mirror chopping and LDR slewing. The dynamic response of two 20-m LDR configurations was studied. Two mirror support configurations were investigated for the Ames concept, the first employs a six-strut secondary mirror support structure, while the second uses a triple-bipod support design. All three configurations were modeled using a tetrahedral truss design for the primary mirror support structure. Response resulting from secondary mirror chopping was obtained for the two Ames configurations, and the response of the primary mirror from slewing was obtained for all three configurations.
On the strong influence of molecular interactions over large distances
Pfennig, Andreas
2018-03-01
Molecular-dynamics simulations of liquid water show deterministic chaos, i.e. an intentionally introduced molecular position shift of an individual molecule increases exponentially by a factor of 10 in 0.23 ps. This is a Lyaponov instability. As soon as it reaches molecular scale, the direction of the resulting shift in molecular motions is unpredictable. The influence of any individual distant particle on an observed molecule will be minute, but the effect will quickly increase to molecular scale and beyond due to this exponential growth. Consequently, any individual particle in the universe will affect the behavior of any molecule within at most 33 ps after the interaction reaches it. A larger distance of the faraway particle does not decrease the influence on an observed molecule, but the effect reaches molecular scale only some ps later. Thus in evaluating the interactions, nearby and faraway molecules have to be equally accounted for. The consequences of this quickly reacting network of interactions on universal scale are fundamental. Even in a strictly deterministic view, molecular behavior is principally unpredictable, and thus has to be regarded random. Corresponding statements apply for any particles interacting. This result leads to a fundamental rethinking of the structure of interactions of molecules and particles as well as the behavior of reality.
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
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
Hydration dynamics in water clusters via quantum molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of
Molecular dynamics simulation of laser shock phenomena
Energy Technology Data Exchange (ETDEWEB)
Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).
2001-10-01
Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)
Molecular dynamic simulation study of molten cesium
Directory of Open Access Journals (Sweden)
Yeganegi Saeid
2017-01-01
Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.
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
Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Cedrix J. Dongmo Foumthuim
2018-01-01
Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
Electron-nuclear corellations for photoinduced dynamics in molecular dimers
Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.
2003-03-01
Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).
Large scale dynamics of protoplanetary discs
Béthune, William
2017-08-01
Planets form in the gaseous and dusty disks orbiting young stars. These protoplanetary disks are dispersed in a few million years, being accreted onto the central star or evaporated into the interstellar medium. To explain the observed accretion rates, it is commonly assumed that matter is transported through the disk by turbulence, although the mechanism sustaining turbulence is uncertain. On the other side, irradiation by the central star could heat up the disk surface and trigger a photoevaporative wind, but thermal effects cannot account for the observed acceleration and collimation of the wind into a narrow jet perpendicular to the disk plane. Both issues can be solved if the disk is sensitive to magnetic fields. Weak fields lead to the magnetorotational instability, whose outcome is a state of sustained turbulence. Strong fields can slow down the disk, causing it to accrete while launching a collimated wind. However, the coupling between the disk and the neutral gas is done via electric charges, each of which is outnumbered by several billion neutral molecules. The imperfect coupling between the magnetic field and the neutral gas is described in terms of "non-ideal" effects, introducing new dynamical behaviors. This thesis is devoted to the transport processes happening inside weakly ionized and weakly magnetized accretion disks; the role of microphysical effects on the large-scale dynamics of the disk is of primary importance. As a first step, I exclude the wind and examine the impact of non-ideal effects on the turbulent properties near the disk midplane. I show that the flow can spontaneously organize itself if the ionization fraction is low enough; in this case, accretion is halted and the disk exhibits axisymmetric structures, with possible consequences on planetary formation. As a second step, I study the launching of disk winds via a global model of stratified disk embedded in a warm atmosphere. This model is the first to compute non-ideal effects from
Molecular dynamics simulations of oscillatory flows in microfluidic channels
DEFF Research Database (Denmark)
Hansen, J.S.; Ottesen, Johnny T.
2006-01-01
In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system...
Quantum-Accurate Molecular Dynamics Potential for Tungsten
Energy Technology Data Exchange (ETDEWEB)
Wood, Mitchell; Thompson, Aidan P.
2017-03-01
The purpose of this short contribution is to report on the development of a Spectral Neighbor Analysis Potential (SNAP) for tungsten. We have focused on the characterization of elastic and defect properties of the pure material in order to support molecular dynamics simulations of plasma-facing materials in fusion reactors. A parallel genetic algorithm approach was used to efficiently search for fitting parameters optimized against a large number of objective functions. In addition, we have shown that this many-body tungsten potential can be used in conjunction with a simple helium pair potential1 to produce accurate defect formation energies for the W-He binary system.
Stability mechanisms of a thermophilic laccase probed by molecular dynamics
DEFF Research Database (Denmark)
Christensen, Niels Johan; Kepp, Kasper Planeta
2013-01-01
Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response...... integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F(-) intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes....
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.
A molecular dynamics simulation study of chloroform
Tironi, Ilario G.; van Gunsteren, Wilfred F.
Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.
Molecular beam studies of reaction dynamics
International Nuclear Information System (INIS)
Lee, Yuan T.
1991-03-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation
A molecular dynamics approach to barrodiffusion
Cooley, James; Marciante, Mathieu; Murillo, Michael
2016-10-01
Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin
Molecular beam studies of reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
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
The Dynamics of Large-Amplitude Motion in Energized Molecules
Energy Technology Data Exchange (ETDEWEB)
Perry, David S. [Univ. of Akron, OH (United States). Dept. of Chemistry
2016-05-27
Chemical reactions involve large-amplitude nuclear motion along the reaction coordinate that serves to distinguish reactants from products. Some reactions, such as roaming reactions and reactions proceeding through a loose transition state, involve more than one large-amplitude degree of freedom. Because of the limitation of exact quantum nuclear dynamics to small systems, one must, in general, define the active degrees of freedom and separate them in some way from the other degrees of freedom. In this project, we use large-amplitude motion in bound model systems to investigate the coupling of large-amplitude degrees of freedom to other nuclear degrees of freedom. This approach allows us to use the precision and power of high-resolution molecular spectroscopy to probe the specific coupling mechanisms involved, and to apply the associated theoretical tools. In addition to slit-jet spectra at the University of Akron, the current project period has involved collaboration with Michel Herman and Nathalie Vaeck of the Université Libre de Bruxelles, and with Brant Billinghurst at the Canadian Light Source (CLS).
Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study
DEFF Research Database (Denmark)
Laradji, Mohamed; Mouritsen, Ole G.
2000-01-01
Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface, corres...
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)
2015-06-28
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
International Nuclear Information System (INIS)
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
International Nuclear Information System (INIS)
Vashishta, Priya; Kalia, Rajiv
2005-01-01
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report
Molecular dynamics simulations of cluster fission and fusion processes
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia
2004-01-01
Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...
Haptization of molecular dynamics simulation with thermal display
International Nuclear Information System (INIS)
Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki
2010-01-01
Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)
Deformation mechanisms in nanotwinned copper by molecular dynamics simulation
Energy Technology Data Exchange (ETDEWEB)
Zhao, Xing [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China); Lu, Cheng, E-mail: chenglu@uow.edu.au [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Tieu, Anh Kiet; Pei, Linqing; Zhang, Liang; Su, Lihong [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Zhan, Lihua [State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China)
2017-02-27
Nanotwinned materials exhibit simultaneous ultrahigh strength and high ductility which is attributed to the interactions between dislocations and twin boundaries but the specific deformation mechanisms are rarely seen in experiments at the atomic level. Here we use large scale molecular dynamics simulations to explore this intricate interplay during the plastic deformation of nanotwinned Cu. We demonstrate that the dominant deformation mechanism transits dynamically from slip transfer to twin boundary migration to slip-twin interactions as the twin boundary orientation changes from horizontal to slant, and then to a vertical direction. Building on the fundamental physics of dislocation processes from computer simulations and combining the available experimental investigations, we unravel the underlying deformation mechanisms for nanotwinned Cu, incorporating all three distinct dislocation processes. Our results give insights into systematically engineering the nanoscale twins to fabricate nanotwinned metals or alloys that have high strength and considerable ductility.
Thermal transpiration: A molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)
2014-12-09
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems
Stanton, L. G.; Glosli, J. N.; Murillo, M. S.
2018-04-01
Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.
How Dynamic Visualization Technology Can Support Molecular Reasoning
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…
Adaptive sampling strategies with high-throughput molecular dynamics
Clementi, Cecilia
Despite recent significant hardware and software developments, the complete thermodynamic and kinetic characterization of large macromolecular complexes by molecular simulations still presents significant challenges. The high dimensionality of these systems and the complexity of the associated potential energy surfaces (creating multiple metastable regions connected by high free energy barriers) does not usually allow to adequately sample the relevant regions of their configurational space by means of a single, long Molecular Dynamics (MD) trajectory. Several different approaches have been proposed to tackle this sampling problem. We focus on the development of ensemble simulation strategies, where data from a large number of weakly coupled simulations are integrated to explore the configurational landscape of a complex system more efficiently. Ensemble methods are of increasing interest as the hardware roadmap is now mostly based on increasing core counts, rather than clock speeds. The main challenge in the development of an ensemble approach for efficient sampling is in the design of strategies to adaptively distribute the trajectories over the relevant regions of the systems' configurational space, without using any a priori information on the system global properties. We will discuss the definition of smart adaptive sampling approaches that can redirect computational resources towards unexplored yet relevant regions. Our approaches are based on new developments in dimensionality reduction for high dimensional dynamical systems, and optimal redistribution of resources. NSF CHE-1152344, NSF CHE-1265929, Welch Foundation C-1570.
A new parallel molecular dynamics algorithm for organic systems
International Nuclear Information System (INIS)
Plimpton, S.; Hendrickson, B.; Heffelfinger, G.
1993-01-01
A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed
Molecular computational elements encode large populations of small objects
Prasanna de Silva, A.; James, Mark R.; McKinney, Bernadine O. F.; Pears, David A.; Weir, Sheenagh M.
2006-10-01
Since the introduction of molecular computation, experimental molecular computational elements have grown to encompass small-scale integration, arithmetic and games, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size (about 1nm) and large `on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100μm) used for synthesis of combinatorial libraries. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a `wash and watch' protocol. Our focus on converting molecular science into technology concerning analog sensors, turns to digital logic devices in the present work.
Molecular beam studies of adsorption dynamics
International Nuclear Information System (INIS)
Arumainayagam, C.R.; McMaster, M.C.; Madix, R.J.
1991-01-01
We have investigated the trapping dynamics of C 1 -C 3 alkanes and Xe on Pt(111) using supersonic molecular beams and a direct technique to measure trapping probabilities. We have extended a one-dimensional model based on classical mechanics to include trapping and have found semiquantitative agreement with experimental results for the dependence of the initial trapping probability on incident translational energy at normal incidence. Our measurements of the initial trapping probability as a function of incident translational energy at normal incidence are in agreement with previous mean translational energy measurements for Xe and CH 4 desorbing near the surface normal, in accordance with detailed balance. However, the angular dependence of the initial trapping probability shows deviations from normal energy scaling, demonstrating the importance of parallel momentum in the trapping process and the inadequacy of one-dimensional models. The dependence of the initial trapping probability of Xe on incident translational energy and angle is quite well fit by three-dimensional stochastic classical trajectory calculations utilizing a Morse potential. Angular distributions of the scattered molecules indicate that the trapping probability is not a sensitive function of surface temperature. The trapping probability increases with surface coverage in quantitative agreement with a modified Kisliuk model which incorporates enhanced trapping onto the monolayer. We have also used the direct technique to study trapping onto a saturated monolayer state to investigate the dynamics of extrinsic precursor adsorption and find that the initial trapping probability onto the monolayer is higher than on the clean surface. The initial trapping probability onto the monolayer scales with total energy, indicating a highly corrugated interaction potential
Molecular dynamics studies of displacement cascades
International Nuclear Information System (INIS)
Averback, R.S.; Hsieh, Horngming; Diaz de la Rubia, T.
1990-02-01
Molecular-dynamics simulations of cascades in Cu and Ni with primary-knock-on energies up to 5 keV and lattice temperatures in the range 0 K--700 K are described. Interatomic forces were represented by either the Gibson II (Cu) or Johnson-Erginsoy (Ni) potentials in most of this work, although some simulations using ''Embedded Atom Method'' potentials, e.g., for threshold events in Ni 3 Al, are also presented. The results indicate that the primary state of damage produced by displacement cascades is controlled by two phenomena, replacement collision sequences during the collisional phase of the cascade and local melting during the thermal spike. As expected, the collisional phase is rather similar in Cu and Ni, however, the thermal spike is of longer duration and has a more pronounced influence in Cu than Ni. When the ambient temperature of the lattice is increased, the melt zones are observed to both increase in size and cool more slowly. This has the effect of reducing defect production and enhancing atomic mixing and disordering. The implications of these results for defect production, cascade collapse, atomic disordering will be discussed. 34 refs., 7 figs., 2 tabs
A molecular dynamics simulation code ISIS
International Nuclear Information System (INIS)
Kambayashi, Shaw
1992-06-01
Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)
Spin-diffusions and diffusive molecular dynamics
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.
A hybrid algorithm for parallel molecular dynamics simulations
Mangiardi, Chris M.; Meyer, R.
2017-10-01
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.
Computing in Large-Scale Dynamic Systems
Pruteanu, A.S.
2013-01-01
Software applications developed for large-scale systems have always been difficult to de- velop due to problems caused by the large number of computing devices involved. Above a certain network size (roughly one hundred), necessary services such as code updating, topol- ogy discovery and data
Bolhuis, Peter
Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.
Large-Area, Ensemble Molecular Electronics: Motivation and Challenges.
Vilan, Ayelet; Aswal, Dinesh; Cahen, David
2017-03-08
We review charge transport across molecular monolayers, which is central to molecular electronics (MolEl), using large-area junctions (NmJ). We strive to provide a wide conceptual overview of three main subtopics. First, a broad introduction places NmJ in perspective to related fields of research and to single-molecule junctions (1mJ) in addition to a brief historical account. As charge transport presents an ultrasensitive probe for the electronic perfection of interfaces, in the second part ways to form both the monolayer and the contacts are described to construct reliable, defect-free interfaces. The last part is dedicated to understanding and analyses of current-voltage (I-V) traces across molecular junctions. Notwithstanding the original motivation of MolEl, I-V traces are often not very sensitive to molecular details and then provide a poor probe for chemical information. Instead, we focus on how to analyze the net electrical performance of molecular junctions, from a functional device perspective. Finally, we point to creation of a built-in electric field as a key to achieve functionality, including nonlinear current-voltage characteristics that originate in the molecules or their contacts to the electrodes. This review is complemented by a another review that covers metal-molecule-semiconductor junctions and their unique hybrid effects.
Large deviations in the presence of cooperativity and slow dynamics
Whitelam, Stephen
2018-06-01
We study simple models of intermittency, involving switching between two states, within the dynamical large-deviation formalism. Singularities appear in the formalism when switching is cooperative or when its basic time scale diverges. In the first case the unbiased trajectory distribution undergoes a symmetry breaking, leading to a change in shape of the large-deviation rate function for a particular dynamical observable. In the second case the symmetry of the unbiased trajectory distribution remains unbroken. Comparison of these models suggests that singularities of the dynamical large-deviation formalism can signal the dynamical equivalent of an equilibrium phase transition but do not necessarily do so.
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.
The Art of Molecular Dynamics Simulation (by D. C. Rapaport)
Molner, Stephen P.
1999-02-01
Cambridge University Press: New York, 1996. 400 pp. ISBN 0 521 44561 2. $74.95. This book describes the extremely powerful techniques of molecular dynamics simulation. The techniques involve solving the classical many-body problems in contexts relevant to the study of matter at the atomic level. The method allows the prediction of static and dynamics properties of substances directly from the underlying interactions between molecules. This is, of course, a very broad subject and the author has adopted a dual approach in that the text is partly tutorial and also contains a large number of computer programs for practical use. Rapaport has adopted the attitude of trying the simplest method first. Atoms are modeled as point particles interacting through point potentials. Molecules are represented by atoms with orientation dependent forces, or as extended structures each containing several interaction sites. The molecules may be rigid, flexible, or somewhere in between, and if there are internal degrees of freedom there will be internal forces as well. The intent of the book is not to discuss the design of molecular models, but rather to make use of existing models, and from a pedagogical viewpoint the simpler the model the better. The aim of the book is to demonstrate the general methodology of molecular dynamics simulation by example, not to review the large body of literature covering the many different kinds of models developed for specific applications. The text is partly tutorial, but also contains a large number of computer programs for practical use. This volume will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner. The material covers a wide range of practical methods and real applications and is organized as a series of case studies. The typical case study includes a summary of the theoretical background used for the formulation of the computational approach. That is described by either a
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
Stability of large scale interconnected dynamical systems
International Nuclear Information System (INIS)
Akpan, E.P.
1993-07-01
Large scale systems modelled by a system of ordinary differential equations are considered and necessary and sufficient conditions are obtained for the uniform asymptotic connective stability of the systems using the method of cone-valued Lyapunov functions. It is shown that this model significantly improves the existing models. (author). 9 refs
Molecular dynamics using quasielastic neutron scattering
Mitra, S
2003-01-01
Quasielastic neutron scattering (QENS) technique is well suited to study the molecular motions (rotations and translations) in solids or liquids. It offers a unique possibility of analysing spatial dimensions of atomic or molecular processes in their development over time. We describe here some of the systems studied using the QENS spectrometer, designed, developed and commissioned at Dhruva reactor in Trombay. We have studied a variety of systems to investigate the molecular motion, for example, simple molecular solids, molecules adsorbed in confined medium like porous systems or zeolites, monolayer-protected nano-sized metal clusters, water in Portland cement as it cures with time, etc. (author)
Photoionization dynamics of excited molecular states
International Nuclear Information System (INIS)
Dehmer, J.L.; O'Halloran, M.A.; Tomkins, F.S.; Dehmer, P.M.; Pratt, S.T.
1987-01-01
Resonance Enhanced Multiphoton Ionization (REMPI) utilizes tunable dye lasers to ionize an atom or molecule by first preparing an excited state by multiphoton absorption and then ionizing that state before it can decay. This process is highly selective with respect to both the initial and resonant intermediate states of the target, and it can be extremely sensitive. In addition, the products of the REMPI process can be detected as needed by analyzing the resulting electrons, ions, fluorescence, or by additional REMPI. This points to a number of opportunities for exploring excited state physics and chemistry at the quantum-state-specific level. Here we will first give a brief overview of the large variety of experimental approaches to excited state phenomena made possible by REMPI. Then we will examine in more detail, recent studies of the three photon resonant, four photon (3 + 1) ionization of H 2 via the C 'PI/sup u/ state. Strong non-Franck-Condon behavior in the photoelectron spectra of this nominally simple Rydberg state has led to the examination of a variety of dynamical mechanisms. Of these, the role of doubly excited autoionizing states now seems decisive. Progress on photoelectron studies of autoionizing states in H 2 , excited in a (2 + 1) REMPI process via the E, F 1 Σ/sub g/ + will also be briefly discussed. 26 refs., 7 figs
Directory of Open Access Journals (Sweden)
Yesylevskyy S. O.
2010-04-01
Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed
International Nuclear Information System (INIS)
Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira
2005-01-01
The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed
CLUSTER DYNAMICS LARGELY SHAPES PROTOPLANETARY DISK SIZES
Energy Technology Data Exchange (ETDEWEB)
Vincke, Kirsten; Pfalzner, Susanne, E-mail: kvincke@mpifr-bonn.mpg.de [Max Planck Institute for Radio Astronomy, Auf dem Hügel 69, D-53121 Bonn (Germany)
2016-09-01
To what degree the cluster environment influences the sizes of protoplanetary disks surrounding young stars is still an open question. This is particularly true for the short-lived clusters typical for the solar neighborhood, in which the stellar density and therefore the influence of the cluster environment change considerably over the first 10 Myr. In previous studies, the effect of the gas on the cluster dynamics has often been neglected; this is remedied here. Using the code NBody6++, we study the stellar dynamics in different developmental phases—embedded, expulsion, and expansion—including the gas, and quantify the effect of fly-bys on the disk size. We concentrate on massive clusters (M {sub cl} ≥ 10{sup 3}–6 ∗ 10{sup 4} M {sub Sun}), which are representative for clusters like the Orion Nebula Cluster (ONC) or NGC 6611. We find that not only the stellar density but also the duration of the embedded phase matters. The densest clusters react fastest to the gas expulsion and drop quickly in density, here 98% of relevant encounters happen before gas expulsion. By contrast, disks in sparser clusters are initially less affected, but because these clusters expand more slowly, 13% of disks are truncated after gas expulsion. For ONC-like clusters, we find that disks larger than 500 au are usually affected by the environment, which corresponds to the observation that 200 au-sized disks are common. For NGC 6611-like clusters, disk sizes are cut-down on average to roughly 100 au. A testable hypothesis would be that the disks in the center of NGC 6611 should be on average ≈20 au and therefore considerably smaller than those in the ONC.
Effective string dynamics in large N QCD
Energy Technology Data Exchange (ETDEWEB)
Iroshnikov, G.S. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)]|[Moskow Inst. of Physics and Technology, Moscow (Russian Federation)
1995-05-01
The semiclassical 1/N expansion in the strong coupling regime for spinor quarks was developed and the form of effective action was obtained. An extremum of the effective action that arises in the calculation of the hadronic correlation functions in the large N limit corresponds to a topologically non-trivial configuration of the gauge field. This configuration forms a chromoelectric Nambu string with additional spinor terms that contain in particular the Polyakov spinor factor. In the case when real quarks forming hadrons are replaced by scalar particles the above correlators yield the standard dual resonance amplitudes. (author). 10 refs, 1 fig.
Crystal structure and pair potentials: A molecular-dynamics study
Energy Technology Data Exchange (ETDEWEB)
Parrinello, M.; Rahman, A.
1980-10-06
With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.
Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation
National Research Council Canada - National Science Library
Johnston, K
1998-01-01
.... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...
Molecular Dynamics and Bioactivity of a Novel Mutated Human ...
African Journals Online (AJOL)
Keywords: Parathyroid hormone, Mutation prediction, Molecular dynamics, RANKL/OPG, UAMS-32P cell. Tropical .... PTH1R were used as MD simulation starting points. A full-atom ... Values of RMSD, Rg, and potential energy evaluation ...
Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting
National Research Council Canada - National Science Library
Low, Tammy K
2006-01-01
.... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...
A molecular dynamics calculation of solid phase of malonic acid ...
Indian Academy of Sciences (India)
Sathya S R R Perumal
Keywords. Hydrogen bond chain; elastic constants; molecular dynamics. 1. Introduction ... theory - a probabilistic model to determine the hydro- gen bonds within the .... compares poorly with the experimental value of 108.5. Similarly β and γ ...
Molecular dynamics calculation of shear viscosity for molten salt
International Nuclear Information System (INIS)
Okamoto, Yoshihiro; Yokokawa, Mitsuo; Ogawa, Toru
1993-12-01
A computer program of molecular dynamics simulation has been made to calculate shear viscosity of molten salt. Correlation function for an off-diagonal component of stress tensor can be obtained as the results of calculation. Shear viscosity is calculated by integration of the correlation function based on the Kubo-type formula. Shear viscosities for a molten KCl ranging in temperature from 1047K to 1273K were calculated using the program. Calculation of 10 5 steps (1 step corresponds to 5 x 10 -15 s) was performed for each temperature in the 216 ions system. The obtained results were in good agreement with the reported experimental values. The program has been vectorized to achieve a faster computation in supercomputer. It makes possible to calculate the viscosity using a large number of statistics amounting to several million MD steps. (author)
Molecular Dynamics Studies of Thermal Induced Chemistry in Tatb
Quenneville, J.; Germann, T. C.; Thompson, A. P.; Kober, E. M.
2007-12-01
A reactive force field (ReaxFF) is used with molecular dynamics to probe the chemistry induced by intense heating (`accelerated cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 32-molecule simulations, we calculate the reaction rate as a function of temperature and compare the Arrhenius-predicted activation energy with experiment. Decomposition product evolution (mainly N2, H2O, CO2 and graphitic carbon clusters) is followed using a 576-molecule larger simulation, which also illustrates the effect of system size on both carbon clustering and reaction rate.
Classical molecular dynamics simulation of electronically non-adiabatic processes.
Miller, William H; Cotton, Stephen J
2016-12-22
Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).
Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer
Directory of Open Access Journals (Sweden)
Casuyac Miqueas
2016-01-01
Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.
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
Next generation extended Lagrangian first principles molecular dynamics.
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.
Dynamical analysis of highly excited molecular spectra
Energy Technology Data Exchange (ETDEWEB)
Kellman, M.E. [Univ. of Oregon, Eugene (United States)
1993-12-01
The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.
Phenomenological dynamics in QCD at large distances
International Nuclear Information System (INIS)
Gogohia, V.Sh.; Kluge, Gy.
1991-07-01
A gauge-invariant, nonperturbative approach to QCD at large distances in the context of the Schwinger-Dyson equations and corresponding Slavnov-Taylor identities in the quark sector is presented. Making only one widely accepted assumption that the full gluon propagator becomes an infrared singular like (q 2 ) -2 in the covariant gauge, we find three and only three confinement-type solutions for the quark propagator (quark confinement theorem.) The approach is free from ghost complications. Also show that multiplication by the quark infrared renormalization constant only, would make all the Green's functions infrared finite (multiplicative renormalizability). The bound-state problem in framework of Bethe-Salpeter equation is discussed as well. Some basic physical parameters of chiral QCD as pion decay constant and quark condensate, have been calculated within our approach. (author) 75 refs.; 14 figs
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...
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)
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 Dynamic Modeling and Simulation for Polymers
National Research Council Canada - National Science Library
Harrell, Anthony
2003-01-01
... the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity...
Molecular dynamics of a proguanil derivative
African Journals Online (AJOL)
pc
Proguanil is a prophylactic antimalarial drug t .... presence of resistance to individual component. ... This is the mathematical ... predicting equilibrium structures of molecular systems ..... for the modeling and subsequent development of.
Visualizing functional motions of membrane transporters with molecular dynamics simulations.
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.
Pseudorotational dynamics of small molecular species
International Nuclear Information System (INIS)
Hagelberg, F.
2002-01-01
The electron nuclear dynamics (END) theory was designed to provide a full description of the dynamic development of the electronic system. It is independent of any potential energy surface constructions. The dynamic behavior of molecules close to the threshold of dissociation was the objective of this study. Thus, simulations based on END theory were performed with the aim to extend the current understanding of the dynamic features of pseudorotational into a non-adiabatic regime. Electron dynamics of triatomic species (H 3 + and Li 3 + ) in terms of electronic angular momentum expectation values were characterized. Finally, it is shown that the expansion coefficients which carry the information about the excitation content of the electronic system at any stage of the motional process can be calculated. (nevyjel)
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.
Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes
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
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...
Reduction of Large Dynamical Systems by Minimization of Evolution Rate
Girimaji, Sharath S.
1999-01-01
Reduction of a large system of equations to a lower-dimensional system of similar dynamics is investigated. For dynamical systems with disparate timescales, a criterion for determining redundant dimensions and a general reduction method based on the minimization of evolution rate are proposed.
On the large-N dynamics of gauge symmetry breaking
International Nuclear Information System (INIS)
Karchev, N.I.
1983-07-01
We consider a Gsub(W)xUsub(TC)(N) gauge theory. A method of colour singlet bilocal collective coordinates is proposed to show, large-N colour dynamics is responsible for the Gsub(W) gauge symmetry breaking if the large-N Schwinger-Dyson equation admits anomalous solutions. The dynamically generated mass matrix is computed through these solutions. The technicolour model is discussed. (author)
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
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
Multiscale molecular dynamics using the matched interface and boundary method
International Nuclear Information System (INIS)
Geng Weihua; Wei, G.W.
2011-01-01
The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.
Implementation of force distribution analysis for molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Seifert Christian
2011-04-01
Full Text Available Abstract Background The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA, a method that allows visualizing strain propagation in macromolecules. Results To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of internal strain upon ligand binding, we previously also successfully revealed the functionality of a stiff allosteric protein. FDA thus has the potential to be a valuable tool in the investigation and rational design of mechanical properties in proteins and nano-materials.
Classical and quantum molecular dynamics in NMR spectra
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 ...
Dynamics of molecular superrotors in an external magnetic field
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.
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)
Molecular dynamics with deterministic and stochastic numerical methods
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...
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.
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
Dynamic response function and large-amplitude dissipative collective motion
International Nuclear Information System (INIS)
Wu Xizhen; Zhuo Yizhong; Li Zhuxia; Sakata, Fumihiko.
1993-05-01
Aiming at exploring microscopic dynamics responsible for the dissipative large-amplitude collective motion, the dynamic response and correlation functions are introduced within the general theory of nuclear coupled-master equations. The theory is based on the microscopic theory of nuclear collective dynamics which has been developed within the time-dependent Hartree-Fock (TDHF) theory for disclosing complex structure of the TDHF-manifold. A systematic numerical method for calculating the dynamic response and correlation functions is proposed. By performing numerical calculation for a simple model Hamiltonian, it is pointed out that the dynamic response function gives an important information in understanding the large-amplitude dissipative collective motion which is described by an ensemble of trajectories within the TDHF-manifold. (author)
LARGE-SCALE TOPOLOGICAL PROPERTIES OF MOLECULAR NETWORKS.
Energy Technology Data Exchange (ETDEWEB)
MASLOV,S.SNEPPEN,K.
2003-11-17
Bio-molecular networks lack the top-down design. Instead, selective forces of biological evolution shape them from raw material provided by random events such as gene duplications and single gene mutations. As a result individual connections in these networks are characterized by a large degree of randomness. One may wonder which connectivity patterns are indeed random, while which arose due to the network growth, evolution, and/or its fundamental design principles and limitations? Here we introduce a general method allowing one to construct a random null-model version of a given network while preserving the desired set of its low-level topological features, such as, e.g., the number of neighbors of individual nodes, the average level of modularity, preferential connections between particular groups of nodes, etc. Such a null-model network can then be used to detect and quantify the non-random topological patterns present in large networks. In particular, we measured correlations between degrees of interacting nodes in protein interaction and regulatory networks in yeast. It was found that in both these networks, links between highly connected proteins are systematically suppressed. This effect decreases the likelihood of cross-talk between different functional modules of the cell, and increases the overall robustness of a network by localizing effects of deleterious perturbations. It also teaches us about the overall computational architecture of such networks and points at the origin of large differences in the number of neighbors of individual nodes.
Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.
Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W
2011-09-22
Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.
Dynamics of polymers in a good solvent - a molecular dynamics study using the Connection Machine
International Nuclear Information System (INIS)
Shannon, S.R.; Choy, T.C.
1996-01-01
In recent times the use of molecular dynamics simulations has become an important tool in modelling and understanding the dynamics of interacting many-body systems. With recent advances in computing power it is now feasible to perform modelling of systems which contain a large number of interacting particles, and thus to simulate the behaviour of real systems reasonably. Our earlier discoveries of anomalous corrections to scaling behaviour of the Edward's polymer were applied to study the dynamical behaviour of two dimensional polymer systems - either a single chain immersed in a fluid, a pure polymer melt, or with any concentration of polymers in the fluid. By choosing a suitable interaction potential between the fluid particles and the monomers, we are able to study the experimentally observable time dependent structure factor of polymers in a good solvent. Simulations were performed using the Connection Machine CM5 supercomputer at the Australian National University which due to its fast multi- processor nearest neighbour communications facility, enables us to easily model large systems of at least 3000 fluid plus monomer particles. Our study is based on a finite difference solution of Newton's equations of motion i.e. the Verlet algorithm, and the results are used to test current theories of polymer dynamics, which were based primarily on the earlier models proposed by Rouse (1953) and Zimm (1956). In particular dynamical scaling predictions is scrutinised to examine the effects due to the anomalous corrections-to-scaling behaviour found in an earlier work using finite-size scaling analysis of Monte-Carlo data and now understood via a new perturbation concept
Directory of Open Access Journals (Sweden)
Kei Moritsugu
Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.
Next Generation Extended Lagrangian Quantum-based Molecular Dynamics
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.
Veld, M.A.J.; Fransson, L.; Palmans, A.R.A.; Meijer, E.W.; Hult, K.
2009-01-01
Size matters: Lactones have extensively been studied as monomers in enzymatic polymerization reactions. Large lactones showed an unexpectedly high reactivity in these reactions. A combination of docking and molecular dynamics studies have been used to explain this high reactivity in terms of
Towards realistic molecular dynamics simulations of grain boundary mobility
International Nuclear Information System (INIS)
Zhou, J.; Mohles, V.
2011-01-01
In order to investigate grain boundary migration by molecular dynamics (MD) simulations a new approach involving a crystal orientation-dependent driving force has been developed by imposing an appropriate driving force on grain boundary atoms and enlarging the effective range of driving force. The new approach has been validated by the work of the driving force associated with the motion of grain boundaries. With the new approach the relation between boundary migration velocity and driving force is found to be nonlinear, as was expected from rate theory for large driving forces applied in MD simulations. By evaluating grain boundary mobility nonlinearly for a set of symmetrical tilt boundaries in aluminum at high temperature, high-angle grain boundaries were shown to move much faster than low-angle grain boundaries. This agrees well with experimental findings for recrystallization and grain growth. In comparison with the available data the simulated mobility of a 38.21 o Σ7 boundary was found to be significantly lower than other MD simulation results and comparable with the experimental values. Furthermore, the average volume involved during atomic jumps for boundary migration is determined in MD simulations for the first time. The large magnitude of the volume indicates that grain boundary migration is accomplished by the correlated motion of atom groups.
A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.
Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E
2017-06-20
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Wu, Bin
spatial instrumental scales, understanding experimental results involves extensive and difficult data analysis based on liquid theory and condensed matter physics. Therefore, a model that successfully describes the inter- and intra-dendrimer correlations is crucial in obtaining and delivering reliable information. On the other hand, making meaningful comparisons between molecular dynamics and neutron scattering is a fundamental challenge to link simulations and experiments at the nano-scale. This challenge stems from our approach to utilize MD simulation to explain the underlying mechanism of experimental observation. The SANS measurements were conducted on a series of SANS spectrometers including the Extended Q-Range Small-Angle Neutron Scattering Diffractometer (EQ-SANS) and the General-Purpose Small-Angle Neutron Scattering Diffractometer (GP-SANS) at the Oak Ridge National Laboratory (ORNL), and NG7 Small Angle Neutron Scattering Spectrometer at National Institute of Standards (NIST) and Technology in U.S.A., large dynamic range small-angle diffractometer D22 at Institut Laue-Langevin (ILL) in France, and 40m-SANS Spectrometer at Korea Atomic Energy Research Institute (KAERI) in Korea. On the other hand, the Amber molecular dynamics simulation package is utilized to carry out the computational study. In this dissertation, the following observations have been revealed. The previously developed theoretical model for polyelectrolyte dendrimers are adopted to analyze SANS measurements and superb model fitting quality is found. Coupling with advanced contrast variation small angle neutron scattering (CVSANS) data analysis scheme reported recently, the intra-dendrimer hydration and hydrocarbon components distributions are revealed experimentally. The results indeed indicate that the maximum density is located in the molecular center rather than periphery, which is consistent to previous SANS studies and the back-folding picture of PAMAM dendrimers. According to this picture
International Nuclear Information System (INIS)
Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M
2010-01-01
Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives
Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C
2013-11-07
Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.
Molecular dynamics study of atomic displacements in disordered solid alloys
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.
Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics
International Nuclear Information System (INIS)
Sanz-Navarro, Carlos F.
2002-01-01
The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)
Dynamic molecular oxygen production in cometary comae
Yao, Yunxi; Giapis, Konstantinos P.
2017-05-01
Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2-. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.
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.
Femtochemistry and femtobiology ultrafast dynamics in molecular science
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
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.
Chain networking revealed by molecular dynamics simulation
Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing
Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)
Energy Technology Data Exchange (ETDEWEB)
Kashiwagi, H [Institute for Molecular Science, Okazaki, Aichi (Japan)
1982-06-01
A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience.
International Nuclear Information System (INIS)
Kashiwagi, H.
1982-01-01
A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience. (orig.)
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp
2012-06-01
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 as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.
International Nuclear Information System (INIS)
Xu, S.
1993-01-01
Molecular dynamics simulations of nucleation and phase transitions in TeF 6 and SeF 6 clusters containing 100-350 molecules were carried out. Simulations successfully reproduced the crystalline structures observed in electron diffraction studies of large clusters (containing about 10 4 molecules) of the same materials. When the clusters were cooled, they spontaneously underwent the same bcc the monoclinic phase transition in simulations as in experiment, despite the million-fold difference in the time scales involved. Other transitions observed included melting and freezing. Several new techniques based on molecular translation and orientation were introduced to identify different condensed phases, to study nucleation and phase transitions, and to define characteristic temperatures of transitions. The solid-state transition temperatures decreased with cluster size in the same way as did the melting temperature, in that the depression of transition temperature was inversely proportional to the cluster radius. Rotational melting temperatures, as inferred from the rotational diffusion of molecules, coincided with those of the solid-state transition. Nucleation in liquid-solid and bcc-monoclinic transitions started in the interior of clusters on cooling, and at the surface on heating. Transition temperatures on cooling were always lower than those on heating due to the barriers to nucleation. Linear growth rates of nuclei in freezing were an order of magnitude lower than those in the bcc-monoclinic transition. Revealing evidence about the molecular behavior associated with phase changes was found. Simulations showed the formation of the actual transition complexes along the transition pathway, i.e., the critical nuclei of the new phase. These nuclei, consisting of a few dozen molecules, were distinguishable in the midst of the surrounding matter
Plastic dislocation motion via nonequilibrium molecular and continuum dynamics
International Nuclear Information System (INIS)
Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.
1980-01-01
The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition
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
Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation
International Nuclear Information System (INIS)
Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.
1991-01-01
We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus
Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd
2014-09-15
The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.
Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics
Halverson, Jonathan D.; Lee, Won Bo; Grest, Gary S.; Grosberg, Alexander Y.; Kremer, Kurt
2011-05-01
Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. The ring melts were found to diffuse faster than their linear counterparts, with both architectures approximately obeying a D ˜ N-2.4 scaling law for large N. The mean-square displacement of the center-of-mass of the rings follows a sub-diffusive behavior for times and distances beyond the ring extension , neither compatible with the Rouse nor the reptation model. The rings relax stress much faster than linear polymers, and the zero-shear viscosity was found to vary as η0 ˜ N1.4 ± 0.2 which is much weaker than the N3.4 behavior of linear chains, not matching any commonly known model for polymer dynamics when compared to the observed mean-square displacements. These findings are discussed in view of the conformational properties of the rings presented in the preceding paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204904 (2011)], 10.1063/1.3587137.
Excited state dynamics & optical control of molecular motors
Wiley, Ted; Sension, Roseanne
2014-03-01
Chiral overcrowded alkenes are likely candidates for light driven rotary molecular motors. At their core, these molecular motors are based on the chromophore stilbene, undergoing ultrafast cis/trans photoisomerization about their central double bond. Unlike stilbene, the photochemistry of molecular motors proceeds in one direction only. This unidirectional rotation is a result of helicity in the molecule induced by steric hindrance. However, the steric hindrance which ensures unidirectional excited state rotation, has the unfortunate consequence of producing large ground state barriers which dramatically decrease the overall rate of rotation. These molecular scale ultrafast motors have only recently been studied by ultrafast spectroscopy. Our lab has studied the photochemistry and photophysics of a ``first generation'' molecular motor with UV-visible transient absorption spectroscopy. We hope to use optical pulse shaping to enhance the efficiency and turnover rate of these molecular motors.
Large, cold, and unusual molecular cloud in Monoceros
International Nuclear Information System (INIS)
Maddalena, R.J.; Thaddeus, P.; and Columbia University)
1985-01-01
Observations of the J = 1 → 0 rotational transition of CO near the galactic plane in Monoceros (lroughly-equal216 0 ) reveal a molecular cloud with unusually low peak CO temperatures (T/sub R/ -1 ) typical of much warmer clouds. At the assumed distance of 3 kpc, the cloud is large (250 x 100 pc), has a mass of 7-11 x 10 5 M/sub sun/, and is well removed from the galactic midplane (130 pc). Except for a possible H II region, all the signs of star formation usually shown by clouds of comparable mass are missing. The cloud, unlike cloud complexes of similar size, is a single, continuous object that apparently has not been torn apart by star formation. Clouds with such properties are rare in the Galaxy; only one or two similar objects have been found. We discuss the possibility that the cloud is young and not yet forming stars but will evolve into a typical cloud complex once star formation begins
Theory of multiexciton dynamics in molecular chains
Wang, Luxia; May, Volkhard
2016-11-01
Ultrafast and strong optical excitation of a molecular system is considered which is formed by a regular one-dimensional arrangement of identical molecules. As it is typical for zinc chlorine-type molecules the transition energy from the ground state to the first excited singlet state is assumed to be smaller than the energy difference between the first excited state and the following one. This enables the creation of many excitons without their immediate quenching due to exciton-exciton annihilation. As a first step into the field of dense Frenkel-exciton systems the present approach stays at a mean-field type of description and ignores vibrational contributions. The resulting nonlinear kinetic equations mix Rabi-type oscillations with those caused by energy transfer and suggest an excitation-dependent narrowing of the exciton band. The indication of this effect in the framework of a two-color pump-probe experiment and of the detection of photon emission is discussed.
Dynamics of Molecular Hydrogen in Hypersaline Microbial Mars
Hoehler, Tori M.; Bebout, Brad M.; Visscher, Pieter T.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)
2000-01-01
Early Earth microbial communities that centered around the anaerobic decomposition of organic molecular hydrogen as a carrier of electrons, regulator of energy metabolism, and facilitator of syntroph'c microbial interactions. The advent of oxygenic photosynthetic organisms added a highly dynamic and potentially dominant term to the hydrogen economy of these communities. We have examined the daily variations of hydrogen concentrations in cyanobacteria-dominated microbial mats from hypersaline ponds in Baja California Sur, Mexico. These mats bring together phototrophic and anaerobic bacteria (along with virtually all other trophic groups) in a spatially ordered and chemically dynamic matrix that provides a good analog for early Earth microbial ecosystems. Hydrogen concentrations in the photic zone of the mat can be three orders of magnitude or more higher than in the photic zone, which are, in turn, an order of magnitude higher than in the unconsolidated sediments underlying the mat community. Within the photic zone, hydrogen concentrations can fluctuate dramatically during the diel (24 hour day-night) cycle, ranging from less than 0.001% during the day to nearly 10% at night. The resultant nighttime flux of hydrogen from the mat to the environment was up to 17% of the daytime oxygen flux. The daily pattern observed is highly dependent on cyanobacterial species composition within the mat, with Lyngbya-dominated systems having a much greater dynamic range than those dominated by Microcoleus; this may relate largely to differing degrees of nitrogen-fixing and fermentative activity in the two mats. The greatest H2 concentrations and fluxes were observed in the absence of oxygen, suggesting an important potential feedback control in the context of the evolution of atmospheric composition. The impact of adding this highly dynamic photosynthetic term to the hydrogen economy of early microbial ecosystems must have been substantial. From an evolutionary standpoint, the H2
Three-stage classical molecular dynamics model for simulation of heavy-ion fusion
Directory of Open Access Journals (Sweden)
Godre Subodh S.
2015-01-01
Full Text Available A three-stage Classical Molecular Dynamics (3S-CMD approach for heavy-ion fusion is developed. In this approach the Classical Rigid-Body Dynamics simulation for heavy-ion collision involving light deformed nucleus is initiated on their Rutherford trajectories at very large initial separation. Collision simulation is then followed by relaxation of the rigid-body constrains for one or both the colliding nuclei at distances close to the barrier when the trajectories of all the nucleons are obtained in a Classical Molecular Dynamics approach. This 3S-CMD approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but also the internal vibrational excitations of one or both the nuclei at distances close to the barrier. The results of the dynamical simulation for 24Mg+208Pb collision show significant modification of the fusion barrier and calculated fusion cross sections due to internal excitations.
Molecular dynamics studies of superionic conductors
International Nuclear Information System (INIS)
Rahman, A.
1979-01-01
Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard
Dynamical photo-induced electronic properties of molecular junctions
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.
Molecular dynamics of the structure and thermodynamics of dusty ...
African Journals Online (AJOL)
The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...
A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS
AHLSTROM, P; BERENDSEN, HJC
1993-01-01
Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)
Structure of hydrogenated amorphous silicon from ab initio molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))
1991-09-15
We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.
Ab initio molecular dynamics simulation of laser melting of silicon
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1996-01-01
The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting
Microsecond atomic-scale molecular dynamics simulations of polyimides
Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.
2013-01-01
We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long
Molecular dynamics study of the silica-water-SDA interactions
Szyja, B.M.; Jansen, A.P.J.; Verstraelen, T.; Santen, van R.A.
2009-01-01
In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species
Toluene model for molecular dynamics simulations in the ranges 298
Fioroni, M.; Vogt, D.
2004-01-01
An all-atom model for toluene is presented in the framework of classical molecular dynamics (MD). The model has been parametrized under the GROMOS96 force field to reproduce the physicochemical properties of the neat liquid. Four new atom types have been introduced, distinguishing between carbons
Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics
Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de
1997-01-01
The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.
Molecular dynamics simulations and free energy profile of ...
Indian Academy of Sciences (India)
aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.
Molecular dynamics simulations of lipid vesicle fusion in atomic detail
Knecht, Volker; Marrink, Siewert-Jan
The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic
Molecular dynamic analysis of the structure of dendrimers
Energy Technology Data Exchange (ETDEWEB)
Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it
2004-01-01
We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.
Molecular dynamic analysis of the structure of dendrimers
International Nuclear Information System (INIS)
Canetta, E.; Maino, G.
2004-01-01
We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques
Molecular dynamics study on the relaxation properties of bilayered ...
Indian Academy of Sciences (India)
2017-08-31
Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...
Metal cluster fission: jellium model and Molecular dynamics simulations
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia
2004-01-01
Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...
Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...
Indian Academy of Sciences (India)
Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...
Free energy from molecular dynamics with multiple constraints
den Otter, Wouter K.; Briels, Willem J.
2000-01-01
In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to
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.
Ownership dynamics with large shareholders : An empirical analysis
Donelli, M.; Urzua Infante, F.; Larrain, B.
2013-01-01
We study the empirical determinants of corporate ownership dynamics in a market where large shareholders are prevalent. We use a unique, hand-collected 20-year dataset on the ownership structure of Chilean companies. Controllers’ blockholdings are on average high -as in continental Europe, for
Worst-Case-Optimal Dynamic Reinsurance for Large Claims
DEFF Research Database (Denmark)
Korn, Ralf; Menkens, Olaf; Steffensen, Mogens
2012-01-01
We control the surplus process of a non-life insurance company by dynamic proportional reinsurance. The objective is to maximize expected (utility of the) surplus under the worst-case claim development. In the large claim case with a worst-case upper limit on claim numbers and claim sizes, we fin...
Dynamic Modeling, Optimization, and Advanced Control for Large Scale Biorefineries
DEFF Research Database (Denmark)
Prunescu, Remus Mihail
with a complex conversion route. Computational fluid dynamics is used to model transport phenomena in large reactors capturing tank profiles, and delays due to plug flows. This work publishes for the first time demonstration scale real data for validation showing that the model library is suitable...
Mechanical properties of irradiated nanowires – A molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
Figueroa, Emilio [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla, 653 Santiago (Chile); Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente, Universidad Tecnológica Metropolitana, Santiago 7800002 (Chile); Tramontina, Diego [Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza (Argentina); Instituto de Bioingeniería, Universidad de Mendoza, 5500 Mendoza (Argentina); Gutiérrez, Gonzalo, E-mail: gonzalo@fisica.ciencias.uchile.cl [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla, 653 Santiago (Chile); Bringa, Eduardo [Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza (Argentina)
2015-12-15
In this work we study, by means of molecular dynamics simulation, the change in the mechanical properties of a gold nanowire with pre-existing radiation damage. The gold nanowire is used as a simple model for a nanofoam, made of connected nanowires. Radiation damage by keV ions leads to the formation of a stacking fault tetrahedron (SFT), and this defect leads to a reduced plastic threshold, as expected, when the nanowire is subjected to tension. We quantify dislocation and twin density during the deformation, and find that the early activation of the SFT as a dislocation source leads to reduced dislocation densities compared to the case without radiation damage. In addition, we observed a total destruction of the SFT, as opposed to a recent simulation study where it was postulated that SFTs might act as self-generating dislocation sources. The flow stress at large deformation is also found to be slightly larger for the irradiated case, in agreement with recent experiments. - Highlights: • Stacking Fault Tetrahedra (SFT) formation proceeds by cascades, containing typically a vacancy cluster and interstitials. • Applied tension leads to the destruction of the SFT, in contrast to a recently reported case of a SFT which soften the NW. • After the initial dislocation activity, strength is controlled by a few surviving dislocations.
Stresses and elastic constants of crystalline sodium, from molecular dynamics
International Nuclear Information System (INIS)
Schiferl, S.K.
1985-02-01
The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the results to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs
Sequence-dependent DNA deformability studied using molecular dynamics simulations.
Fujii, Satoshi; Kono, Hidetoshi; Takenaka, Shigeori; Go, Nobuhiro; Sarai, Akinori
2007-01-01
Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.
Cleaning graphene: A first quantum/classical molecular dynamics approach
Energy Technology Data Exchange (ETDEWEB)
Delfour, L.; Magaud, L., E-mail: emilie.despiau-pujo@cea.fr, E-mail: laurence.magaud@grenoble.cnrs.fr [Institut Néel, CNRS/Université Grenoble Alpes, 25 Avenue des Martyrs, 38054 Grenoble (France); Davydova, A.; Despiau-Pujo, E., E-mail: emilie.despiau-pujo@cea.fr, E-mail: laurence.magaud@grenoble.cnrs.fr; Cunge, G. [LTM, CNRS/Université Grenoble Alpes/CEA, 17 Avenue des Martyrs, 38054 Grenoble (France); Graves, D. B. [Department of Chemical and Biomolecular Engineering, University of California at Berkeley, Berkeley, California 94720 (United States)
2016-03-28
Graphene outstanding properties created a huge interest in the condensed matter community and unprecedented fundings at the international scale in the hope of application developments. Recently, there have been several reports of incomplete removal of the polymer resists used to transfer as-grown graphene from one substrate to another, resulting in altered graphene transport properties. Finding a large-scale solution to clean graphene from adsorbed residues is highly desirable and one promising possibility would be to use hydrogen plasmas. In this spirit, we couple here quantum and classical molecular dynamics simulations to explore the kinetic energy ranges required by atomic hydrogen to selectively etch a simple residue—a CH{sub 3} group—without irreversibly damaging the graphene. For incident energies in the 2–15 eV range, the CH{sub 3} radical can be etched by forming a volatile CH{sub 4} compound which leaves the surface, either in the CH{sub 4} form or breaking into CH{sub 3} + H fragments, without further defect formation. At this energy, adsorption of H atoms on graphene is possible and further annealing will be required to recover pristine graphene.
Molecular dynamics studies of radiation effects in silicon carbide
International Nuclear Information System (INIS)
Diaz de la Rubia, T.; Caturla, M.J.; Tobin, M.
1995-01-01
We discuss results of molecular dynamics computer simulation studies of 3 keV and 5 keV displacement cascades in β-SIC, and compare them to results of 5 keV cascades in pure silicon. The SiC simulations are performed with the Tersoff potential. For silicon we use the Stillinger-Weber potential. Simulations were carried out for Si recoils in 3 dimensional cubic computational cells With periodic boundary conditions and up to 175,616 atoms. The cascade lifetime in SiC is found to be extremely short. This, combined with the high melting temperature of SiC, precludes direct lattice amorphization during the cascade. Although large disordered regions result, these retain their basic crystalline structure. These results are in contrast with observations in pure silicon where direct-impact amorphization from the cascade is seen to take place. The SiC results also show anisotropy in the number of Si and C recoils as well as in the number of replacements in each sublattice. Details of the damage configurations obtained will be discussed
Molecular Dynamics Studies of Overbased Detergents on a Water Surface.
Bodnarchuk, M S; Dini, D; Heyes, D M; Breakspear, A; Chahine, S
2017-07-25
Molecular dynamics (MD) simulations are reported of model overbased detergent nanoparticles on a model water surface which mimic their behavior on a Langmuir trough or large water droplet in engine oil. The simulations predict that the structure of the nanoparticle on a water surface is different to when it is immersed in a bulk hydrophobic solvent. The surfactant tails are partly directed out of the water, while the carbonate core maximizes its extent of contact with the water. Umbrella sampling calculations of the potential of mean force between two particles showed that they are associated with varying degrees with a maximum binding free energy of ca. 10 k B T for the salicylate stabilized particle, ca. 8 k B T for a sulfurized alkyl phenate stabilized particle, and ca. 5 k B T for a sulfonate stabilized particle. The differences in the strength of attraction depend on the proximity of nearest approach and the energy penalty associated with the disruption of the hydration shell of water molecules around the calcium carbonate core when the two particles approach. This is greatest for the sulfonate particle, which partially loses the surfactant ions to the solution, and least for the salicylate, which forms the weakest water "cage". The particles are separated by a water hydration layer, even at the point of closest approach.
Dynamical spin accumulation in large-spin magnetic molecules
Płomińska, Anna; Weymann, Ireneusz; Misiorny, Maciej
2018-01-01
The frequency-dependent transport through a nanodevice containing a large-spin magnetic molecule is studied theoretically in the Kondo regime. Specifically, the effect of magnetic anisotropy on dynamical spin accumulation is of primary interest. Such accumulation arises due to finite components of frequency-dependent conductance that are off diagonal in spin. Here, employing the Kubo formalism and the numerical renormalization group method, we demonstrate that the dynamical transport properties strongly depend on the relative orientation of spin moments in electrodes of the device, as well as on intrinsic parameters of the molecule. In particular, the effect of dynamical spin accumulation is found to be greatly affected by the type of magnetic anisotropy exhibited by the molecule, and it develops for frequencies corresponding to the Kondo temperature. For the parallel magnetic configuration of the device, the presence of dynamical spin accumulation is conditioned by the interplay of ferromagnetic-lead-induced exchange field and the Kondo correlations.
Large N dynamics in QED in a magnetic field
International Nuclear Information System (INIS)
Gusynin, V.P.; Miransky, V.A.; Shovkovy, I.A.
2003-01-01
The expression for the dynamical mass of fermions in QED in a magnetic field is obtained for a large number of the fermion flavor N in the framework of 1/N expansion. The existence of a threshold value N thr , dividing the theories with essentially different dynamics, is established. For the number of flavors N thr , the dynamical mass is very sensitive to the value of the coupling constant α b , related to the magnetic scale μ=√(vertical bar eB vertical bar). For N of the order of N thr or larger, a dynamics similar to that in the Nambu-Jona-Lasinio model with a cutoff of the order of √(vertical bar eB vertical bar) and the dimensional coupling constant G∼1/(N vertical bar eB vertical bar) takes place. In this case, the value of the dynamical mass is essentially α b independent (the dynamics with an infrared stable fixed point). The value of N thr separates a weak coupling dynamics (with α-tilde b ≡Nα b b > or approx. 1) and is of the order of 1/α b
Molecular dynamics for irradiation driven chemistry: application to the FEBID process*
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-10-01
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 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 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 capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.
Multiscale equation-free algorithms for molecular dynamics
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.
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...
Large mass hierarchies from strongly-coupled dynamics
Energy Technology Data Exchange (ETDEWEB)
Athenodorou, Andreas [Department of Physics, University of Cyprus,B.O. Box 20537, 1678 Nicosia (Cyprus); Bennett, Ed [Department of Physics, College of Science, Swansea University,Singleton Park, Swansea SA2 8PP (United Kingdom); Kobayashi-Maskawa Institute for the Origin of Particles and the Universe (KMI),Nagoya University,Furo, Chikusa, Nagoya 464-8602 (Japan); Bergner, Georg [Albert Einstein Center for Fundamental Physics, Institute for Theoretical Physics,University of Bern,Sidlerstrasse 5, CH-3012 Bern (Switzerland); Elander, Daniel [National Institute for Theoretical Physics, School of Physics andMandelstam Institute for Theoretical Physics, University of the Witwatersrand,1 Jan Smuts Avenue, Johannesburg, Wits 2050 (South Africa); Lin, C.-J. David [Institute of Physics, National Chiao-Tung University,1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China); CNRS, Aix Marseille Université, Université de Toulon, Centre de Physique Théorique,UMR 7332, F-13288 Marseille (France); Lucini, Biagio; Piai, Maurizio [Department of Physics, College of Science, Swansea University,Singleton Park, Swansea SA2 8PP (United Kingdom)
2016-06-20
Besides the Higgs particle discovered in 2012, with mass 125 GeV, recent LHC data show tentative signals for new resonances in diboson as well as diphoton searches at high center-of-mass energies (2 TeV and 750 GeV, respectively). If these signals are confirmed (or other new resonances are discovered at the TeV scale), the large hierarchies between masses of new bosons require a dynamical explanation. Motivated by these tentative signals of new physics, we investigate the theoretical possibility that large hierarchies in the masses of glueballs could arise dynamically in new strongly-coupled gauge theories extending the standard model of particle physics. We study lattice data on non-Abelian gauge theories in the (near-)conformal regime as well as a simple toy model in the context of gauge/gravity dualities. We focus our attention on the ratio R between the mass of the lightest spin-2 and spin-0 resonances, that for technical reasons is a particularly convenient and clean observable to study. For models in which (non-perturbative) large anomalous dimensions arise dynamically, we show indications that this mass ratio can be large, with R>5. Moreover, our results suggest that R might be related to universal properties of the IR fixed point. Our findings provide an interesting step towards understanding large mass ratios in the non-perturbative regime of quantum field theories with (near) IR conformal behaviour.
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...
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
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.
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.
Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms
Directory of Open Access Journals (Sweden)
Dirk-Sören Lühmann
2015-08-01
Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.
Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.
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.
Corticomuscular synchronization with small and large dynamic force output
Andrykiewicz, Agnieszka; Patino, Luis; Naranjo, Jose Raul; Witte, Matthias; Hepp-Reymond, Marie-Claude; Kristeva, Rumyana
2007-01-01
Background Over the last few years much research has been devoted to investigating the synchronization between cortical motor and muscular activity as measured by EEG/MEG-EMG coherence. The main focus so far has been on corticomuscular coherence (CMC) during static force condition, for which coherence in beta-range has been described. In contrast, we showed in a recent study [1] that dynamic force condition is accompanied by gamma-range CMC. The modulation of the CMC by various dynamic force amplitudes, however, remained uninvestigated. The present study addresses this question. We examined eight healthy human subjects. EEG and surface EMG were recorded simultaneously. The visuomotor task consisted in isometric compensation for 3 forces (static, small and large dynamic) generated by a manipulandum. The CMC, the cortical EEG spectral power (SP), the EMG SP and the errors in motor performance (as the difference between target and exerted force) were analyzed. Results For the static force condition we found the well-documented, significant beta-range CMC (15–30 Hz) over the contralateral sensorimotor cortex. Gamma-band CMC (30–45 Hz) occurred in both small and large dynamic force conditions without any significant difference between both conditions. Although in some subjects beta-range CMC was observed during both dynamic force conditions no significant difference between conditions could be detected. With respect to the motor performance, the lowest errors were obtained in the static force condition and the highest ones in the dynamic condition with large amplitude. However, when we normalized the magnitude of the errors to the amplitude of the applied force (relative errors) no significant difference between both dynamic conditions was observed. Conclusion These findings confirm that during dynamic force output the corticomuscular network oscillates at gamma frequencies. Moreover, we show that amplitude modulation of dynamic force has no effect on the gamma CMC
Corticomuscular synchronization with small and large dynamic force output
Directory of Open Access Journals (Sweden)
Witte Matthias
2007-11-01
Full Text Available Abstract Background Over the last few years much research has been devoted to investigating the synchronization between cortical motor and muscular activity as measured by EEG/MEG-EMG coherence. The main focus so far has been on corticomuscular coherence (CMC during static force condition, for which coherence in beta-range has been described. In contrast, we showed in a recent study 1 that dynamic force condition is accompanied by gamma-range CMC. The modulation of the CMC by various dynamic force amplitudes, however, remained uninvestigated. The present study addresses this question. We examined eight healthy human subjects. EEG and surface EMG were recorded simultaneously. The visuomotor task consisted in isometric compensation for 3 forces (static, small and large dynamic generated by a manipulandum. The CMC, the cortical EEG spectral power (SP, the EMG SP and the errors in motor performance (as the difference between target and exerted force were analyzed. Results For the static force condition we found the well-documented, significant beta-range CMC (15–30 Hz over the contralateral sensorimotor cortex. Gamma-band CMC (30–45 Hz occurred in both small and large dynamic force conditions without any significant difference between both conditions. Although in some subjects beta-range CMC was observed during both dynamic force conditions no significant difference between conditions could be detected. With respect to the motor performance, the lowest errors were obtained in the static force condition and the highest ones in the dynamic condition with large amplitude. However, when we normalized the magnitude of the errors to the amplitude of the applied force (relative errors no significant difference between both dynamic conditions was observed. Conclusion These findings confirm that during dynamic force output the corticomuscular network oscillates at gamma frequencies. Moreover, we show that amplitude modulation of dynamic force has no
Molecular dynamics simulations of bubble nucleation in dark matter detectors.
Denzel, Philipp; Diemand, Jürg; Angélil, Raymond
2016-01-01
Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)PFLDAS0031-917110.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α-particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.
Nonlinear Dynamics of Carbon Nanotubes Under Large Electrostatic Force
Xu, Tiantian
2015-06-01
Because of the inherent nonlinearities involving the behavior of CNTs when excited by electrostatic forces, modeling and simulating their behavior is challenging. The complicated form of the electrostatic force describing the interaction of their cylindrical shape, forming upper electrodes, to lower electrodes poises serious computational challenges. This presents an obstacle against applying and using several nonlinear dynamics tools typically used to analyze the behavior of complicated nonlinear systems undergoing large motion, such as shooting, continuation, and integrity analysis techniques. This works presents an attempt to resolve this issue. We present an investigation of the nonlinear dynamics of carbon nanotubes when actuated by large electrostatic forces. We study expanding the complicated form of the electrostatic force into enough number of terms of the Taylor series. Then, we utilize this form along with an Euler-Bernoulli beam model to study for the first time the dynamic behavior of CNTs when excited by large electrostatic force. The geometric nonlinearity and the nonlinear electrostatic force are considered. An efficient reduced-order model (ROM) based on the Galerkin method is developed and utilized to simulate the static and dynamic responses of the CNTs. Several results are generated demonstrating softening and hardening behavior of the CNTs near their primary and secondary resonances. The effects of the DC and AC voltage loads on the behavior have been studied. The impacts of the initial slack level and CNT diameter are also demonstrated.
NONLINEAR DYNAMICS OF CARBON NANOTUBES UNDER LARGE ELECTROSTATIC FORCE
Xu, Tiantian
2015-06-01
Because of the inherent nonlinearities involving the behavior of CNTs when excited by electrostatic forces, modeling and simulating their behavior is challenging. The complicated form of the electrostatic force describing the interaction of their cylindrical shape, forming upper electrodes, to lower electrodes poises serious computational challenges. This presents an obstacle against applying and using several nonlinear dynamics tools typically used to analyze the behavior of complicated nonlinear systems undergoing large motion, such as shooting, continuation, and integrity analysis techniques. This works presents an attempt to resolve this issue. We present an investigation of the nonlinear dynamics of carbon nanotubes when actuated by large electrostatic forces. We study expanding the complicated form of the electrostatic force into enough number of terms of the Taylor series. Then, we utilize this form along with an Euler-Bernoulli beam model to study for the first time the dynamic behavior of CNTs when excited by large electrostatic force. The geometric nonlinearity and the nonlinear electrostatic force are considered. An efficient reduced-order model (ROM) based on the Galerkin method is developed and utilized to simulate the static and dynamic responses of the CNTs. Several results are generated demonstrating softening and hardening behavior of the CNTs near their primary and secondary resonances. The effects of the DC and AC voltage loads on the behavior have been studied. The impacts of the initial slack level and CNT diameter are also demonstrated.
Takamoto, So; Yamasaki, Takahiro; Nara, Jun; Ohno, Takahisa; Kaneta, Chioko; Hatano, Asuka; Izumi, Satoshi
2018-03-01
Thermal decomposition of silicon carbide is a promising approach for the fabrication of graphene. However, the atomistic growth mechanism of graphene remains unclear. This paper describes the development of a new charge-transfer interatomic potential. Carbon bonds with a wide variety of characteristics can be reproduced by the proposed vectorized bond-order term. A large-scale thermal decomposition simulation enables us to observe the continuous growth process of the multiring carbon structure. The annealing simulation reveals the atomistic process by which the multiring carbon structure is transformed to flat graphene involving only six-membered rings. Also, it is found that the surface atoms of the silicon carbide substrate enhance the homogeneous graphene formation.
Energy Technology Data Exchange (ETDEWEB)
Tringe, J.W., E-mail: tringe2@llnl.gov [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Ileri, N. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Levie, H.W. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Stroeve, P.; Ustach, V.; Faller, R. [Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Renaud, P. [Swiss Federal Institute of Technology, Lausanne, (EPFL) (Switzerland)
2015-08-18
Highlights: • WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo. • Protein surface coverage characterized by atomic force microscopy. • Models indicate transport characteristics depend strongly on surface coverage. • Results resolve of a four orders of magnitude difference in diffusion coefficient values. - Abstract: We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik; Szepessy, Anders
2010-01-01
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik
2010-03-17
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
Molecular electron recollision dynamics in intense circularly polarized laser pulses
Bandrauk, André D.; Yuan, Kai-Jun
2018-04-01
Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.
Efficient characterisation of large deviations using population dynamics
Brewer, Tobias; Clark, Stephen R.; Bradford, Russell; Jack, Robert L.
2018-05-01
We consider population dynamics as implemented by the cloning algorithm for analysis of large deviations of time-averaged quantities. We use the simple symmetric exclusion process with periodic boundary conditions as a prototypical example and investigate the convergence of the results with respect to the algorithmic parameters, focussing on the dynamical phase transition between homogeneous and inhomogeneous states, where convergence is relatively difficult to achieve. We discuss how the performance of the algorithm can be optimised, and how it can be efficiently exploited on parallel computing platforms.
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
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
Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.
Cooke, Ben; Schmidler, Scott C
2008-10-28
We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.
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)
MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Bonding and vibrational dynamics of a large π-conjugated molecule on a metal surface
International Nuclear Information System (INIS)
Temirov, R; Soubatch, S; Lassise, A; Tautz, F S
2008-01-01
The interplay between the substrate bonding of a large π-conjugated semiconductor molecule and the dynamical properties of the metal-organic interface is studied, employing the prototypical PTCDA/Ag(111) monolayer as an example. Both the coupling of molecular vibrations to the electron-hole-pair continuum of the metal surface and the inelastic scattering of tunnelling electrons by the molecular vibrations on their passage through the molecule are considered. The results of both types of experiment are consistent with the findings of measurements which probe the geometric and electronic structure of the adsorbate-substrate complex directly; generally speaking, they can be understood in the framework of standard theories for the electron-vibron coupling. While the experiments reported here in fact provide additional qualitative insights into the substrate bonding of our π-conjugated model molecule, their detailed quantitative understanding would require a full calculation of the dynamical interface properties, which is currently not available
Molecular dynamics of TBP and DBP studied by neutron transmission
International Nuclear Information System (INIS)
Salles Filho, J.B.V.; Refinetti, M.E.; Fulfaro, R.; Vinhas, L.A.
1984-04-01
Differences between the properties of TBP and DBP, concerning the uranium extraction processes, may be related to certain characteristics of the molecular dynamics of each compound. In order to investigate the dynamical behaviour of hydrogen in these molecules, neutron transmission of TBP and DBP has been measured as a function of neutron wavelenght in the range 4.0 - 6.0 A, at room temperature. Scattering cross sections per hydrogen atom have been obtained. From the comparison with results previously obtained for n-butanol, similar dynamical behaviour of butyl radicals in these compounds could be observed. This similarity indicates that the presence of two or three butyl radicals in butylphosphate molecules does not exert influence in the hydrogen motion of methyl and methylene groups. This suggests that the different chemical behaviour between TBP and DBP is related to the dynamics of the hydrogen directly bound to the DBP phosphate group.(Author) [pt
Langevin dynamics simulations of large frustrated Josephson junction arrays
International Nuclear Information System (INIS)
Groenbech-Jensen, N.; Bishop, A.R.; Lomdahl, P.S.
1991-01-01
Long-time Langevin dynamics simulations of large (N x N,N = 128) 2-dimensional arrays of Josephson junctions in a uniformly frustrating external magnetic field are reported. The results demonstrate: (1) Relaxation from an initially random flux configuration as a universal fit to a glassy stretched-exponential type of relaxation for the intermediate temperatures T(0.3 T c approx-lt T approx-lt 0.7 T c ), and an activated dynamic behavior for T ∼ T c ; (2) a glassy (multi-time, multi-length scale) voltage response to an applied current. Intrinsic dynamical symmetry breaking induced by boundaries as nucleation sites for flux lattice defects gives rise to transverse and noisy voltage response
Langevin dynamics simulations of large frustrated Josephson junction arrays
International Nuclear Information System (INIS)
Gronbech-Jensen, N.; Bishop, A.R.; Lomdahl, P.S.
1991-01-01
Long-time Langevin dynamics simulations of large (N x N, N = 128) 2-dimensional arrays of Josephson junctions in a uniformly frustrating external magnetic field are reported. The results demonstrate: Relaxation from an initially random flux configuration as a ''universal'' fit to a ''glassy'' stretched-exponential type of relaxation for the intermediate temperatures T (0.3 T c approx-lt T approx-lt 0.7 T c ), and an ''activated dynamic'' behavior for T ∼ T c A glassy (multi-time, multi-length scale) voltage response to an applied current. Intrinsic dynamical symmetry breaking induced by boundaries as nucleation sites for flux lattice defects gives rise to transverse and noisy voltage response
Dynamic Soil-Pile Interaction for large diameter monopile foundations
DEFF Research Database (Denmark)
Zania, Varvara
2013-01-01
of the study is to analyse the dynamic interaction of the soil and a single pile embedded in it by accounting for the geometric and stiffness properties of the pile. In doing so, a semi – analytical approach is adopted based on the fundamental solution of horizontal pile vibration by Novak and Nogami (1977...... eigenfrequencies of the soil layer do not affect the soil – pile interaction. The decrease of the eigefrequency of the OWT depends on the aforementioned variation of the dynamic stiffness and the slenderness ratio of the monopile.......Monopile foundations have been used in a large extent to support offshore wind turbines (OWT), being considered as a reliable and cost effective design solution. The accurate estimation of their dynamic response characteristics is essential, since the design of support structures for OWTs has been...
Srivastava, Deepak; Saini, Subhash (Technical Monitor)
1998-01-01
The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.
International Nuclear Information System (INIS)
Wang, J.; Gutierre, M.S.
2010-01-01
This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.
Microscopic theory of dynamical subspace for large amplitude collective motion
International Nuclear Information System (INIS)
Sakata, Fumihiko; Marumori, Toshio; Ogura, Masanori.
1986-01-01
A full quantum theory appropriate for describing large amplitude collective motion is proposed by exploiting the basic idea of the semi-classical theory so far developed within the time-depedent Hartree-Fock theory. A central problem of the quantum theory is how to determine an optimal representation called a dynamical representation specific for the collective subspace where the large amplitude collective motion is replicated as precisely as possible. As an extension of the semi-classical theory where the concept of an approximate integral surface played an important role, the collective subspace is properly characterized by introducing a concept of an approximate invariant subspace of the Hamiltonian. (author)
Tezuka, Kyoichi; Taguchi, Tatsuhiko; Alavi, Saman; Sum, Amadeu K.; Ohmura, Ryo
2012-01-01
This paper report analyses of thermodynamic stability of structure-H clathrate hydrates formed with methane and large guest molecules in terms of their gas phase molecular sizes and molar masses for the selection of a large guest molecule providing better hydrate stability. We investigated the correlation among the gas phase molecular sizes, the molar masses of large molecule guest substances, and the equilibrium pressures. The results suggest that there exists a molecular-size value for the ...
Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study
National Research Council Canada - National Science Library
Isaev, Olexandr; Kholod, Yana; Gorb, Leonid; Qasim, Mohammad; Fredrickson, Herb; Leszczynski, Jerzy
2006-01-01
.... In the present study molecular structure, electrostatic potential, vibrational spectrum and dynamics of thermal decomposition of CL-20 have been investigated by static and dynamic methods of ab...
Secure Group Communications for Large Dynamic Multicast Group
Institute of Scientific and Technical Information of China (English)
Liu Jing; Zhou Mingtian
2003-01-01
As the major problem in multicast security, the group key management has been the focus of research But few results are satisfactory. In this paper, the problems of group key management and access control for large dynamic multicast group have been researched and a solution based on SubGroup Secure Controllers (SGSCs) is presented, which solves many problems in IOLUS system and WGL scheme.
Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories
Directory of Open Access Journals (Sweden)
Jenny Farmer
2017-11-01
Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.
Czech Academy of Sciences Publication Activity Database
Chocholoušová, Jana; Feig, M.
2006-01-01
Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006
Coalescence of silver unidimensional structures by molecular dynamics simulation
International Nuclear Information System (INIS)
Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.
2007-01-01
The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)
Microscopic study of nuclear 'pasta' by quantum molecular dynamics
International Nuclear Information System (INIS)
Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu
2002-01-01
Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. and be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape. We also observe intermediate phases, which has complicated nuclear shapes. Geometrical structures of matter are analyzed with Minkowski functionals, and it is found out that intermediate phases can be characterized as ones with negative Euler characteristic. Our result suggests the existence of these kinds of phases in addition to the simple 'pasta' phases in neutron star crusts. (author)
Nonlinear dynamics of zigzag molecular chains (in Russian)
DEFF Research Database (Denmark)
Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth
1999-01-01
models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...
The chaos and order in nuclear molecular dynamics
International Nuclear Information System (INIS)
Srokowski, T.
1995-01-01
The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or 12 C, 16 O and 20 Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs
Walcott, Sam
2014-10-01
Molecular motors, by turning chemical energy into mechanical work, are responsible for active cellular processes. Often groups of these motors work together to perform their biological role. Motors in an ensemble are coupled and exhibit complex emergent behavior. Although large motor ensembles can be modeled with partial differential equations (PDEs) by assuming that molecules function independently of their neighbors, this assumption is violated when motors are coupled locally. It is therefore unclear how to describe the ensemble behavior of the locally coupled motors responsible for biological processes such as calcium-dependent skeletal muscle activation. Here we develop a theory to describe locally coupled motor ensembles and apply the theory to skeletal muscle activation. The central idea is that a muscle filament can be divided into two phases: an active and an inactive phase. Dynamic changes in the relative size of these phases are described by a set of linear ordinary differential equations (ODEs). As the dynamics of the active phase are described by PDEs, muscle activation is governed by a set of coupled ODEs and PDEs, building on previous PDE models. With comparison to Monte Carlo simulations, we demonstrate that the theory captures the behavior of locally coupled ensembles. The theory also plausibly describes and predicts muscle experiments from molecular to whole muscle scales, suggesting that a micro- to macroscale muscle model is within reach.
DyNet: visualization and analysis of dynamic molecular interaction networks.
Goenawan, Ivan H; Bryan, Kenneth; Lynn, David J
2016-09-01
: The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most 'rewired' nodes across many network states. DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). david.lynn@sahmri.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
Statistical ensembles and molecular dynamics studies of anisotropic solids. II
International Nuclear Information System (INIS)
Ray, J.R.; Rahman, A.
1985-01-01
We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities
Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ
DEFF Research Database (Denmark)
Euro, Liliya; Haapanen, Outi; Róg, Tomasz
2017-01-01
of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...
Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates
Energy Technology Data Exchange (ETDEWEB)
Zhang Junfang [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia); Rivero, Mayela [CSIRO Petroleum, PO Box 1130, Bentley, Western Australia, 6102 (Australia); Choi, S K [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia)
2007-02-14
We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 A. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.
Fermionic molecular dynamics for ground states and collisions of nuclei
International Nuclear Information System (INIS)
Feldmeier, H.; Bieler, K.; Schnack, J.
1994-08-01
The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)
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.)
Molecular Dynamics Simulations of displacement cascades in metallic systems
International Nuclear Information System (INIS)
Doan, N.V.; Tietze, H.
1995-01-01
We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)
Enhancing protein adsorption simulations by using accelerated molecular dynamics.
Directory of Open Access Journals (Sweden)
Christian Mücksch
Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.
Stereochemical errors and their implications for molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Freddolino Peter L
2011-05-01
Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.
Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite
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
High-temperature annealing of graphite: A molecular dynamics study
Petersen, Andrew; Gillette, Victor
2018-05-01
A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
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.
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
Energy Technology Data Exchange (ETDEWEB)
Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche
1997-09-01
Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.
Incorporation of quantum statistical features in molecular dynamics
International Nuclear Information System (INIS)
Ohnishi, Akira; Randrup, J.
1995-01-01
We formulate a method for incorporating quantum fluctuations into molecular-dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous transitions to occur between the wave packets which are not energy eigenstates. The ensuing diffusive evolution in the space of the wave packet parameters exhibits appealing physical properties, including relaxation towards quantum-statistical equilibrium. (author)
Molecular Dynamics Simulations of Tensile Behavior of Copper
Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.
2014-01-01
Molecular dynamics simulations on tensile deformation of initially defect free single crystal copper nanowire oriented in {100} has been carried out at 10 K under adiabatic and isothermal loading conditions. The tensile behaviour was characterized by sharp rise in stress in elastic regime followed by sudden drop at the point of dislocation nucleation. The important finding is that the variation in dislocation density is correlated with the observed stress-strain response. Several interesting ...
Automated processing of data generated by molecular dynamics
International Nuclear Information System (INIS)
Lobato Hoyos, Ivan; Rojas Tapia, Justo; Instituto Peruano de Energia Nuclear, Lima
2008-01-01
A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane
Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping
2012-01-01
We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present new results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition...
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
International Nuclear Information System (INIS)
Swygenhoven, H. van; Caro, A.
1997-01-01
Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young's modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs
Accelerating Molecular Dynamic Simulation on Graphics Processing Units
Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.
2009-01-01
We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. PMID:19191337
Molecular dynamics simulation of cascade damage in gold
International Nuclear Information System (INIS)
Alonso, E.; Caturla, M.J.; Tang, M.; Huang, H.; Diaz de la Rubia, T.
1997-01-01
High-energy cascades have been simulated in gold using molecular dynamics with a modified embedded atom method potential. The results show that both vacancy and interstitial clusters form with high probability as a result of intracascade processes. The formation of clusters has been interpreted in terms of the high pressures generated in the core of the cascade during the early stages. The authors provide evidence that correlation between interstitial and vacancy clustering exists
Thermal conductivity of ZnTe investigated by molecular dynamics
International Nuclear Information System (INIS)
Wang Hanfu; Chu Weiguo
2009-01-01
The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.
Fragmentation dynamics of molecular hydrogen in strong ultrashort laser pulses
International Nuclear Information System (INIS)
Rudenko, A; Feuerstein, B; Zrost, K; Jesus, V L B de; Ergler, T; Dimopoulou, C; Schroeter, C D; Moshammer, R; Ullrich, J
2005-01-01
We present the results of a systematic experimental study of dissociation and Coulomb explosion of molecular hydrogen induced by intense ultrashort (7-25 fs) laser pulses. Using coincident recoil-ion momentum spectroscopy we can distinguish the contributions from dissociation and double ionization even if they result in the same kinetic energies of the fragments. The dynamics of all fragmentation channels drastically depends on the pulse duration, and for 7 fs pulses becomes extremely sensitive to the pulse shape
Stability mechanisms of a thermophilic laccase probed by molecular dynamics.
Directory of Open Access Journals (Sweden)
Niels J Christensen
Full Text Available Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K, probing structural changes associated with enthalpy-entropy compensation. Approaching T opt (∼350 K from 300 K, this change correlated with a beginning "unzipping" of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive at 400 K, suggesting a general salt stabilization effect. In contrast, F(- (but not Cl(- specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F(- intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes.
Molecular dynamics simulation of phosphorylated KID post-translational modification.
Directory of Open Access Journals (Sweden)
Hai-Feng Chen
2009-08-01
Full Text Available Kinase-inducible domain (KID as transcriptional activator can stimulate target gene expression in signal transduction by associating with KID interacting domain (KIX. NMR spectra suggest that apo-KID is an unstructured protein. After post-translational modification by phosphorylation, KID undergoes a transition from disordered to well folded protein upon binding to KIX. However, the mechanism of folding coupled to binding is poorly understood.To get an insight into the mechanism, we have performed ten trajectories of explicit-solvent molecular dynamics (MD for both bound and apo phosphorylated KID (pKID. Ten MD simulations are sufficient to capture the average properties in the protein folding and unfolding.Room-temperature MD simulations suggest that pKID becomes more rigid and stable upon the KIX-binding. Kinetic analysis of high-temperature MD simulations shows that bound pKID and apo-pKID unfold via a three-state and a two-state process, respectively. Both kinetics and free energy landscape analyses indicate that bound pKID folds in the order of KIX access, initiation of pKID tertiary folding, folding of helix alpha(B, folding of helix alpha(A, completion of pKID tertiary folding, and finalization of pKID-KIX binding. Our data show that the folding pathways of apo-pKID are different from the bound state: the foldings of helices alpha(A and alpha(B are swapped. Here we also show that Asn139, Asp140 and Leu141 with large Phi-values are key residues in the folding of bound pKID. Our results are in good agreement with NMR experimental observations and provide significant insight into the general mechanisms of binding induced protein folding and other conformational adjustment in post-translational modification.
Analyzing machupo virus-receptor binding by molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Austin G. Meyer
2014-02-01
Full Text Available In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein–protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host–virus protein–protein interface. We use steered molecular dynamics (SMD to computationally pull the machupo virus (MACV spike glycoprotein (GP1 away from the human transferrin receptor (hTfR1. We then approximate affinity using the maximum applied force of separation and the area under the force-versus-distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-crystal structure shows two large hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein–protein interactions.
Analyzing machupo virus-receptor binding by molecular dynamics simulations
Sawyer, Sara L.; Ellington, Andrew D.; Wilke, Claus O.
2014-01-01
In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein–protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host–virus protein–protein interface. We use steered molecular dynamics (SMD) to computationally pull the machupo virus (MACV) spike glycoprotein (GP1) away from the human transferrin receptor (hTfR1). We then approximate affinity using the maximum applied force of separation and the area under the force-versus-distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-crystal structure shows two large hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein–protein interactions. PMID:24624315
Empirical molecular-dynamics study of diffusion in liquid semiconductors
Yu, W.; Wang, Z. Q.; Stroud, D.
1996-11-01
We report the results of an extensive molecular-dynamics study of diffusion in liquid Si and Ge (l-Si and l-Ge) and of impurities in l-Ge, using empirical Stillinger-Weber (SW) potentials with several choices of parameters. We use a numerical algorithm in which the three-body part of the SW potential is decomposed into products of two-body potentials, thereby permitting the study of large systems. One choice of SW parameters agrees very well with the observed l-Ge structure factors. The diffusion coefficients D(T) at melting are found to be approximately 6.4×10-5 cm2/s for l-Si, in good agreement with previous calculations, and about 4.2×10-5 and 4.6×10-5 cm2/s for two models of l-Ge. In all cases, D(T) can be fitted to an activated temperature dependence, with activation energies Ed of about 0.42 eV for l-Si, and 0.32 or 0.26 eV for two models of l-Ge, as calculated from either the Einstein relation or from a Green-Kubo-type integration of the velocity autocorrelation function. D(T) for Si impurities in l-Ge is found to be very similar to the self-diffusion coefficient of l-Ge. We briefly discuss possible reasons why the SW potentials give D(T)'s substantially lower than ab initio predictions.
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...
Molecular dynamics simulation of bubble nucleation in explosive boiling
International Nuclear Information System (INIS)
Zou Yu; Chinese Academy of Sciences, Beijing; Huai Xiulan; Liang Shiqiang
2009-01-01
Molecular dynamics (MD) simulation is carried out for the bubble nucleation of liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. The results indicate that the initial equilibrium temperature of liquid and molecular cluster size affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of bubble nucleation, the potential energy of the system slowly increases. In the bubble nucleation of explosive boiling, the lower the initial equilibrium temperature, the larger the size of the molecular cluster, and the more the heat transferred into the system of the simulation cell, causing the increase potential energy in a larger range. (authors)
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
International Nuclear Information System (INIS)
Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid
2015-01-01
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields
Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics
Directory of Open Access Journals (Sweden)
Wei Zhang
2017-07-01
Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.
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.
Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations
International Nuclear Information System (INIS)
Kim, Woongkee; Kaviany, Massoud; Shim, J. H.
2014-01-01
It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments
Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets
Lehmann, Kevin K.
2003-03-01
Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.
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.
Molecular dynamics simulations of solutions at constant chemical potential
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.
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.
Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele
2003-01-01
The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metady- namics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.
A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations
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
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,
Energy Dynamics of an Infinitely Large Offshore Wind Farm
DEFF Research Database (Denmark)
Frandsen, Sten Tronæs; Barthelmie, R.J.; Pryor, S.C.
, particularly in the near-term, can be expected in the higher resource, moderate water depths of the North Sea rather than the Mediterranean. There should therefore be significant interest in understanding the energy dynamics of the infinitely large wind farm – how wakes behave and whether the extraction...... of energy by wind turbines over a large area has a significant and lasting impact on the atmospheric boundary layer. Here we focus on developing understanding of the infinite wind farm through a combination of theoretical considerations, data analysis and modeling. Initial evaluation of power losses due...... is of about the same magnitude as for the infinitely large wind farm. We will examine whether this can be proved theoretically or is indicated by data currently available. We will also evaluate whether energy extraction at the likely scale of development in European Seas can be expected to modulate...
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
Dynamics of Large Systems of Nonlinearly Evolving Units
Lu, Zhixin
The dynamics of large systems of many nonlinearly evolving units is a general research area that has great importance for many areas in science and technology, including biology, computation by artificial neural networks, statistical mechanics, flocking in animal groups, the dynamics of coupled neurons in the brain, and many others. While universal principles and techniques are largely lacking in this broad area of research, there is still one particular phenomenon that seems to be broadly applicable. In particular, this is the idea of emergence, by which is meant macroscopic behaviors that "emerge" from a large system of many "smaller or simpler entities such that...large entities" [i.e., macroscopic behaviors] arise which "exhibit properties the smaller/simpler entities do not exhibit." In this thesis we investigate mechanisms and manifestations of emergence in four dynamical systems consisting many nonlinearly evolving units. These four systems are as follows. (a) We first study the motion of a large ensemble of many noninteracting particles in a slowly changing Hamiltonian system that undergoes a separatrix crossing. In such systems, we find that separatrix-crossing induces a counterintuitive effect. Specifically, numerical simulation of two sets of densely sprinkled initial conditions on two energy curves appears to suggest that the two energy curves, one originally enclosing the other, seemingly interchange their positions. This, however, is topologically forbidden. We resolve this paradox by introducing a numerical simulation method we call "robust" and study its consequences. (b) We next study the collective dynamics of oscillatory pacemaker neurons in Suprachiasmatic Nucleus (SCN), which, through synchrony, govern the circadian rhythm of mammals. We start from a high-dimensional description of the many coupled oscillatory neuronal units within the SCN. This description is based on a forced Kuramoto model. We then reduce the system dimensionality by using
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...
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....
Molecular dynamics investigation of tracer diffusion in a simple liquid
International Nuclear Information System (INIS)
Ould-Kaddour, F.; Barrat, J.L.
1991-05-01
Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs
Molecular dynamics of coalescence and collisions of silver nanoparticles
Energy Technology Data Exchange (ETDEWEB)
Guevara-Chapa, Enrique, E-mail: enrique_guevara@hotmail.com [Universidad Autónoma de Nuevo León, Facultad de Ciencias Físico Matemáticas (Mexico); Mejía-Rosales, Sergio [Universidad Autónoma de Nuevo León, Center for Innovation, Research and Development in Engineering and Technology (CIIDIT), and CICFIM-Facultad de Ciencias Físico Matemáticas (Mexico)
2014-12-15
We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy.
Molecular dynamics simulations of lysozyme in water/sugar solutions
Energy Technology Data Exchange (ETDEWEB)
Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)
2008-04-18
Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.
Molecular dynamics of coalescence and collisions of silver nanoparticles
International Nuclear Information System (INIS)
Guevara-Chapa, Enrique; Mejía-Rosales, Sergio
2014-01-01
We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy
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
The classical and quantum dynamics of molecular spins on graphene
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2016-02-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.
Large-scale dynamic compaction of natural salt
International Nuclear Information System (INIS)
Hansen, F.D.; Ahrens, E.H.
1996-01-01
A large-scale dynamic compaction demonstration of natural salt was successfully completed. About 40 m 3 of salt were compacted in three, 2-m lifts by dropping a 9,000-kg weight from a height of 15 m in a systematic pattern to achieve desired compaction energy. To enhance compaction, 1 wt% water was added to the relatively dry mine-run salt. The average compacted mass fractional density was 0.90 of natural intact salt, and in situ nitrogen permeabilities averaged 9X10 -14 m 2 . This established viability of dynamic compacting for placing salt shaft seal components. The demonstration also provided compacted salt parameters needed for shaft seal system design and performance assessments of the Waste Isolation Pilot Plant
Machine learning molecular dynamics for the simulation of infrared spectra.
Gastegger, Michael; Behler, Jörg; Marquetand, Philipp
2017-10-01
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.
Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy
Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks
2016-06-01
Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.
Chaotic Traversal (CHAT): Very Large Graphs Traversal Using Chaotic Dynamics
Changaival, Boonyarit; Rosalie, Martin; Danoy, Grégoire; Lavangnananda, Kittichai; Bouvry, Pascal
2017-12-01
Graph Traversal algorithms can find their applications in various fields such as routing problems, natural language processing or even database querying. The exploration can be considered as a first stepping stone into knowledge extraction from the graph which is now a popular topic. Classical solutions such as Breadth First Search (BFS) and Depth First Search (DFS) require huge amounts of memory for exploring very large graphs. In this research, we present a novel memoryless graph traversal algorithm, Chaotic Traversal (CHAT) which integrates chaotic dynamics to traverse large unknown graphs via the Lozi map and the Rössler system. To compare various dynamics effects on our algorithm, we present an original way to perform the exploration of a parameter space using a bifurcation diagram with respect to the topological structure of attractors. The resulting algorithm is an efficient and nonresource demanding algorithm, and is therefore very suitable for partial traversal of very large and/or unknown environment graphs. CHAT performance using Lozi map is proven superior than the, commonly known, Random Walk, in terms of number of nodes visited (coverage percentage) and computation time where the environment is unknown and memory usage is restricted.
Directory of Open Access Journals (Sweden)
Elena ePapaleo
2015-05-01
Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us 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 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 their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular 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.
Challenges in parameter identification of large structural dynamic systems
International Nuclear Information System (INIS)
Koh, C.G.
2001-01-01
In theory, it is possible to determine the parameters of a structural or mechanical system by subjecting it to some dynamic excitation and measuring the response. Considerable research has been carried out in this subject area known as the system identification over the past two decades. Nevertheless, the challenges associated with numerical convergence are still formidable when the system is large in terms of the number of degrees of freedom and number of unknowns. While many methods work for small systems, the convergence becomes difficult, if not impossible, for large systems. In this keynote lecture, both classical and non-classical system identification methods for dynamic testing and vibration-based inspection are discussed. For classical methods, the extended Kalman filter (EKF) approach is used. On this basis, a substructural identification method has been developed as a strategy to deal with large structural systems. This is achieved by reducing the problem size, thereby significantly improving the numerical convergence and efficiency. Two versions of this method are presented each with its own merits. A numerical example of frame structure with 20 unknown parameters is illustrated. For non-classical methods, the Genetic Algorithm (GA) is shown to be applicable with relative ease due to its 'forward analysis' nature. The computational time is, however, still enormous for large structural systems due to the combinatorial explosion problem. A model GA method has been developed to address this problem and tested with considerable success on a relatively large system of 50 degrees of freedom, accounting for input and output noise effects. An advantages of this GA-based identification method is that the objective function can be defined in response measured. Numerical studies show that the method is relatively robust, as it does in response measured. Numerical studies show that the method is relatively robust, as it dos not require good initial guess and the
Accelerated molecular dynamics methods: introduction and recent developments
International Nuclear Information System (INIS)
Uberuaga, Blas Pedro; Voter, Arthur F.; Perez, Danny; Shim, Y.; Amar, J.G.
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) (10, 19, 23) to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what
Accelerated molecular dynamics methods: introduction and recent developments
Energy Technology Data Exchange (ETDEWEB)
Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what
Moffett, Alexander S; Bender, Kyle W; Huber, Steven C; Shukla, Diwakar
2017-07-28
The structural motifs responsible for activation and regulation of eukaryotic protein kinases in animals have been studied extensively in recent years, and a coherent picture of their activation mechanisms has begun to emerge. In contrast, non-animal eukaryotic protein kinases are not as well understood from a structural perspective, representing a large knowledge gap. To this end, we investigated the conformational dynamics of two key Arabidopsis thaliana receptor-like kinases, brassinosteroid-insensitive 1 (BRI1) and BRI1-associated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphorylated kinase domains. Molecular dynamics simulations calculate the motion of each atom in a protein based on classical approximations of interatomic forces, giving researchers insight into protein function at unparalleled spatial and temporal resolutions. We found that in an otherwise "active" BAK1 the αC helix is highly disordered, a hallmark of deactivation, whereas the BRI1 αC helix is moderately disordered and displays swinging behavior similar to numerous animal kinases. An analysis of all known sequences in the A. thaliana kinome found that αC helix disorder may be a common feature of plant kinases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
Spinodal decomposition in multicomponent fluid mixtures: A molecular dynamics study
DEFF Research Database (Denmark)
Laradji, Mohamed; Mouritsen, Ole G.; Toxvaerd, Søren
1996-01-01
parameter, leading to large growth-exponent values, the dynamics in multicomponent fluids (p = 3, 4) is found to follow a t(1/3) growth law, where t is time, which we relate to a long-wavelength evaporation-condensation process. These findings, which are proposed to be consequences of the compact domain...
International Nuclear Information System (INIS)
Hafez Haghighat, S.M.; Schaeublin, R.; Fivel, M.C.
2007-01-01
Full text of publication follows: multi-scale modeling, including molecular dynamics (MD) and discrete dislocation dynamics (DDD) methods, appears as a significant tool for the description of plasticity and mechanical properties of materials. This research is on the investigation of the subsequence effects of irradiation on the plasticity of pure Fe and focuses on the interaction of a single dislocation and a spherical cavity, as void or He bubble. Extensive MD simulations of the interaction under imposed strain rate [1, 2] have shown that various temperatures and cavity sizes result in different release stresses depending on dislocation bow out. It appears that a temperature increase and cavity size decrease reduce the cavity strength. MD simulation shows that the elastic field around the cavity is largely anisotropic. This anisotropy may influence the way the dislocation unpins from the cavity. Following the MD simulations, the interaction of a single dislocation and a spherical cavity is now simulated using a DDD discrete dislocation dynamics model. The simulation accounts for the non-Schmidt effect induced by the bcc structure of Fe through local rules derived from MD simulations [3]. The cavity is introduced in the simulation by computing the image forces using a finite element technique. The effective stress applied on the dislocation is then obtained as the superimposition of the applied stress field, the image stress field and the internal stresses. Note that such a model only uses elasticity theory and no core effect of dislocations is taken into account. One of the objectives of this work is to check whether elasticity is responsible of the behaviour observed by MD. Several cases are tested. First an edge dislocation in a (110) plane is pushed against the cavity under a pure shear loading. The local reaction of the dislocations and the cavity are compared to the MD simulations. Then, the case of a screw dislocation is studied. Finally, other loading
Molecular-dynamics simulations of urea nucleation from aqueous solution.
Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele
2015-01-06
Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.
Molecular-dynamics simulations of urea nucleation from aqueous solution
Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele
2015-01-01
Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete. PMID:25492932
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.
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.
Planar dynamics of large-deformation rods under moving loads
Zhao, X. W.; van der Heijden, G. H. M.
2018-01-01
We formulate the problem of a slender structure (a rod) undergoing large deformation under the action of a moving mass or load motivated by inspection robots crawling along bridge cables or high-voltage power lines. The rod is described by means of geometrically exact Cosserat theory which allows for arbitrary planar flexural, extensional and shear deformations. The equations of motion are discretised using the generalised-α method. The formulation is shown to handle the discontinuities of the problem well. Application of the method to a cable and an arch problem reveals interesting nonlinear phenomena. For the cable problem we find that large deformations have a resonance detuning effect on cable dynamics. The problem also offers a compelling illustration of the Timoshenko paradox. For the arch problem we find a stabilising (delay) effect on the in-plane collapse of the arch, with failure suppressed entirely at sufficiently high speed.
Validating clustering of molecular dynamics simulations using polymer models
Directory of Open Access Journals (Sweden)
Phillips Joshua L
2011-11-01
Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our
DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS
JUFFER, AH; BERENDSEN, HJC
1993-01-01
A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the
Risselada, H. Jelger; Marrink, Siewert J.
2009-01-01
The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high
Marrink, SJ; Mark, AE
2003-01-01
Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at
Czech Academy of Sciences Publication Activity Database
Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.
2004-01-01
Roč. 70, č. 6 (2004), 0611031-0611034 ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant - others:NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004
Chiral dynamics and partonic structure at large transverse distances
Energy Technology Data Exchange (ETDEWEB)
Strikman, M. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Physics; Weiss, C. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States). Theory Center
2009-12-30
In this paper, we study large-distance contributions to the nucleon’s parton densities in the transverse coordinate (impact parameter) representation based on generalized parton distributions (GPDs). Chiral dynamics generates a distinct component of the partonic structure, located at momentum fractions x≲M_{π}/M_{N} and transverse distances b~1/M_{π}. We calculate this component using phenomenological pion exchange with a physical lower limit in b (the transverse “core” radius estimated from the nucleon’s axial form factor, R_{core}=0.55 fm) and demonstrate its universal character. This formulation preserves the basic picture of the “pion cloud” model of the nucleon’s sea quark distributions, while restricting its application to the region actually governed by chiral dynamics. It is found that (a) the large-distance component accounts for only ~1/3 of the measured antiquark flavor asymmetry d¯-u¯ at x~0.1; (b) the strange sea quarks s and s¯ are significantly more localized than the light antiquark sea; (c) the nucleon’s singlet quark size for x<0.1 is larger than its gluonic size, (b^{2})_{q+q¯}>(b^{2})_{g}, as suggested by the t-slopes of deeply-virtual Compton scattering and exclusive J/ψ production measured at HERA and FNAL. We show that our approach reproduces the general N_{c}-scaling of parton densities in QCD, thanks to the degeneracy of N and Δ intermediate states in the large-N_{c} limit. Finally, we also comment on the role of pionic configurations at large longitudinal distances and the limits of their applicability at small x.
Physical properties of Cu nanoparticles: A molecular dynamics study
International Nuclear Information System (INIS)
Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.
2014-01-01
Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index
Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors
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.
Large scale IRAM 30 m CO-observations in the giant molecular cloud complex W43
Carlhoff, P.; Nguyen Luong, Q.; Schilke, P.; Motte, F.; Schneider, N.; Beuther, H.; Bontemps, S.; Heitsch, F.; Hill, T.; Kramer, C.; Ossenkopf, V.; Schuller, F.; Simon, R.; Wyrowski, F.
2013-12-01
We aim to fully describe the distribution and location of dense molecular clouds in the giant molecular cloud complex W43. It was previously identified as one of the most massive star-forming regions in our Galaxy. To trace the moderately dense molecular clouds in the W43 region, we initiated W43-HERO, a large program using the IRAM 30 m telescope, which covers a wide dynamic range of scales from 0.3 to 140 pc. We obtained on-the-fly-maps in 13CO (2-1) and C18O (2-1) with a high spectral resolution of 0.1 km s-1 and a spatial resolution of 12''. These maps cover an area of ~1.5 square degrees and include the two main clouds of W43 and the lower density gas surrounding them. A comparison to Galactic models and previous distance calculations confirms the location of W43 near the tangential point of the Scutum arm at approximately 6 kpc from the Sun. The resulting intensity cubes of the observed region are separated into subcubes, which are centered on single clouds and then analyzed in detail. The optical depth, excitation temperature, and H2 column density maps are derived out of the 13CO and C18O data. These results are then compared to those derived from Herschel dust maps. The mass of a typical cloud is several 104 M⊙ while the total mass in the dense molecular gas (>102 cm-3) in W43 is found to be ~1.9 × 106 M⊙. Probability distribution functions obtained from column density maps derived from molecular line data and Herschel imaging show a log-normal distribution for low column densities and a power-law tail for high densities. A flatter slope for the molecular line data probability distribution function may imply that those selectively show the gravitationally collapsing gas. Appendices are available in electronic form at http://www.aanda.orgThe final datacubes (13CO and C18O) for the entire survey are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/560/A24
Correlations and symmetry of interactions influence collective dynamics of molecular motors
International Nuclear Information System (INIS)
Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B
2015-01-01
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)
A lattice with no transition and large dynamic aperture
International Nuclear Information System (INIS)
Guignard, G.
1989-01-01
In the case of a one-ring high-energy scheme for an advanced hadron facility, beam losses can be reduced if the ring lattice accomodates the beam from injection to maximum energy without crossing the transition. Since there is no synchrotron booster in such a scheme and the injection energy is relatively low, this requirement implies a negative compaction factor and an imaginary transition energy. This can be achieved by making the horizontal dispersion negative in some regions of the arcs so that the average value taken in the dipoles is globally also negative. Such a modulation of the dispersion may result in an increasing difficulty to obtain a large enough dynamic aperture in the presence of sextupoles. A careful optimization is therefore necessary and the possibility of modifying the linear lattice in order to include the requirements associated with chromaticity adjustments has to be studied. This paper summarizes the work done along this line and based on previous searches for a race track lattice that can be used in a hadron facility main ring. It describes an alternative lattice design, which tends to minimize the effects of the nonlinear aberrations introduced by sextupoles and to achieve a large dynamic aperture, keeping the betatron amplitudes as low as possible. 7 refs., 6 figs., 1 tab
International Nuclear Information System (INIS)
Dellerue, Serge
2000-01-01
Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr
Parallel computing and molecular dynamics of biological membranes
International Nuclear Information System (INIS)
La Penna, G.; Letardi, S.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Salina, G.
1998-01-01
In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)
Rheology of liquid n-triacontane: Molecular dynamics simulation
International Nuclear Information System (INIS)
Kondratyuk, N D; Norman, G E; Stegailov, V V
2016-01-01
Molecular dynamics is applied to calculate diffusion coefficients of n-triacontane C 30 H 62 using Einstein-Smoluchowski and Green-Kubo relations. The displacement 〈Δr 2 〉( t ) has a subdiffusive part 〈Δr 2 〉 ∼ t α , caused by molecular crowding at low temperatures. Longtime asymptotes of 〈v(0)v(t)〉 are collated with the hydrodynamic tail t -3/2 demonstrated for atomic liquids. The influence of these asymptotes on the compliance of Einstein-Smoluchowski and Green-Kubo methods is analyzed. The effects of the force field parameters on the diffusion process are treated. The results are compared with experimental data. (paper)
Sugar transport across lactose permease probed by steered molecular dynamics
DEFF Research Database (Denmark)
Jensen, Morten Østergaard; Yin, Ying; Tajkhorshid, Emad
2007-01-01
Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic...... details of lactose interaction with the lumen of LacY during its permeation. Lactose induces a widening of the narrowest parts of the channel during permeation, the widening being largest within the periplasmic half-channel. During permeation, the water-filled lumen of LacY only partially hydrates lactose......, forcing it to interact with channel lining residues. Lactose forms a multitude of direct sugar-channel hydrogen bonds, predominantly with residues of the flexible N-domain, which is known to contribute a major part of LacY's affinity for lactose. In the periplasmic half-channel lactose predominantly...
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane.
Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping
2012-12-01
We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.
Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar
This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...... of enzyme kinetics in non-aqueous media, it has been a fruitful approach to fix the enzyme hydration level by controlling the water activity of the medium. In this work, a protocol is therefore developed for determining the water activity in non-aqueous protein simulations. The method relies on determining...... integration, while for small systems, it seems to be even better. The method is applied to compute the excess Gibbs energy of the mixtures of water and organic solvents used in the simulations of CALB. This allows to determine the water activity of the simulated systems and thus to compare protein properties...
Directory of Open Access Journals (Sweden)
Peng Sang
Full Text Available Although the crystal structures of the HIV-1 gp120 core bound and pre-bound by CD4 are known, the details of dynamics involved in conformational equilibrium and transition in relation to gp120 function have remained elusive. The homology models of gp120 comprising the N- and C-termini and loops V3 and V4 in the CD4-bound and CD4-unbound states were built and subjected to molecular dynamics (MD simulations to investigate the differences in dynamic properties and molecular motions between them. The results indicate that the CD4-bound gp120 adopted a more compact and stable conformation than the unbound form during simulations. For both the unbound and bound gp120, the large concerted motions derived from essential dynamics (ED analyses can influence the size/shape of the ligand-binding channel/cavity of gp120 and, therefore, were related to its functional properties. The differences in motion direction between certain structural components of these two forms of gp120 were related to the conformational interconversion between them. The free energy calculations based on the metadynamics simulations reveal a more rugged and complex free energy landscape (FEL for the unbound than for the bound gp120, implying that gp120 has a richer conformational diversity in the unbound form. The estimated free energy difference of ∼-6.0 kJ/mol between the global minimum free energy states of the unbound and bound gp120 indicates that gp120 can transform spontaneously from the unbound to bound states, revealing that the bound state represents a high-probability "ground state" for gp120 and explaining why the unbound state resists crystallization. Our results provide insight into the dynamics-and-function relationship of gp120, and facilitate understandings of the thermodynamics, kinetics and conformational control mechanism of HIV-1 gp120.
Accurate Kirkwood-Buff Integrals from Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar; O'Connell, John P.; Peters, Günther H.J.
2010-01-01
A method is proposed for obtaining thermodynamic properties via Kirkwood–Buff (KB) integrals from molecular simulations. In order to ensure that the KB integration converges, the pair distribution function is extrapolated to large distances using the extension method of Verlet, which enforces...... of state fitted to simulation results. Good agreement is achieved for both fluids at densities larger than 1.5 times the critical density....
Molecular dynamics study of lubricant depletion by pulsed laser heating
Seo, Young Woo; Rosenkranz, Andreas; Talke, Frank E.
2018-05-01
In this study, molecular dynamics simulations were performed to numerically investigate the effect of pulsed laser heating on lubricant depletion. The maximum temperature, the lubricant depletion width, the number of evaporated lubricant beads and the number of fragmented lubricant chains were studied as a function of laser peak power, pulse duration and repetition rate. A continuous-wave laser and a square pulse laser were simulated and compared to a Gaussian pulse laser. With increasing repetition rate, pulsed laser heating was found to approach continuous-wave laser heating.
Thermal conductivity of water: Molecular dynamics and generalized hydrodynamics results
Bertolini, Davide; Tani, Alessandro
1997-10-01
Equilibrium molecular dynamics simulations have been carried out in the microcanonical ensemble at 300 and 255 K on the extended simple point charge (SPC/E) model of water [Berendsen et al., J. Phys. Chem. 91, 6269 (1987)]. In addition to a number of static and dynamic properties, thermal conductivity λ has been calculated via Green-Kubo integration of the heat current time correlation functions (CF's) in the atomic and molecular formalism, at wave number k=0. The calculated values (0.67+/-0.04 W/mK at 300 K and 0.52+/-0.03 W/mK at 255 K) are in good agreement with the experimental data (0.61 W/mK at 300 K and 0.49 W/mK at 255 K). A negative long-time tail of the heat current CF, more apparent at 255 K, is responsible for the anomalous decrease of λ with temperature. An analysis of the dynamical modes contributing to λ has shown that its value is due to two low-frequency exponential-like modes, a faster collisional mode, with positive contribution, and a slower one, which determines the negative long-time tail. A comparison of the molecular and atomic spectra of the heat current CF has suggested that higher-frequency modes should not contribute to λ in this temperature range. Generalized thermal diffusivity DT(k) decreases as a function of k, after an initial minor increase at k=kmin. The k dependence of the generalized thermodynamic properties has been calculated in the atomic and molecular formalisms. The observed differences have been traced back to intramolecular or intermolecular rotational effects and related to the partial structure functions. Finally, from the results we calculated it appears that the SPC/E model gives results in better agreement with experimental data than the transferable intermolecular potential with four points TIP4P water model [Jorgensen et al., J. Chem. Phys. 79, 926 (1983)], with a larger improvement for, e.g., diffusion, viscosities, and dielectric properties and a smaller one for thermal conductivity. The SPC/E model shares
Molecular hydrodynamic approach to dynamical correlations in quantum liquids
International Nuclear Information System (INIS)
Rabani, Eran; Reichman, David R.
2002-01-01
A quantum molecular hydrodynamic formalism is developed for the study of dynamics in quantum liquids. The method combines exact static input, generated by path-integral Monte Carlo, and an approximate form of the quantum memory function for the solution of the exact quantum generalized Langevin equation under consideration. This methodology is applied to the study of the spectrum of density fluctuations in liquid para-H 2 . Using a physically motivated approximation for the memory function, semiquantitative agreement is obtained for S(k,ω) in comparison to the recent experiments of Bermejo et al. [Phys. Rev. Lett. 84, 5359 (2000)]. Improvement of the methodology and future applications are discussed
Molecular Dynamics Simulations on Evaporation of Droplets with Dissolved Salts
Jin-Liang Xu; Min Chen; Xiao-Dong Wang; Bing-Bing Wang
2013-01-01
Molecular dynamics simulations are used to study the evaporation of water droplets containing either dissolved LiCl, NaCl or KCl salt in a gaseous surrounding (nitrogen) with a constant high temperature of 600 K. The initial droplet has 298 K temperature and contains 1,120 water molecules, 0, 40, 80 or 120 salt molecules. The effects of the salt type and concentration on the evaporation rate are examined. Three stages with different evaporation rates are observed for all cases. In the initial...
Molecular nonlinear dynamics and protein thermal uncertainty quantification
Xia, Kelin; Wei, Guo-Wei
2014-01-01
This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. PMID:24697365
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
International Nuclear Information System (INIS)
Mugnai, Mauro L.; Elber, Ron
2015-01-01
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide
Full quantum treatment of charge dynamics in amorphous molecular semiconductors
de Vries, Xander; Friederich, Pascal; Wenzel, Wolfgang; Coehoorn, Reinder; Bobbert, Peter A.
2018-02-01
We present a treatment of charge dynamics in amorphous molecular semiconductors that accounts for the coupling of charges to all intramolecular phonon modes in a fully quantum mechanical way. Based on ab initio calculations, we derive charge transfer rates that improve on the widely used semiclassical Marcus rate and obtain benchmark results for the mobility and energetic relaxation of electrons and holes in three semiconductors commonly applied in organic light-emitting diodes. Surprisingly, we find very similar results when using the simple Miller-Abrahams rate. We conclude that extracting the disorder strength from temperature-dependent charge transport studies is very possible but extracting the reorganization energy is not.
The density functional theory and the charged fluid molecular dynamics
International Nuclear Information System (INIS)
Hansen, J.P.; Zerah, G.
1993-01-01
Car and Parrinello had the idea of combining the density functional theory (Hohenberg, Kohn and Sham) to the 'molecular dynamics' numerical modelling method, in order to simulate metallic or co-valent solids and liquids from the first principles. The objective of this paper is to present a simplified version of this method ab initio, applicable to classical and quantal charged systems. The method is illustrated with recent results on charged colloidal suspensions and highly correlated electron-proton plasmas. 1 fig., 21 refs
Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.
2009-01-01
and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...... computations of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems.3,16,17,18 For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence...
Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations
Directory of Open Access Journals (Sweden)
Wolfgang Schreiner
2012-01-01
Full Text Available Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt has reached a stationary shape, the simulation has not yet converged.
Molecular dynamics computer simulations based on NMR data
International Nuclear Information System (INIS)
Vlieg, J. de.
1989-01-01
In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs
Thermodynamics of small clusters of atoms: A molecular dynamics simulation
DEFF Research Database (Denmark)
Damgaard Kristensen, W.; Jensen, E. J.; Cotterill, Rodney M J
1974-01-01
The thermodynamic properties of clusters containing 55, 135, and 429 atoms have been calculated using the molecular dynamics method. Structural and vibrational properties of the clusters were examined at different temperatures in both the solid and the liquid phase. The nature of the melting...... transition was investigated, and a number of properties, such as melting temperature, latent heat of melting, and premelting phenomena, were found to vary with cluster size. These properties were also found to depend on the structure of the solid phase. In this phase the configuration of lowest free energy...
Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution
Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.
2011-01-01
Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molec...
Ti and Zr surfaces studied by molecular dynamics
International Nuclear Information System (INIS)
Pascuet, Maria I.; Passianot, Roberto C.; Monti, Ana M.
2003-01-01
The interaction between point defects technique and the (0001), (1-210), (10-10) surfaces in Ti and Zr is studied by the molecular dynamics technique. Both of metals are in the hexagonal structure and within a temperature range of 100 to 900 K. The atomic interactions are modeled by EAM-type many-body potentials, that were used previously in static simulations. New migration mechanisms are unraveled and others are verified with respect to those already proposed in the static studies. Also included is an analysis of the vacancy stability in the sub-surface layers of the prismatic surfaces. (author)
Nonlinear rotor dynamics of 2D molecular array: topology reconstruction
International Nuclear Information System (INIS)
Lykah, V.A.; Syrkin, E.S.
2011-01-01
Molecular layers with rotational degrees of freedom and quadrupolar interaction between linear molecules are investigated theoretically. We found earlier that alternative orientation of the molecules along and perpendicular to an axis of the rectangular lattice is preferable. Here we find the integral of motion and give the topology analysis of the possible dynamical phases and special points in the long-wave limit. We find the strong anisotropy in the angle space: directions of easy excitation ('valleys') exist. We show the potential relief reconstruction in dependence on the adsorbed lattice anisotropy.
Dynamical image-charge effect in molecular tunnel junctions
DEFF Research Database (Denmark)
Jin, Chengjun; Thygesen, Kristian Sommer
2014-01-01
the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z(2), where Z is the quasiparticle renormalization factor, compared to the static IC approximation...... that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels....
Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics
Mathiazhagan, S.; Anup, S.
2016-08-01
Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.
Porting of serial molecular dynamics code on MIMD platforms
International Nuclear Information System (INIS)
Celino, M.
1995-05-01
A molecular Dynamics (MD) code, utilized for the study of atomistic models of metallic systems has been parallelized for MIMD (Multiple Instructions Multiple Data) parallel platforms by means of the Parallel Virtual Machine (PVM) message passing library. Since the parallelization implies modifications of the sequential algorithms, these are described from the point of view of the Statistical Mechanics theory. Furthermore, techniques and parallelization strategies utilized and the MD parallel code are described in detail. Benchmarks on several MIMD platforms (IBM SP1 and SP2, Cray T3D, Cluster of workstations) allow performances evaluation of the code versus the different characteristics of the parallel platforms
Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals
International Nuclear Information System (INIS)
Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon
2000-01-01
We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the direction form intersecting stacking faults by slippage along {111} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
Energy Technology Data Exchange (ETDEWEB)
Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)
1994-12-31
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.
Molecular dynamics simulation of radiation damage cascades in diamond
Energy Technology Data Exchange (ETDEWEB)
Buchan, J. T. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Robinson, M. [Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia); Christie, H. J.; Roach, D. L.; Ross, D. K. [Physics and Materials Research Centre, School of Computing, Science and Engineering, University of Salford, Salford, Greater Manchester M5 4WT (United Kingdom); Marks, N. A. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia)
2015-06-28
Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.
Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.
2009-01-01
and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...... dynamics (MD) simulations of a hydrophilic air-water-silica system using the MD package FASTTUBE. We employ quantum chemistry calculation to obtain air-silica interaction parameters for the simulations. Our simulations are based in the following force fields: i) The silica-silica interaction is based...... of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems. For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence of air. Hence...
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
International Nuclear Information System (INIS)
Wei Gu; Garcia, A.E.; Schoenborn, B.P.
1994-01-01
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies
Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts
Directory of Open Access Journals (Sweden)
Kazuaki Z. Takahashi
2017-01-01
Full Text Available Long-timescale molecular dynamics simulations were performed to estimate the actual physical nature of a united-atom model of polyethylene (PE. Several scaling laws for representative polymer properties are compared to theoretical predictions. Internal structure results indicate a clear departure from theoretical predictions that assume ideal chain statics. Chain motion deviates from predictions that assume ideal motion of short chains. With regard to linear viscoelasticity, the presence or absence of entanglements strongly affects the duration of the theoretical behavior. Overall, the results indicate that Gaussian statics and dynamics are not necessarily established for real atomistic models of PE. Moreover, the actual physical nature should be carefully considered when using atomistic models for applications that expect typical polymer behaviors.
First Principles Modelling of Shape Memory Alloys Molecular Dynamics Simulations
Kastner, Oliver
2012-01-01
Materials sciences relate the macroscopic properties of materials to their microscopic structure and postulate the need for holistic multiscale research. The investigation of shape memory alloys is a prime example in this regard. This particular class of materials exhibits strong coupling of temperature, strain and stress, determined by solid state phase transformations of their metallic lattices. The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and covers thermodynamical, micro-mechanical and crystallographical aspects. It addresses scientists in these research fields and thei...
Molecular dynamics simulations of glycerol glass-forming liquid
International Nuclear Information System (INIS)
Blieck, J.; Affouard, F.; Bordat, P.; Lerbret, A.; Descamps, M.
2005-01-01
Structural and dynamical properties of liquid glycerol have been investigated by Molecular Dynamics simulations. An improved model based on a slight reparametrisation of the all-atoms AMBER force field used in [R. Chelli, P. Procacci, G. Cardini, R.G.D. Valle, S. Califano, Phys. Chem. Chem. Phys. 1 (1999) 871] is presented. The structure remains satisfactory, qualitatively similar to that obtained from the original model. This new model is also found to reproduce significantly better the diffusion coefficient and the correlations times as they can be deduced from neutron spin echo (NSE) experiments. Structural heterogeneities revealed as a pre-peak of the static structure factor S(Q) close to Q ∼ 0.6 A -1 are observed. Our results are also found compatible with predictions of the Mode Coupling Theory
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.
2013-03-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.
Molecular dynamics simulations of a lithium/sodium carbonate mixture.
Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo
2016-03-01
The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates.
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.; Allen, J.W.; Green, W.H.
2013-01-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
2016-05-01
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.
Charge Carrier Dynamics at Silver Nanocluster-Molecular Acceptor Interfaces
Almansaf, Abdulkhaleq
2017-07-01
A fundamental understanding of interfacial charge transfer at donor-acceptor interfaces is very crucial as it is considered among the most important dynamical processes for optimizing performance in many light harvesting systems, including photovoltaics and photo-catalysis. In general, the photo-generated singlet excitons in photoactive materials exhibit very short lifetimes because of their dipole-allowed spin radiative decay and short diffusion lengths. In contrast, the radiative decay of triplet excitons is dipole forbidden; therefore, their lifetimes are considerably longer. The discussion in this thesis primarily focuses on the relevant parameters that are involved in charge separation (CS), charge transfer (CT), intersystem crossing (ISC) rate, triplet state lifetime, and carrier recombination (CR) at silver nanocluster (NCs) molecular-acceptors interfaces. A combination of steady-state and femto- and nanosecond broadband transient absorption spectroscopies were used to investigate the charge carrier dynamics in various donor-acceptor systems. Additionally, this thesis was prolonged to investigate some important factors that influence the charge carrier dynamics in Ag29 silver NCs donor-acceptor systems, such as the metal doping and chemical structure of the nanocluster and molecular acceptors. Interestingly, clear correlations between the steady-state measurements and timeresolved spectroscopy results are found. In the first study, we have investigated the interfacial charge transfer dynamics in positively charged meso units of 5, 10, 15, 20-tetra (1- methyl-4-pyridino)-porphyrin tetra (p-toluene sulfonate) (TMPyP) and neutral charged 5, 10, 15, 20-tetra (4-pyridyl)-porphyrin (TPyP), with negatively charged undoped and gold (Au)- doped silver Ag29 NCs. Moreover, this study showed the impact of Au doping on the charge carrier dynamics of the system. In the second study, we have investigated the interfacial charge transfer dynamics in [Pt2 Ag23 Cl7 (PPh3
Energy Technology Data Exchange (ETDEWEB)
Saiz, Fernan [Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, London, SW7 2A7 (United Kingdom); Gamero-Castaño, Manuel, E-mail: mgameroc@uci.edu [Department of Mechanical and Aerospace Engineering, University of California, Irvine, California, 92697 (United States)
2016-06-15
The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.
International Nuclear Information System (INIS)
Saiz, Fernan; Gamero-Castaño, Manuel
2016-01-01
The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.
A self-learning algorithm for biased molecular dynamics
Tribello, Gareth A.; Ceriotti, Michele; Parrinello, Michele
2010-01-01
A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences. PMID:20876135
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
Dynamic coherence in excitonic molecular complexes under various excitation conditions
Energy Technology Data Exchange (ETDEWEB)
Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz
2014-08-17
Highlights: • Dynamic coherence does not improve energy transfer efficiency in natural conditions. • Photo-induced quantum jumps are discussed in classical context. • Natural time scale of a light excitation event is identified. • Coherence in FMO complex averages out under excitation by neighboring antenna. • This result is valid even in absence of dissipation. - Abstract: We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity – an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna–Matthews–Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.
Wong, Sun; Del Genio, Anthony; Wang, Tao; Kahn, Brian; Fetzer, Eric J.; L'Ecuyer, Tristan S.
2015-01-01
Goals: Water budget-related dynamical phase space; Connect large-scale dynamical conditions to atmospheric water budget (including precipitation); Connect atmospheric water budget to cloud type distributions.
Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers.
Deng, Xiang; Zhironkina, Oxana A; Cherepanynets, Varvara D; Strelkova, Olga S; Kireev, Igor I; Belmont, Andrew S
2016-09-26
In higher eukaryotic interphase nuclei, the 100- to >1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significant changes in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change in the overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.
Memory effects in nonadiabatic molecular dynamics at metal surfaces
DEFF Research Database (Denmark)
Olsen, Thomas; Schiøtz, Jakob
2010-01-01
We study the effect of temporal correlation in a Langevin equation describing nonadiabatic dynamics at metal surfaces. For a harmonic oscillator, the Langevin equation preserves the quantum dynamics exactly and it is demonstrated that memory effects are needed in order to conserve the ground state...... energy of the oscillator. We then compare the result of Langevin dynamics in a harmonic potential with a perturbative master equation approach and show that the Langevin equation gives a better description in the nonperturbative range of high temperatures and large friction. Unlike the master equation......, this approach is readily extended to anharmonic potentials. Using density functional theory, we calculate representative Langevin trajectories for associative desorption of N-2 from Ru(0001) and find that memory effects lower the dissipation of energy. Finally, we propose an ab initio scheme to calculate...
Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics
International Nuclear Information System (INIS)
White, Alexander J.; Gorshkov, Vyacheslav N.; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry
2014-01-01
Modeling the dynamics of photophysical and (photo)chemical reactions in extended molecular systems is a new frontier for quantum chemistry. Many dynamical phenomena, such as intersystem crossing, non-radiative relaxation, and charge and energy transfer, require a non-adiabatic description which incorporate transitions between electronic states. Additionally, these dynamics are often highly sensitive to quantum coherences and interference effects. Several methods exist to simulate non-adiabatic dynamics; however, they are typically either too expensive to be applied to large molecular systems (10's-100's of atoms), or they are based on ad hoc schemes which may include severe approximations due to inconsistencies in classical and quantum mechanics. We present, in detail, an algorithm based on Monte Carlo sampling of the semiclassical time-dependent wavefunction that involves running simple surface hopping dynamics, followed by a post-processing step which adds little cost. The method requires only a few quantities from quantum chemistry calculations, can systematically be improved, and provides excellent agreement with exact quantum mechanical results. Here we show excellent agreement with exact solutions for scattering results of standard test problems. Additionally, we find that convergence of the wavefunction is controlled by complex valued phase factors, the size of the non-adiabatic coupling region, and the choice of sampling function. These results help in determining the range of applicability of the method, and provide a starting point for further improvement
Sex speeds adaptation by altering the dynamics of molecular evolution.
McDonald, Michael J; Rice, Daniel P; Desai, Michael M
2016-03-10
Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.
Molecular Dynamics Approach in Designing Thermostable Aspergillus niger Xylanase
Malau, N. D.; Sianturi, M.
2017-03-01
Molecular dynamics methods we have applied as a tool in designing thermostable Aspergillus niger Xylanase, by examining Root Mean Square Deviation (RMSD) and The Stability of the Secondary Structure of enzymes structure at its optimum temperature and compare with its high temperature behavior. As RMSD represents structural fluctuation at a particular temperature, a better understanding of this factor will suggest approaches to bioengineer these enzymes to enhance their thermostability. In this work molecular dynamic simulations of Aspergillus niger xylanase (ANX) have been carried at 400K (optimum catalytic temperature) for 2.5 ns and 500K (ANX reported inactive temperature) for 2.5 ns. Analysis have shown that the Root Mean Square Deviation (RMSD) significant increase at higher temperatures compared at optimum temperature and some of the secondary structures of ANX that have been damaged at high temperature. Structural analysis revealed that the fluctuations of the α-helix and β-sheet regions are larger at higher temperatures compared to the fluctuations at optimum temperature.
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing
2012-01-01
The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
Directory of Open Access Journals (Sweden)
Ji-Long Zhang
Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.
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.
Step by step parallel programming method for molecular dynamics code
International Nuclear Information System (INIS)
Orii, Shigeo; Ohta, Toshio
1996-07-01
Parallel programming for a numerical simulation program of molecular dynamics is carried out with a step-by-step programming technique using the two phase method. As a result, within the range of a certain computing parameters, it is found to obtain parallel performance by using the level of parallel programming which decomposes the calculation according to indices of do-loops into each processor on the vector parallel computer VPP500 and the scalar parallel computer Paragon. It is also found that VPP500 shows parallel performance in wider range computing parameters. The reason is that the time cost of the program parts, which can not be reduced by the do-loop level of the parallel programming, can be reduced to the negligible level by the vectorization. After that, the time consuming parts of the program are concentrated on less parts that can be accelerated by the do-loop level of the parallel programming. This report shows the step-by-step parallel programming method and the parallel performance of the molecular dynamics code on VPP500 and Paragon. (author)
The molecular dynamics simulation of ion-induced ripple growth
International Nuclear Information System (INIS)
Suele, P.; Heinig, K.-H.
2009-01-01
The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength (λ) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths (λ 35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in λ long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for λ>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.
Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
Okumura, Hisashi
2008-09-28
Partial multicanonical algorithm is proposed for molecular dynamics and Monte Carlo simulations. The partial multicanonical simulation samples a wide range of a part of the potential-energy terms, which is necessary to sample the conformational space widely, whereas a wide range of total potential energy is sampled in the multicanonical algorithm. Thus, one can concentrate the effort to determine the weight factor only on the important energy terms in the partial multicanonical simulation. The partial multicanonical, multicanonical, and canonical molecular dynamics algorithms were applied to an alanine dipeptide in explicit water solvent. The canonical simulation sampled the states of P(II), C(5), alpha(R), and alpha(P). The multicanonical simulation covered the alpha(L) state as well as these states. The partial multicanonical simulation also sampled the C(7) (ax) state in addition to the states that were sampled by the multicanonical simulation. In the partial multicanonical simulation, furthermore, backbone dihedral angles phi and psi rotated more frequently than those in the multicanonical and canonical simulations. These results mean that the partial multicanonical algorithm has a higher sampling efficiency than the multicanonical and canonical algorithms.
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel
International Nuclear Information System (INIS)
Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.
2011-01-01
This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12σ, 14σ and 16σ and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.
Huge-scale molecular dynamics simulation of multibubble nuclei
Watanabe, Hiroshi
2013-12-01
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.
Zhao, Lei; Cheng, Jiangtao
2017-09-07
In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.
International Nuclear Information System (INIS)
Bhowmik, Rahul; Katti, Kalpana S.; Verma, Devendra; Katti, Dinesh R.
2007-01-01
Polymer-hydroxyapatite (HAP) composites are widely investigated for their potential use as bone replacement materials. The molecular interactions at mineral polymer interface are known to have significant role of mechanical response of the composite system. Modeling interactions between such dissimilar molecules using molecular dynamics (MD) is an area of current interest. Molecular dynamics studies require potential function or force field parameters. Some force fields are described in literature that represents the structure of hydroxyapatite reasonably well. Yet, the applicability of these force fields for studying the interaction between dissimilar materials (such as mineral and polymer) is limited, as there is no accurate representation of polymer in these force fields. We have obtained the parameters of consistent valence force field (CVFF) for monoclinic hydroxyapatite. Validation of parameters was done by comparing the computationally obtained unit cell parameters, vibrational spectra and atomic distances with XRD and FTIR experiments. Using the obtained parameters of HAP, and available parameters of polymer (polyacrylic acid), interaction study was performed with MD simulations. The MD simulations showed that several hydrogen bonds may form between HAP and polyacrylic acid depending upon the exposed surface of HAP. Also there are some favourable planes of HAP where polyacrylic acid is most likely to attach. We have also simulated the mineralization of HAP using a 'synthetic biomineralization'. These modeling studies are supported by photoacoustic spectroscopy experiments on both porous and non porous composite samples for potential joint replacement and bone tissue engineering applications
Dynamics of large rotors on spring supported foundations
Energy Technology Data Exchange (ETDEWEB)
Puttonen, J. [IVO Power Engineering Ltd., Vantaa (Finland)] Luukkanen, P. [Imatran Voima Oy, Vantaa (Finland)
1998-12-31
This article presents some case studies relating to the dynamics of the large machines on spring isolated foundations. The studies comprise both vibration calculations and measurements also introducing the accuracy of numerical methods available in practical engineering. A summary of the pros and cons of spring isolated foundations in power plants is included. The cases described are from the lately built power plants of the IVO-group. The auxiliary feed water pump analysed consists of an electric motor (7 MW), a gear and two pumps. During the trial runs, severe vibrations were observed calling for thorough vibration measurements. The modelling of the whole vibrating entity in the rotating machinery, including the shaft train, oil films of bearings and the foundation is demonstrated by a turbine generator set of 100 MW. Finally, some results of a test comparing the acoustic emission and traditional vibration measurements for recognizing the rub between the shaft and the hydrodynamic bearing are presented. (orig.) 6 refs.
Dynamics of large rotors on spring supported foundations
Energy Technology Data Exchange (ETDEWEB)
Puttonen, J. [IVO Power Engineering Ltd., Vantaa (Finland)] Luukkanen, P. [Imatran Voima Oy, Vantaa (Finland)
1997-12-31
This article presents some case studies relating to the dynamics of the large machines on spring isolated foundations. The studies comprise both vibration calculations and measurements also introducing the accuracy of numerical methods available in practical engineering. A summary of the pros and cons of spring isolated foundations in power plants is included. The cases described are from the lately built power plants of the IVO-group. The auxiliary feed water pump analysed consists of an electric motor (7 MW), a gear and two pumps. During the trial runs, severe vibrations were observed calling for thorough vibration measurements. The modelling of the whole vibrating entity in the rotating machinery, including the shaft train, oil films of bearings and the foundation is demonstrated by a turbine generator set of 100 MW. Finally, some results of a test comparing the acoustic emission and traditional vibration measurements for recognizing the rub between the shaft and the hydrodynamic bearing are presented. (orig.) 6 refs.
Large wood budget and transport dynamics on a large river using radio telemetry
Schenk, Edward R.; Moulin, Bertrand; Hupp, Cliff R.; Richte, Jean M.
2014-01-01
Despite the abundance of large wood (LW) river studies there is still a lack of understanding of LW transport dynamics on large low gradient rivers. This study used 290 radio frequency identification tagged (RFID) LW and 54 metal (aluminum) tagged LW, to quantify the percent of in-channel LW that moves per year and what variables play a role in LW transport dynamics. Aluminum tags were installed and monitored on LW in-transit during the rising limb of a flood, the mean distance traveled by those pieces during the week was 13.3 river kilometers (km) with a maximum distance of 72 km. RFID tagged LW moved a mean of 11.9 km/yr with a maximum observed at 101.1 km/yr. Approximately 41% of LW low on the bank moves per year. The high rate of transport and distance traveled is likely due to the lack of interaction between LW floating in the channel and the channel boundaries, caused primarily by the width of the channel relative to length of the LW. Approximately 80% of the RFID tags moved past a fixed reader during the highest 20% of river stage per year. LW transport and logjam dynamics are complicated at high flows as pieces form temporary jams that continually expand and contract. Unlike most other studies, key members that create a logjam were defined more by stability than jam size or channel/hydrologic conditions. Finally, using an existing geomorphic database for the river, and data from this study, we were able to develop a comprehensive LW budget showing that 5% of the in-channel LW population turns over each year (input from mass wasting and fluvial erosion equals burial, decomposition, and export out of system) and another 16% of the population moving within the system.
Blended particle filters for large-dimensional chaotic dynamical systems
Majda, Andrew J.; Qi, Di; Sapsis, Themistoklis P.
2014-01-01
A major challenge in contemporary data science is the development of statistically accurate particle filters to capture non-Gaussian features in large-dimensional chaotic dynamical systems. Blended particle filters that capture non-Gaussian features in an adaptively evolving low-dimensional subspace through particles interacting with evolving Gaussian statistics on the remaining portion of phase space are introduced here. These blended particle filters are constructed in this paper through a mathematical formalism involving conditional Gaussian mixtures combined with statistically nonlinear forecast models compatible with this structure developed recently with high skill for uncertainty quantification. Stringent test cases for filtering involving the 40-dimensional Lorenz 96 model with a 5-dimensional adaptive subspace for nonlinear blended filtering in various turbulent regimes with at least nine positive Lyapunov exponents are used here. These cases demonstrate the high skill of the blended particle filter algorithms in capturing both highly non-Gaussian dynamical features as well as crucial nonlinear statistics for accurate filtering in extreme filtering regimes with sparse infrequent high-quality observations. The formalism developed here is also useful for multiscale filtering of turbulent systems and a simple application is sketched below. PMID:24825886
Vision-Augmented Molecular Dynamics Simulation of Nanoindentation
Directory of Open Access Journals (Sweden)
Rajab Al-Sayegh
2015-01-01
Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.
Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.
Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei
2018-06-05
The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.
Lattice dynamics of a crystal with a molecular impurity
International Nuclear Information System (INIS)
Sahoo, D.; Venkataraman, G.
1975-01-01
The dynamics of a crystal containing a molecular impurity is discussed with allowance for the effects of internal vibrations of the molecule. Cartesian coordinates are used to describe internal vibrations, angular oscillations and centre of mass translations of the impurity, and the displacement of atoms of the host lattice. Next the Hamiltonian is set up and the equations of motion derived. In this process, use is made of Dirac brackets when dealing with vibrational coordinates (of the molecule) which have redundancy and constraints. A method of solution of the normal modes of the system is indicated by using the defect space matrixpartitioning technique. The special case of a rigid molecular impurity is then discussed along with the relevance of the present formalism in the interpretation of a recent neutron scattering experiment. It is also shown how the results of crystal-field approximation model and those of the molecular model approximation are obtained as further special cases of the present formalism. A comparison of the present work with those of others has been made. (author)
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.
DEFF Research Database (Denmark)
Peters, Günther H.j.; Frimurer, T. M.; Andersen, J. N.
2000-01-01
Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme...... to substrate binding. Based on essential dynamics analysis of the PTP1B/DADEpYL trajectory, it is shown that internal motions in the binding pocket occur in a subspace of only a few degrees of freedom. in particular, relatively large flexibilities are observed along several eigenvectors in the segments: Arg(24...... for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein...
Narimani, Zahra; Beigy, Hamid; Ahmad, Ashar; Masoudi-Nejad, Ali; Fröhlich, Holger
2017-01-01
Inferring the structure of molecular networks from time series protein or gene expression data provides valuable information about the complex biological processes of the cell. Causal network structure inference has been approached using different methods in the past. Most causal network inference techniques, such as Dynamic Bayesian Networks and ordinary differential equations, are limited by their computational complexity and thus make large scale inference infeasible. This is specifically true if a Bayesian framework is applied in order to deal with the unavoidable uncertainty about the correct model. We devise a novel Bayesian network reverse engineering approach using ordinary differential equations with the ability to include non-linearity. Besides modeling arbitrary, possibly combinatorial and time dependent perturbations with unknown targets, one of our main contributions is the use of Expectation Propagation, an algorithm for approximate Bayesian inference over large scale network structures in short computation time. We further explore the possibility of integrating prior knowledge into network inference. We evaluate the proposed model on DREAM4 and DREAM8 data and find it competitive against several state-of-the-art existing network inference methods.
Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben
2017-08-22
A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.
Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions
Gkionis, Konstantinos
2014-07-23
The properties of liquids in a confined environment are known to differ from those in the bulk. Extending this knowledge to geometries defined by two metallic layers in contact with the ends of a carbon nanotube is important for describing a large class of nanodevices that operate in non-aqueous environments. Here we report a series of classical molecular dynamics simulations for gold-electrode junctions in acetone, cyclohexane and N,N-dimethylformamide solutions and analyze the structure and the dynamics of the solvents in different regions of the nanojunction. The presence of the nanotube has little effect on the ordering of the solvents along its axis, while in the transversal direction deviations are observed. Importantly, the orientational dynamics of the solvents at the electrode-nanotube interface differ dramatically from that found when only the electrodes are present.
Energy Technology Data Exchange (ETDEWEB)
Car, R.; Parrinello, M.
1988-01-18
An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.
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
Molecular dynamics simulation of electron trapping in the sapphire lattice
International Nuclear Information System (INIS)
Rambaut, C.; Oh, K.H.; Fayeulle, S.; Kohanoff, J.
1995-10-01
Energy storage and release in dielectric materials can be described on the basis of the charge trapping mechanism. Most phenomenological aspects have been recently rationalized in terms of the space charge mode. Dynamical aspects are studied here by performing Molecular Dynamics simulations. We show that an excess electron introduced into the sapphire lattice (α -Al 2 O 3 ) can be trapped only at a limited number of sites. The energy gained by allowing the electron to localize in these sites is of the order of 4-5 eV, in good agreement with the results of the space charge model. Displacements of the neighboring ions due to the implanted charge are shown to be localized in a small region of about 5 A. Detrapping is observed at 250 K. The ionic displacements turn out to play an important role in modifying the potential landscape by lowering, in a dynamical way, the barriers that cause localization at low temperature. (author). 18 refs, 7 figs, 2 tabs
Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies
Simon, A.; Rapacioli, M.; Rouaut, G.; Trinquier, G.; Gadéa, F. X.
2017-03-01
We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica
2012-10-09
NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.
Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions
Energy Technology Data Exchange (ETDEWEB)
Fattebert, J.-L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Richards, D.F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Glosli, J.N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2012-12-01
We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·10^{6} particles on 65,536 MPI tasks.
The MOLDY short-range molecular dynamics package
Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.
2011-12-01
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as
Dynamic Model Averaging in Large Model Spaces Using Dynamic Occam’s Window*
Onorante, Luca; Raftery, Adrian E.
2015-01-01
Bayesian model averaging has become a widely used approach to accounting for uncertainty about the structural form of the model generating the data. When data arrive sequentially and the generating model can change over time, Dynamic Model Averaging (DMA) extends model averaging to deal with this situation. Often in macroeconomics, however, many candidate explanatory variables are available and the number of possible models becomes too large for DMA to be applied in its original form. We propose a new method for this situation which allows us to perform DMA without considering the whole model space, but using a subset of models and dynamically optimizing the choice of models at each point in time. This yields a dynamic form of Occam’s window. We evaluate the method in the context of the problem of nowcasting GDP in the Euro area. We find that its forecasting performance compares well with that of other methods. PMID:26917859
Dynamic Model Averaging in Large Model Spaces Using Dynamic Occam's Window.
Onorante, Luca; Raftery, Adrian E
2016-01-01
Bayesian model averaging has become a widely used approach to accounting for uncertainty about the structural form of the model generating the data. When data arrive sequentially and the generating model can change over time, Dynamic Model Averaging (DMA) extends model averaging to deal with this situation. Often in macroeconomics, however, many candidate explanatory variables are available and the number of possible models becomes too large for DMA to be applied in its original form. We propose a new method for this situation which allows us to perform DMA without considering the whole model space, but using a subset of models and dynamically optimizing the choice of models at each point in time. This yields a dynamic form of Occam's window. We evaluate the method in the context of the problem of nowcasting GDP in the Euro area. We find that its forecasting performance compares well with that of other methods.
Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.
Yang, Qian; Sing-Long, Carlos A; Reed, Evan J
2017-08-01
We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.
Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.
Yagasaki, Takuma; Saito, Shinji
2009-09-15
Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is
Molecular dynamics of interfacial water and cations associated with clay minerals
International Nuclear Information System (INIS)
Cygan, Randall T.; Greathouse, Jeffery A.; Teich-McGoldrick, Stephanie L.; Nenoff, Tina M.; Daemen, Luke L.
2012-01-01
Document available in extended abstract form only. Clay mineral interfaces, including interlayer and external surfaces, play an essential role in many geochemical processes. Adsorption, dissolution, precipitation, nucleation, and growth mechanisms, in particular, are controlled by the interplay of structure, thermodynamics, kinetics, and transport at clay mineral-water interfaces. Molecular details of these geochemical processes are especially important in evaluating the fate of radionuclide waste in the environment. Such details are typically beyond the sensitivity of experimental and analytical methods and therefore require accurate models and simulations. Also, the basal surfaces and interlayers of clay minerals offer structurally constrained interfacial environments to better evaluate the local molecular chemistry. We have developed and used classical and quantum methods to examine the complex behavior of clay mineral-water interfaces and dynamics of interlayer species. Bulk structures, swelling behavior, diffusion, and adsorption processes are evaluated and compared to experimental and spectroscopic findings. In particular, inelastic neutron scattering methods provide a successful probe of vibrational behavior of interlayer species to help guide the simulations. Librations involving rock, wag, and twist motions of water molecules are particularly sensitive to the interlayer environment of smectite minerals such as montmorillonite and beidellite. Trends in librational modes for interlayer water as a function of clay structure and cation hydration energy are readily explained using structural and vibrational analysis derived from molecular simulation. Molecular dynamics simulations of virtual phases, including hydrated pyrophyllite, help to explain the behavior of interlayer water that is not associated with cation species. Additionally, we use large-scale molecular dynamics simulations of other layered minerals, such as muscovite, to evaluate adsorption
Time-dependent theoretical treatments of the dynamics of electrons and nuclei in molecular systems
International Nuclear Information System (INIS)
Deumens, E.; Diz, A.; Longo, R.; Oehrn, Y.
1994-01-01
An overview is presented of methods for time-dependent treatments of molecules as systems of electrons and nuclei. The theoretical details of these methods are reviewed and contrasted in the light of a recently developed time-dependent method called electron-nuclear dynamics. Electron-nuclear dynamics (END) is a formulation of the complete dynamics of electrons and nuclei of a molecular system that eliminates the necessity of constructing potential-energy surfaces. Because of its general formulation, it encompasses many aspects found in other formulations and can serve as a didactic device for clarifying many of the principles and approximations relevant in time-dependent treatments of molecular systems. The END equations are derived from the time-dependent variational principle applied to a chosen family of efficiently parametrized approximate state vectors. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. The approach leads to a simple formulation of the fully nonlinear time-dependent Hartree-Fock theory including nuclear dynamics. The nonlinear END equations with the ab initio Coulomb Hamiltonian have been implemented at this level of theory in a computer program, ENDyne, and have been shown feasible for the study of small molecular systems. Implementation of the Austin Model 1 semiempirical Hamiltonian is discussed as a route to large molecular systems. The linearized END equations at this level of theory are shown to lead to the random-phase approximation for the coupled system of electrons and nuclei. The qualitative features of the general nonlinear solution are analyzed using the results of the linearized equations as a first approximation. Some specific applications of END are presented, and the comparison with experiment and other theoretical approaches is discussed