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.
Molecular Scale Dynamics of Large Ring Polymers
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.
A large scale molecular dynamics calculation of a lipid bilayer
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Okazaki, Susumu [Tokyo Inst. of Tech. (Japan)
1998-03-01
Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nose-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such a atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2 chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made. (author)
Large Scale Molecular Dynamics Simulations of Homogeneous Nucleation
Tanaka, Kyoko K
2013-01-01
We present results from large-scale molecular dynamics (MD) simulations of homogeneous vapor-to-liquid nucleation. The simulations contain between one and eight billion Lennard-Jones (LJ) atoms, covering up to 1.2 {\\mu}s (56 million time-steps). They cover a wide range of supersaturation ratios, S=1.55 to 10^4, and temperatures from kT = 0.3 to 1.0 {\\epsilon} (where {\\epsilon} is the depth of the LJ potential, and k the Boltzmann constant). We have resolved nucleation rates as low as 10^{17} cm^{-3} s^{-1} (in the argon system), and critical cluster sizes as large as 100 atoms. Recent argon nucleation experiments probe nucleation rates in an overlapping range, making the first direct comparison between laboratory experiments and molecular dynamics simulations possible: We find very good agreement within the uncertainties, which are mainly due to the extrapolations of argon and LJ saturation curves to very low temperatures. The self-consistent, modified classical nucleation model of Girshick and Chiu [J. Chem....
Lightweight computational steering of very large scale molecular dynamics simulations
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Beazley, D.M. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Computer Science; Lomdahl, P.S. [Los Alamos National Lab., NM (United States)
1996-09-01
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.
Large scale molecular dynamics study of polymer-surfactant complex
Goswami, Monojoy; Sumpter, Bobby
2012-02-01
In this work, we study the self-assembly of cationic polyelectrolytes mediated by anionic surfactants in dilute or semi-dilute and gel states. The understanding of the dilute system is a requirement for the understanding of gel states. The importance of polyelectrolyte with oppositely charged colloidal particles can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. With the same understanding, interaction of surfactants with polyelectrolytes shows intriguing phenomena that are important for both in academic research as well as industrial applications. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered ring-string structures that have been observed experimentally in biological systems. We will investigate many different properties of PE-surfactant complexation which will be helpful for pharmaceutical, engineering and biological applications.
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Wang, Z.; Lupo, J.; Patnaik, S.S.; McKenney, A.; Pachter, R.
1999-07-01
The Fast Multipole Method (FMM) offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling more realistic molecular dynamics simulations of large molecular systems. The performance of the fast molecular dynamics (FMD) code, a parallel MD code being developed in the group, using the three-dimensional fast multipole method, shows a good speedup. The application to the full atomic-scale molecular dynamics simulation of a liquid crystalline droplet of 4-n-pentyl-4{prime}-cyanobiphenyl (5CB) molecules, of size 35,872 atoms, shows strong surface effects on various orientational order parameters.
The dynamical complexity of work-hardening: a large-scale molecular dynamics simulation
Institute of Scientific and Technical Information of China (English)
Markus J. Buehler; Alexander Hartmaier; Mark A. Duchaineau; Farid F. Abraham; Huajian Gao
2005-01-01
We analyze a large-scale molecular dynamics simulation of work hardening in a model system of a ductile solid.With tensile loading, we observe emission of thousands of dislocations from two sharp cracks. The dislocations interact in a complex way, revealing three fundamental mechanisms of work-hardening in this ductile material. These are (1) dislocation cutting processes, jog formation and generation of trails of point defects; (2) activation of secondary slip systems by Frank-Read and cross-slip mechanisms; and (3) formation of sessile dislocations such as Lomer-Cottrell locks.We report the discovery of a new class of point defects referred to as trail of partial point defects, which could play an important role in situations when partial dislocations dominate plasticity. Another important result of the present work is the rediscovery of the Fleischer-mechanism of cross-slip of partial dislocations that was theoretically proposed more than 50 years ago, and is now, for the first time, confirmed by atomistic simulation. On the typical time scale of molecular dynamics simulations, the dislocations self-organize into a complex sessile defect topology. Our analysis illustrates numerous mechanisms formerly only conjectured in textbooks and observed indirectly in experiments. It is the first time that such a rich set of fundamental phenomena have been revealed in a single computer simulation, and its dynamical evolution has been studied. The present study exemplifies the simulation and analysis of the complex nonlinear dynamics of a many-particle system during failure using ultra-large scale computing.
Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems
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Miller, William H.
2006-04-27
The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.
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Ladd, A.J.C.
1988-08-01
The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.
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Samela, Juha, E-mail: juha.samela@helsinki.fi [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, FI-00014 University of Helsinki (Finland); Norris, Scott A. [Southern Methodist University, Dallas, TX 75205 (United States); Nordlund, Kai [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, FI-00014 University of Helsinki (Finland); Aziz, Michael J. [School of Engineering and Applied Sciences, Harvard University, 29 Oxford St., Cambridge, MA 02138 (United States)
2011-07-15
A practical method to create optimized amorphous silicon and silica structures for molecular dynamics simulations is developed and tested. The method is based on the Wooten, Winer, and Weaire algorithm and combination of small optimized blocks to larger structures. The method makes possible to perform simulations of either very large cluster hypervelocity impacts on amorphous targets or small displacements induced by low energy ion impacts in silicon.
Bergstra, J.A.; Bethke, I.
2002-01-01
Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model
Stone, John E; McGreevy, Ryan; Isralewitz, Barry; Schulten, Klaus
2014-01-01
Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally-determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithms vis-à-vis existing tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods.
Molecular dynamics simulations of sputtering of organic overlayers by slow, large clusters
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Rzeznik, L.; Czerwinski, B. [Jagiellonian University, Smoluchowski Institute of Physics, ul. Reymonta 4, 30-059 Krakow (Poland); Garrison, B.J.; Winograd, N. [104 Chemistry Building, Department of Chemistry, Pennsylvania State University, University Park, PA 16802 (United States); Postawa, Z. [Jagiellonian University, Smoluchowski Institute of Physics, ul. Reymonta 4, 30-059 Krakow (Poland)], E-mail: zp@castor.if.uj.edu.pl
2008-12-15
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{l_brace}1 1 1{r_brace}, 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{sub 60}, Au{sub 3} and SF{sub 5} at tens of keV energies.
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
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Shimojo, Fuyuki; Hattori, Shinnosuke [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Kunaseth, Manaschai [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); National Nanotechnology Center, Pathumthani 12120 (Thailand); Ohmura, Satoshi [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Department of Physics, Kyoto University, Kyoto 606-8502 (Japan); Shimamura, Kohei [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Fukuoka 819-0395 (Japan)
2014-05-14
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{sup 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
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Schiffmann, Florian; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch [Nanoscale Simulations, Department of Materials, ETH Zürich, Wolfgang-Pauli-Str. 27, CH-8093 Zürich (Switzerland)
2015-06-28
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.
ls1 mardyn: The massively parallel molecular dynamics code for large systems
Niethammer, Christoph; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin
2014-01-01
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales which were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multi-center rigid potential models based on Lennard-Jones sites, point charges and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, e.g. for fluids at interfaces, as well as non-equilibrium molecular dynamics simulation of heat and mass ...
Hou, Z Y; Dong, K J; Tian, Z A; Liu, R S; Wang, Z; Wang, J G
2016-06-29
The effect of the cooling rate on the solidification process of liquid aluminium is studied using a large-scale molecular dynamics method. It is found that there are various types of short-range order (SRO) structures in the liquid, among which the icosahedral (ICO)-like structures are dominant. These SRO structures are in dynamic fluctuation and transform each other. The effect of the cooling rate on the microstructure is very weak at high temperatures and in supercooled liquids, and it appears only below the liquid-solid transition temperature. Fast cooling rates favour the formation of amorphous structures with ICO-like features, while slow cooling rates favour the formation of FCC crystalline structures. Furthermore, FCC and HCP structures can coexist in crystalline structures. It is also found that nanocrystalline aluminium can be achieved at appropriate cooling rates, and its formation mechanism is thoroughly investigated by tracing the evolution of nanoclusters. The arrangement of FCC and HCP atoms in the nanograins displays various twinned structures as observed using visualization analysis, which is different from the layering or phase separation structures observed in the solidification of Lennard-Jones fluids and some metal liquids.
Homogeneous SPC/E water nucleation in large molecular dynamics simulations
Angelil, R; Tanaka, K; Tanaka, H
2015-01-01
We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to $\\sim 4\\cdot 10^6$ molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to $\\sim 10^{19}\\,\\textrm{cm}^{-3}\\textrm{s}^{-1}$, helping close the gap between experimentally measured rates $\\sim 10^{17}\\,\\textrm{cm}^{-3}\\textrm{s}^{-1}$. 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 avera...
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.
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Rudd, R E
2009-02-05
Recent advances in the ability to generate extremes of pressure and temperature in dynamic experiments and to probe the response of materials has motivated the need for special materials optimized for those conditions as well as a need for a much deeper understanding of the behavior of materials subjected to high pressure and/or temperature. Of particular importance is the understanding of rate effects at the extremely high rates encountered in those experiments, especially with the next generation of laser drives such as at the National Ignition Facility. Here we use large-scale molecular dynamics (MD) simulations of the high-rate deformation of nanocrystalline tantalum to investigate the processes associated with plastic deformation for strains up to 100%. We use initial atomic configurations that were produced through simulations of solidification in the work of Streitz et al [Phys. Rev. Lett. 96, (2006) 225701]. These 3D polycrystalline systems have typical grain sizes of 10-20 nm. We also study a rapidly quenched liquid (amorphous solid) tantalum. We apply a constant volume (isochoric), constant temperature (isothermal) shear deformation over a range of strain rates, and compute the resulting stress-strain curves to large strains for both uniaxial and biaxial compression. We study the rate dependence and identify plastic deformation mechanisms. The identification of the mechanisms is facilitated through a novel technique that computes the local grain orientation, returning it as a quaternion for each atom. This analysis technique is robust and fast, and has been used to compute the orientations on the fly during our parallel MD simulations on supercomputers. We find both dislocation and twinning processes are important, and they interact in the weak strain hardening in these extremely fine-grained microstructures.
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Rzeznik, L., E-mail: rzeznik@lippmann.lu [University of Information Technology and Management, Sucharskiego 2, 35-225 Rzeszów (Poland); Postawa, Z. [Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków (Poland)
2014-05-01
Molecular dynamics computer simulations have been used to probe the role of the projectile composition on the emission efficiency and the sample damage. A benzene crystal was bombarded by 15 keV large heterogeneous noble gas clusters containing 2953 atoms. The projectiles used in this study are two-component clusters composed of Ne, Ar, and Kr atoms directed at 0° and 60° relative to the surface normal. It has been found that for normal incidence the total sputtering yield decreases with the projectile mass, whereas for 60° impact angle the yield increases with this quantity. For both 0° and 60° impact angles the observed sputtering yield for heterogeneous clusters cannot be calculated as a sum of sputtering yields obtained for homogeneous projectiles multiplied by the concentration of each component in the multi-component cluster. The difference in deposition scenarios of the primary kinetic energy is shown to be responsible for the observed behavior of the total sputtering yield.
Modeling ramp compression experiments using large-scale molecular dynamics simulation.
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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.
Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles
2004-07-15
Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Molecular dynamics of large systems with quantum corrections for the nuclei
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Gu, Bing; Garashchuk, Sophya, E-mail: garashchuk@sc.edu [Department of Chemistry & Biochemistry, University of South Carolina, Columbia, SC 29208 (United States)
2015-12-31
This paper describes an approximate approach to quantum dynamics based on the quantum trajectory formulation of the Schrödinger equation. The quantum-mechanical effects are incorporated through the quantum potential of the mean-field type, acting on a trajectory ensemble in addition to the classical potential. Efficiency for large systems is achieved by using the quantum corrections for selected degrees of freedom and introduction of empirical friction into the ground-state energy calculations. The classical potential, if needed, can be computed on-the-fly using the Density Functional Tight Binding method of electronic structure merged with the quantum trajectory dynamics code. The approach is practical for a few hundred atoms. Applications include a study of adsorption of quantum hydrogen colliding with the graphene model, C{sub 37}H{sub 15} and a calculation of the ground state of solid {sup 4}He simulated by a cell 180-atoms.
Substructured multibody molecular dynamics.
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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.
Norris, Scott A; Samela, Juha; Bukonte, Laura; Backman, Marie; Djurabekova, Flyura; Nordlund, Kai; Madi, Charbel S; Brenner, Michael P; Aziz, Michael J
2011-01-01
Energetic particle irradiation can cause surface ultra-smoothening, self-organized nanoscale pattern formation or degradation of the structural integrity of nuclear reactor components. A fundamental understanding of the mechanisms governing the selection among these outcomes has been elusive. Here we predict the mechanism governing the transition from pattern formation to flatness using only parameter-free molecular dynamics simulations of single-ion impacts as input into a multiscale analysis, obtaining good agreement with experiment. Our results overturn the paradigm attributing these phenomena to the removal of target atoms via sputter erosion: the mechanism dominating both stability and instability is the impact-induced redistribution of target atoms that are not sputtered away, with erosive effects being essentially irrelevant. We discuss the potential implications for the formation of a mysterious nanoscale topography, leading to surface degradation, of tungsten plasma-facing fusion reactor walls. Consideration of impact-induced redistribution processes may lead to a new design criterion for stability under irradiation.
Vadali, Ramkumar V; Shi, Yan; Kumar, Sameer; Kale, Laxmikant V; Tuckerman, Mark E; Martyna, Glenn J
2004-12-01
Many systems of great importance in material science, chemistry, solid-state physics, and biophysics require forces generated from an electronic structure calculation, as opposed to an empirically derived force law to describe their properties adequately. The use of such forces as input to Newton's equations of motion forms the basis of the ab initio molecular dynamics method, which is able to treat the dynamics of chemical bond-breaking and -forming events. However, a very large number of electronic structure calculations must be performed to compute an ab initio molecular dynamics trajectory, making the efficiency as well as the accuracy of the electronic structure representation critical issues. One efficient and accurate electronic structure method is the generalized gradient approximation to the Kohn-Sham density functional theory implemented using a plane-wave basis set and atomic pseudopotentials. The marriage of the gradient-corrected density functional approach with molecular dynamics, as pioneered by Car and Parrinello (R. Car and M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated to be capable of elucidating the atomic scale structure and dynamics underlying many complex systems at finite temperature. However, despite the relative efficiency of this approach, it has not been possible to obtain parallel scaling of the technique beyond several hundred processors on moderately sized systems using standard approaches. Consequently, the time scales that can be accessed and the degree of phase space sampling are severely limited. To take advantage of next generation computer platforms with thousands of processors such as IBM's BlueGene, a novel scalable parallelization strategy for Car-Parrinello molecular dynamics is developed using the concept of processor virtualization as embodied by the Charm++ parallel programming system. Charm++ allows the diverse elements of a Car-Parrinello molecular dynamics calculation to be interleaved with low
Goldsmith, Paul F; Narayanan, Gopal; Snell, Ronald; Li, Di; Brunt, Chris
2008-01-01
We report the results of a 100 square degree survey of the Taurus Molecular Cloud region in the J = 1-0 transition of 12CO and 13CO. The image of the cloud in each velocity channel includes ~ 3 million Nyquist sampled pixels on a 20" grid. The high sensitivity and large linear dynamic range of the maps in both isotopologues reveal a very complex, highly structured cloud morphology. There are large scale correlated structures evident in 13CO emission having very fine dimensions, including filaments, cavities, and rings. The 12CO emission shows a quite different structure, with particularly complex interfaces between regions of greater and smaller column density defining the boundaries of the largest-scale cloud structures. The axes of the striations seen in the 12CO emission from relatively diffuse gas are aligned with the direction of the magnetic field. Using a column density-dependent model for the CO fractional abundance, we derive the mass of the region mapped to be 24,000 solar masses, a factor of three ...
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.
Energy Technology Data Exchange (ETDEWEB)
Osei-Kuffuor, Daniel [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Fattebert, Jean-Luc [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10^{-4} Ha/Bohr.
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-31
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101,952 atoms on 23,328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10(-4) Ha/Bohr.
Nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Energy Technology Data Exchange (ETDEWEB)
Pask, J E; Sukumar, N; Guney, M; Hu, W
2011-02-28
completely general, applicable to any crystal symmetry and to both metals and insulators alike. We have developed and implemented a full self-consistent Kohn-Sham method, including both total energies and forces for molecular dynamics, and developed a full MPI parallel implementation for large-scale calculations. We have applied the method to the gamut of physical systems, from simple insulating systems with light atoms to complex d- and f-electron systems, requiring large numbers of atomic-orbital enrichments. In every case, the new PU FE method attained the required accuracies with substantially fewer degrees of freedom, typically by an order of magnitude or more, than the current state-of-the-art PW method. Finally, our initial MPI implementation has shown excellent parallel scaling of the most time-critical parts of the code up to 1728 processors, with clear indications of what will be required to achieve comparable scaling for the rest. Having shown that the key remaining disadvantage of real-space methods can in fact be overcome, the work has attracted significant attention: with sixteen invited talks, both domestic and international, so far; two papers published and another in preparation; and three new university and/or national laboratory collaborations, securing external funding to pursue a number of related research directions. Having demonstrated the proof of principle, work now centers on the necessary extensions and optimizations required to bring the prototype method and code delivered here to production applications.
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....
Leimkuhler, Ben; Tuckerman, Mark E
2013-01-01
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case, however, that the interparticle forces drive motion on many time scales, and the efficiency of a calculation is limited by the choice of time step, which must be sufficiently small that the fastest force components are accurately integrated. Multiple time-stepping algorithms partially alleviate this inefficiency by assigning to each time scale an appropriately chosen step-size. However, such approaches are limited by resonance phenomena, wherein motion on the fastest time scales limits the step sizes associated with slower time scales. In atomistic models of biomolecular systems, for example, resonances limit the largest time step to around 5-6 fs. In this paper, we introduce a set of stochastic isokinetic equations of motion that are shown to be rigorously ergodic and that can b...
A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations
Energy Technology Data Exchange (ETDEWEB)
Osei-Kuffuor, Daniel [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Fattebert, Jean-Luc [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2014-01-01
Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N^{3}) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix, based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.
MDplot: Visualise Molecular Dynamics.
Margreitter, Christian; Oostenbrink, Chris
2017-05-10
The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.
Mizumoto, Yoshihiko; Ohtsuki, Yukiyoshi
2011-01-01
Path integral molecular dynamics simulation is used to study the rotational motion of a CO molecule doped in a large para-hydrogen (p-H2) cluster. The quasi-free rotational motion of CO in a p-H2 cluster with a reduced rotational constant is derived from the imaginary-time orientational correlation functions, and is in good agreement with recent experimental observations. We attribute the reduced rotational constant to the low-viscous fluid-like behavior of the host p-H2 cluster.
Directory of Open Access Journals (Sweden)
Giuseppina Raffaini
2016-01-01
Full Text Available Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents.
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
Dynamical Non-Equilibrium Molecular Dynamics
Directory of Open Access Journals (Sweden)
Giovanni Ciccotti
2013-12-01
Full Text Available In this review, we discuss the Dynamical approach to Non-Equilibrium Molecular Dynamics (D-NEMD, which extends stationary NEMD to time-dependent situations, be they responses or relaxations. Based on the original Onsager regression hypothesis, implemented in the nineteen-seventies by Ciccotti, Jacucci and MacDonald, the approach permits one to separate the problem of dynamical evolution from the problem of sampling the initial condition. D-NEMD provides the theoretical framework to compute time-dependent macroscopic dynamical behaviors by averaging on a large sample of non-equilibrium trajectories starting from an ensemble of initial conditions generated from a suitable (equilibrium or non-equilibrium distribution at time zero. We also discuss how to generate a large class of initial distributions. The same approach applies also to the calculation of the rate constants of activated processes. The range of problems treatable by this method is illustrated by discussing applications to a few key hydrodynamic processes (the “classical” flow under shear, the formation of convective cells and the relaxation of an interface between two immiscible liquids.
Scalable molecular dynamics with NAMD.
Phillips, James C; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D; Kalé, Laxmikant; Schulten, Klaus
2005-12-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. (c) 2005 Wiley Periodicals, Inc.
Goldsmith, Paul F.
2008-01-01
Viewgraph topics include: optical image of Taurus; dust extinction in IR has provided a new tool for probing cloud morphology; observations of the gas can contribute critical information on gas temperature, gas column density and distribution, mass, and kinematics; the Taurus molecular cloud complex; average spectra in each mask region; mas 2 data; dealing with mask 1 data; behavior of mask 1 pixels; distribution of CO column densities; conversion to H2 column density; variable CO/H2 ratio with values much less than 10(exp -4) at low N indicated by UV results; histogram of N(H2) distribution; H2 column density distribution in Taurus; cumulative distribution of mass and area; lower CO fractional abundance in mask 0 and 1 regions greatly increases mass determined in the analysis; masses determined with variable X(CO) and including diffuse regions agrees well with the found from L(CO); distribution of young stars as a function of molecular column density; star formation efficiency; star formation rate and gas depletion; and enlarged images of some of the regions with numerous young stars. Additional slides examine the origin of the Taurus molecular cloud, evolution from HI gas, kinematics as a clue to its origin, and its relationship to star formation.
Goldsmith, Paul F.
2008-01-01
Viewgraph topics include: optical image of Taurus; dust extinction in IR has provided a new tool for probing cloud morphology; observations of the gas can contribute critical information on gas temperature, gas column density and distribution, mass, and kinematics; the Taurus molecular cloud complex; average spectra in each mask region; mas 2 data; dealing with mask 1 data; behavior of mask 1 pixels; distribution of CO column densities; conversion to H2 column density; variable CO/H2 ratio with values much less than 10(exp -4) at low N indicated by UV results; histogram of N(H2) distribution; H2 column density distribution in Taurus; cumulative distribution of mass and area; lower CO fractional abundance in mask 0 and 1 regions greatly increases mass determined in the analysis; masses determined with variable X(CO) and including diffuse regions agrees well with the found from L(CO); distribution of young stars as a function of molecular column density; star formation efficiency; star formation rate and gas depletion; and enlarged images of some of the regions with numerous young stars. Additional slides examine the origin of the Taurus molecular cloud, evolution from HI gas, kinematics as a clue to its origin, and its relationship to star formation.
Molecular Dynamics and Protein Function
National Research Council Canada - National Science Library
M. Karplus; J. Kuriyan; Bruce J. Berne
2005-01-01
.... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...
Molecular Dynamics of Lipid Bilayers
1989-08-09
The aim of this work is to study, by molecular dynamics simulations, the properties of lipid bilayers. We have applied the vectorizable, order-N...fast angle-dependent force/potential algorithms to treat angle bending and torsion. Keywords: Molecular dynamics , Lipid bilayers.
Wang, Jinan; Shao, Qiang; Xu, Zhijian; Liu, Yingtao; Yang, Zhuo; Cossins, Benjamin P; Jiang, Hualiang; Chen, Kaixian; Shi, Jiye; Zhu, Weiliang
2014-01-09
Large-scale conformational changes of proteins are usually associated with the binding of ligands. Because the conformational changes are often related to the biological functions of proteins, understanding the molecular mechanisms of these motions and the effects of ligand binding becomes very necessary. In the present study, we use the combination of normal-mode analysis and umbrella sampling molecular dynamics simulation to delineate the atomically detailed conformational transition pathways and the associated free-energy landscapes for three well-known protein systems, viz., adenylate kinase (AdK), calmodulin (CaM), and p38α kinase in the absence and presence of respective ligands. For each protein under study, the transient conformations along the conformational transition pathway and thermodynamic observables are in agreement with experimentally and computationally determined ones. The calculated free-energy profiles reveal that AdK and CaM are intrinsically flexible in structures without obvious energy barrier, and their ligand binding shifts the equilibrium from the ligand-free to ligand-bound conformation (population shift mechanism). In contrast, the ligand binding to p38α leads to a large change in free-energy barrier (ΔΔG ≈ 7 kcal/mol), promoting the transition from DFG-in to DFG-out conformation (induced fit mechanism). Moreover, the effect of the protonation of D168 on the conformational change of p38α is also studied, which reduces the free-energy difference between the two functional states of p38α and thus further facilitates the conformational interconversion. Therefore, the present study suggests that the detailed mechanism of ligand binding and the associated conformational transition is not uniform for all kinds of proteins but correlated to their respective biological functions.
Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto
Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.
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
Molecular dynamics of silicon indentation
Energy Technology Data Exchange (ETDEWEB)
Kallman, J.S.; Hoover, W.G.; Hoover, C.G.; De Groot, A.J.; Lee, S.M.; Wooten, F. (Department of Applied Science Davis-Livermore, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States))
1993-04-01
We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.
Molecular modelling and molecular dynamics of CFTR.
Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul
2017-01-01
The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.
Multiscale Reactive Molecular Dynamics
2012-08-15
as a linear combination of several possible bond- ing topologies ( diabatic states) that are coupled to one an- other through the off-diagonal elements...adapts and dynamically identifies bonding topolo- gies to include as the simulation progresses. These bonding topologies form a basis of diabatic ...the original geometric factor. The diabatic correction term, VCORR , used here was labeled in previous MS-EVB models as a repulsive interaction, VREP
State-Dependent Molecular Dynamics
Directory of Open Access Journals (Sweden)
Ciann-Dong Yang
2014-10-01
Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
Molecular dynamics simulation of pyridine
Trumpakaj, Zygmunt; Linde, Bogumił
2015-04-01
Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.
Dynamic molecular graphs: "hopping" structures.
Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María
2014-05-05
This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Molecular dynamics simulation of diffusivity
Institute of Scientific and Technical Information of China (English)
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Optical dynamics of molecular aggregates
de Boer, Steven
2006-01-01
The subject of this thesis is the spectroscopy and dynamics of molecular aggregates in amorphous matrices. Aggregates of three different molecules were studied. The molecules are depicted in Fig. (1.1). Supersaturated solutions of these molecules show aggregate formation. Aggregation is a process si
Grand canonical Molecular Dynamics Simulations
Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K
2011-01-01
For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.
From Molecular Dynamics to Brownian Dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
Available Instruments for Analyzing Molecular Dynamics Trajectories.
Likhachev, I V; Balabaev, N K; Galzitskaya, O V
2016-01-01
Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed.
Molecular Dynamics for Dense Matter
Maruyama, Toshiki; Chiba, Satoshi
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the 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 on 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 the 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 increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...
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.
Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-01-01
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and
Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-01-01
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and
Rheology via nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
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.
Molecular dynamics simulations of classical stopping power.
Grabowski, Paul E; Surh, Michael P; Richards, David F; Graziani, Frank R; Murillo, Michael S
2013-11-22
Molecular dynamics can provide very accurate tests of classical kinetic theory; for example, unambiguous comparisons can be made for classical particles interacting via a repulsive 1/r potential. The plasma stopping power problem, of great interest in its own right, provides an especially stringent test of a velocity-dependent transport property. We have performed large-scale (~10(4)-10(6) particles) molecular dynamics simulations of charged-particle stopping in a classical electron gas that span the weak to moderately strong intratarget coupling regimes. Projectile-target coupling is varied with projectile charge and velocity. Comparisons are made with disparate kinetic theories (both Boltzmann and Lenard-Balescu classes) and fully convergent theories to establish regimes of validity. We extend these various stopping models to improve agreement with the MD data and provide a useful fit to our results.
Better, Cheaper, Faster Molecular Dynamics
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
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.
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.
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
Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng
2016-01-14
To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Application of optimal prediction to molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Barber, IV, John Letherman [Univ. of California, Berkeley, CA (United States)
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is δ-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
Monoamine transporters: Insights from molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Julie eGrouleff
2015-10-01
Full Text Available The human monoamine transporters facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia and Parkinson’s disease. Inhibition of the monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the monoamine transporters, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.
Monoamine transporters: insights from molecular dynamics simulations
Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit
2015-01-01
The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185
Molecular crowding and protein enzymatic dynamics.
Echeverria, Carlos; Kapral, Raymond
2012-05-21
The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding.
Molecular Dynamics Simulations of Interface Failure
Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.
2007-03-01
The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.
Molecular Dynamics and Picosecond Vibrational Spectra.
1980-07-01
and Identify by block number) molecular dynamics picosecond infra-red spectra crmputer simulation vibrational spectra array processor linear rcsponse...that for molecular dynamics theoretical computation is now long enough, to significantly overlap. This overlap of theory and experiment can, at least...to discover these microscopic atomic trajectories, i.e. the molecular dynamics of solution processes, we must be able to both theoretically compute
Molecular Dynamics in the Vacuum Ultraviolet
1989-01-30
CLASSIFICATION OF THIS PAGE COMPLETED PROJECT SUMMARY TITLE: Molecular dynamics in the Vacuum Ultraviolet PRINCIPAL INVESTIGATOR: Paul L. Houston...DTIC TAB 0 Unannounced 0 By Distr ibution I Availability Codes Avail and I or Dist Special I Molecular Dynamics In the Vacuum Ultraviolet Final Technical...Further development of tunable vacuum ultraviolet sources has opened wide areas of molecular dynamics for study. Completed Research Photodissociation of
Molecular dynamics simulation of benzene
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Brownian motion from molecular dynamics
Shin, Hyun Kyung; Talkner, Peter; Lee, Eok Kyun
2010-01-01
Brownian motion of single particles with various masses M and diameters D is studied by molecular dynamics simulations. Besides the momentum auto-correlation function of the Brownian particle the memory function and the fluctuating force which enter the generalized Langevin equation of the Brownian particle are determined and their dependence on mass and diameter are investigated for two different fluid densities. Deviations of the fluctuating force distribution from a Gaussian form are observed for small particle diameters. For heavy particles the deviations of the fluctuating force from the total force acting on the Brownian particle decrease linearly with the mass ratio m/M where m denotes the mass of a fluid particle.
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 of membrane proteins.
Energy Technology Data Exchange (ETDEWEB)
Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); Crozier, Paul Stewart; Stevens, Mark Jackson
2004-10-01
Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.
Programming an Interpreter Using Molecular Dynamics
Directory of Open Access Journals (Sweden)
C.A. Middelburg
2007-01-01
Full Text Available PGA (ProGram Algebra is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.
Molecular dynamics in high electric fields
Apostol, M.; Cune, L. C.
2016-06-01
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.
Programming an interpreter using molecular dynamics
2008-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primari...
Programming an Interpreter Using Molecular Dynamics
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily...
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.
Very Large System Dynamics Models - Lessons Learned
Energy Technology Data Exchange (ETDEWEB)
Jacob J. Jacobson; Leonard Malczynski
2008-10-01
This paper provides lessons learned from developing several large system dynamics (SD) models. System dynamics modeling practice emphasize the need to keep models small so that they are manageable and understandable. This practice is generally reasonable and prudent; however, there are times that large SD models are necessary. This paper outlines two large SD projects that were done at two Department of Energy National Laboratories, the Idaho National Laboratory and Sandia National Laboratories. This paper summarizes the models and then discusses some of the valuable lessons learned during these two modeling efforts.
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...
De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe
2014-12-09
A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.
Molecular Dynamics Simulations of Hypervelocity Impacts
Owens, Eli T.; Bachlechner, Martina E.
2007-03-01
Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.
Nanodrop contact angles from molecular dynamics simulations
Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim
2016-11-01
The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.
Trust dynamics in a large system implementation
DEFF Research Database (Denmark)
Schlichter, Bjarne Rerup; Rose, Jeremy
2013-01-01
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...... 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...... to vary in large-scale implementations (which can take several years), and cannot be taken for granted. Previous studies have largely focused on the taxonomic deconstruction of the trust construct, through point-in-time variance studies. They have identified the relationship between trust and project...
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
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Modeling the Hydrogen Bond within Molecular Dynamics
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
ELASTIC: A Large Scale Dynamic Tuning Environment
Directory of Open Access Journals (Sweden)
Andrea Martínez
2014-01-01
Full Text Available The spectacular growth in the number of cores in current supercomputers poses design challenges for the development of performance analysis and tuning tools. To be effective, such analysis and tuning tools must be scalable and be able to manage the dynamic behaviour of parallel applications. In this work, we present ELASTIC, an environment for dynamic tuning of large-scale parallel applications. To be scalable, the architecture of ELASTIC takes the form of a hierarchical tuning network of nodes that perform a distributed analysis and tuning process. Moreover, the tuning network topology can be configured to adapt itself to the size of the parallel application. To guide the dynamic tuning process, ELASTIC supports a plugin architecture. These plugins, called ELASTIC packages, allow the integration of different tuning strategies into ELASTIC. We also present experimental tests conducted using ELASTIC, showing its effectiveness to improve the performance of large-scale parallel applications.
Molecular dynamics studies of entangled polymer chains
Bulacu, Monica Iulia
2008-01-01
The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a
A thread calculus with molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2010-01-01
We present a theory of threads, interleaving of threads, and interaction between threads and services with features of molecular dynamics, a model of computation that bears on computations in which dynamic data structures are involved. Threads can interact with services of which the states consist o
Programming an interpreter using molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programmi
Programming an interpreter using molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the
Modeling hybrid perovskites by molecular dynamics.
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Modeling hybrid perovskites by molecular dynamics
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Molecular Dynamics Studies of Matrix Metalloproteases.
Díaz, Natalia; Suárez, Dimas
2017-01-01
Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.
Dynamic molecular crystals with switchable physical properties.
Sato, Osamu
2016-06-21
The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials.
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...
Enhanced sampling techniques in molecular dynamics simulations of biological systems.
Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus
2015-05-01
Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.
Random Matrix Theory in molecular dynamics analysis.
Palese, Luigi Leonardo
2015-01-01
It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes.
Exciton dynamics in molecular aggregates
Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A
2006-01-01
The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the characteri
Exciton dynamics in molecular aggregates
Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A
2006-01-01
The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the
Liouville-von Neumann molecular dynamics
Jakowski, Jacek; Morokuma, Keiji
2009-06-01
We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.
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...
Visualizing global properties of a molecular dynamics trajectory.
Zhou, Hao; Li, Shangyang; Makowski, Lee
2016-01-01
Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule.
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
Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers
2017-01-01
Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition
Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-02-21
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular
Molecular dynamics model of dimethyl ether
Energy Technology Data Exchange (ETDEWEB)
Lin, B.; Halley, W.J. [Univ. of Minnesota, Minneapolis, MN (United States)
1995-11-02
We report a molecular dynamics model of the monomeric liquid dimethyl ether. The united atom approach is used to treat CH{sub 3} groups as point source centers. Partial charges are derived from the experimental dipole moment. Harmonic force constants are used for intramolecular interactions, and their values are so chosen that the model`s fundamental frequencies agree with experimental results. Because we are interested in solvation properties, the model contains flexible molecules, allowing molecular distortion and internal dynamical quantities. We report radial distribution functions and the static structure factors as well as some dynamical quantities such as the dynamical structure factor, infrared absorption, and Raman scattering spectra. Calculated results agree reasonably well with experimental and other simulation results. 25 refs., 8 figs., 1 tab.
Molecular dynamic simulations of ocular tablet dissolution.
Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire
2013-11-25
Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies.
Neutron Star Crust and Molecular Dynamics Simulation
Horowitz, C J; Schneider, A; Berry, D K
2011-01-01
In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.
Quantum molecular dynamics simulations of dense matter
Energy Technology Data Exchange (ETDEWEB)
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
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.)
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.
Molecular dynamics modeling of structural battery components
Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.
2015-01-01
A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion compo
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
Molecular Exchange Dynamics in Block Copolymer Micelles
Bates, Frank; Lu, Jie; Choi, Soohyung; Lodge, Timothy
2012-02-01
Poly(styrene-b-ethylene propylene) (PS-PEP) diblock copolymers were mixed with squalane (C30H62) at 1% by weight resulting in the formation of spherical micelles. The structure and dynamics of molecular exchange were characterized by synchrotron small-angle x-ray scattering (SAXS) and time resolved small-angle neutron scattering (TR-SANS), respectively, between 100 C and 160 C. TR-SANS measurements were performed with solutions initially containing deuterium labeled micelle cores and normal cores dispersed in a contrast matched squalane. Monitoring the reduction in scattering intensity as a function of time at various temperatures revealed molecular exchange dynamics highly sensitive to the core molecular weight and molecular weight distribution. Time-temperature superposition of data acquired at different temperatures produced a single master curve for all the mixtures. Experiments conducted with isotopically labeled micelle cores, each formed from two different but relatively mondisperse PS blocks, confirmed a simple dynamical model based on first order kinetics and core Rouse single chain relaxation. These findings demonstrate a dramatic transition to nonergodicity with increasing micelle core molecular weight and confirm the origins of the logarithmic exchange kinetics in such systems.
Dynamical Decompactification and Three Large Dimensions
Greene, Brian; Marnerides, Stefanos
2009-01-01
We study string gas dynamics in the early universe and seek to realize the Brandenberger-Vafa mechanism - a goal that has eluded earlier works - that singles out three or fewer spatial dimensions as the number which grow large cosmologically. To this end, we consider a dilute gas of strings on a large torus, so that strings typically interact at significant impact parameters. A strong exponential suppression in the interaction rates for d>3 spatial dimensions reflects the classical argument that string worldsheets generically only intersect in four or fewer spacetime dimensions. As a consequence of this suppression, a scan over initial conditions establishes that in the dilute regime decompactification of d=3 spatial dimensions is favored over d>3.
Multiscale coupling of molecular dynamics and peridynamics
Tong, Qi; Li, Shaofan
2016-10-01
We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.
MDMovie: a molecular dynamics viewing tool.
Greenberg, J P
1996-10-01
The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.
Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori
2009-10-01
We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.
Dynamics and Thermodynamics of Molecular Machines
DEFF Research Database (Denmark)
Golubeva, Natalia
2014-01-01
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...... 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...... of the important trade-off between power output and efficiency. Steric motor-motor interactions are shown to play an important thermodynamic role by enhancing the EMP as compared to the noninteracting case. Remarkably, the enhancement occurs at biologically relevant parameters. Finally, a generic model of motor...
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.
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A
2012-12-11
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.
Ice Formation on Kaolinite: Insights from Molecular Dynamics Simulations
Sosso, Gabriele C; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos
2016-01-01
The formation of ice affects many aspects of our everyday life as well as technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even via state-of-the-art experimental techniques. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long timescales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaol...
Dynamic assembly of molecularly imprinted polymer nanoparticles.
Gong, Haiyue; Hajizadeh, Solmaz; Jiang, Lingdong; Ma, Huiting; Ye, Lei
2017-09-11
Manipulation of specific binding and recycling of materials are two important aspects for practical applications of molecularly imprinted polymers. In this work, we developed a new approach to control the dynamic assembly of molecularly imprinted nanoparticles by surface functionalization. Molecularly imprinted polymer nanoparticles with a well-controlled core-shell structure were synthesized using precipitation polymerization. The specific binding sites were created in the core during the first step imprinting reaction. In the second polymerization step, epoxide groups were introduced into the particle shell to act asan intermediate linker to immobilize phenylboronic acids, as well as to introduce cis-diol structures on surface. The imprinted polymer nanoparticles modified with boronic acid and cis-diol structures maintained high molecular binding specificity, and the nanoparticles could be induced to form dynamic particle aggregation that responded to pH variation and chemical stimuli. The possibility of modulating molecular binding and nanoparticle assembly in a mutually independent fashion can be exploited in a number of applications where repeated use of precious nanoparticles is needed. Copyright © 2017 Elsevier Inc. All rights reserved.
Large-scale dynamics of magnetic helicity
Linkmann, Moritz; Dallas, Vassilios
2016-11-01
In this paper we investigate the dynamics of magnetic helicity in magnetohydrodynamic (MHD) turbulent flows focusing at scales larger than the forcing scale. Our results show a nonlocal inverse cascade of magnetic helicity, which occurs directly from the forcing scale into the largest scales of the magnetic field. We also observe that no magnetic helicity and no energy is transferred to an intermediate range of scales sufficiently smaller than the container size and larger than the forcing scale. Thus, the statistical properties of this range of scales, which increases with scale separation, is shown to be described to a large extent by the zero flux solutions of the absolute statistical equilibrium theory exhibited by the truncated ideal MHD equations.
Institute of Scientific and Technical Information of China (English)
蔡文生; Christophe Chipot
2013-01-01
The main thrust of this contribution is to review applications of numerical simulations to biological systems over the past 35 years-specifically classical molecular-dynamics simulations and related preferential sampling approaches aimed at exploring selected degrees of freedom of the molecular assembly. Arguably enough, structural biology and biophysics represent one of the greatest challenges for molecular dynamics, owing to the size of the biological objects of interest and the time scales spanned by the molecular processes of the cell machinery in which these objects are prominent actors. The reader is assumed to be fully familiarized with the basic theoretical underpinnings of molecular-dynamics simulations, which will be discussed here from a biological standpoint, emphasizing how the enterprise of modeling increasingly larger molecular assemblies over physiologically relevant times has shaped the field. This review article will further show how the unbridled race to dilate both the spatial and the temporal scales, in an effort to bridge the gap between the latter, has greatly benefitted from groundbreaking advances on the hardware, computational front-notably through the development of massively parallel and dedicated architectures, as well as on the methodological, algorithmic front. The current trends in this research field, boosted by recent, cutting-edge achievements, wherein molecular dynamics has reached new frontiers, provide the basis for an introspective reflection and a prospective outlook into the future of biologically-oriented, high-performance numerical simulations. Furthermore, alternatives to brute-force molecular dynamics towards connecting time and size scales will be discussed, in particular a class of approaches relying upon the preferential sampling of judiciously chosen, important degrees of freedom of the biological object at hand. These methods, targeted primarily at providing a detailed thermodynamic picture of the molecular process
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Directory of Open Access Journals (Sweden)
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
Open quantum system parameters from molecular dynamics
Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander
2015-01-01
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...
Characterization of Rare Events in Molecular Dynamics
Directory of Open Access Journals (Sweden)
Carsten Hartmann
2013-12-01
Full Text Available A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.
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...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...
Clustering molecular dynamics trajectories for optimizing docking experiments.
De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C
2015-01-01
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.
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.
Study of Nanowires Using Molecular Dynamics Simulations
Monk, Joshua D
2007-01-01
In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...
Molecular dynamics modelling of solidification in metals
Energy Technology Data Exchange (ETDEWEB)
Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)
1997-12-31
Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.
Bead-Fourier path integral molecular dynamics
Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto
2003-06-01
Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.
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...
Control-volume representation of molecular dynamics.
Smith, E R; Heyes, D M; Dini, D; Zaki, T A
2012-05-01
A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑ(i) for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [Todd et al., Phys. Rev. E 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.
Learning generative models of molecular dynamics.
Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J
2012-01-01
We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 regularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories.
Non-Maxwellian Molecular Velocity Distribution at Large Knudsen Numbers
Shim, Jae Wan
2012-01-01
We have derived a non-Maxwellian molecular velocity distribution at large Knudsen numbers for ideal gas. This distribution approaches Maxwellian molecular velocity distribution as the Knudsen number approaches zero. We have found that the expectation value of the square of velocity is the same in the non-Maxwellian molecular velocity distribution as it is in the Maxwellian distribution; however, the expectation value of the speed is not the same.
Dynamic Maintenance and Visualization of Molecular Surfaces
Energy Technology Data Exchange (ETDEWEB)
Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N
2004-12-16
Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.
Molecular dynamics simulations of magnetized dusty plasmas
Piel, Alexander; Reichstein, Torben; Wilms, Jochen
2012-10-01
The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
Energy Technology Data Exchange (ETDEWEB)
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-03-14
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.
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
WANG; Hui(
2001-01-01
［1］Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.［2］Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.［3］Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.［4］Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.［5］Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.［6］Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.［7］Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.［8］Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.［9］Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.［10］Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.［11］Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.［12］Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.［13］Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Large scale dynamics of protoplanetary discs
BÃ©thune, 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
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.
Molecular dynamics studies of aromatic hydrocarbon liquids
Energy Technology Data Exchange (ETDEWEB)
McLaughlin, E.; Gupta, S.
1990-01-01
This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules.
Attosecond VUV Coherent Control of Molecular Dynamics
Ranitovic, P; Riviere, P; Palacios, A; Tong, X M; Toshima, N; Gonzalez-Castrillo, A; Martin, L; Martin, F; Murnane, M M; Kapteyn, H C
2014-01-01
High harmonic light sources make it possible to access attosecond time-scales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized. This is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep ultraviolet, which have not yet been synthesized. Here, we present a novel approach using attosecond vacuum ultraviolet pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly-ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipula...
Molecular Dynamics Studies of Nanofluidic Devices
DEFF Research Database (Denmark)
Zambrano Rodriguez, Harvey Alexander
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...... in transport caused by the walls become more dominant and the fluid consists of fewer molecules. Carbon nanotubes are tubular graphite molecules which can be imagined to function as nanoscale pipes or conduits. Another important material for nanofluidics applications is silica. Nowadays, silica nanochannels...... 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...
Arntsen, Christopher; Chen, Chen; Voth, Gregory A.
2017-09-01
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.
[Oligoglycine surface structures: molecular dynamics simulation].
Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V
2010-01-01
The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.
Implementing peridynamics within a molecular dynamics code.
Energy Technology Data Exchange (ETDEWEB)
Lehoucq, Richard B.; Silling, Stewart Andrew; Plimpton, Steven James; Parks, Michael L.
2007-12-01
Peridynamics (PD) is a continuum theory that employs a nonlocal model to describe material properties. In this context, nonlocal means that continuum points separated by a finite distance may exert force upon each other. A meshless method results when PD is discretized with material behavior approximated as a collection of interacting particles. This paper describes how PD can be implemented within a molecular dynamics (MD) framework, and provides details of an efficient implementation. This adds a computational mechanics capability to an MD code, enabling simulations at mesoscopic or even macroscopic length and time scales.
Exchange frequency in replica exchange molecular dynamics
Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.
2008-01-01
The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.
Extension of Isospin Dependent Quantum Molecular Dynamics
Institute of Scientific and Technical Information of China (English)
FengZhaoqing; ZhangFengshou; LiWenfei; JinGenming
2003-01-01
Isospin dependent molecular dynamics (IQMD) has been used with success for studying isospin effects in heavy ion collisions at intermediate energies[1,2]. However, this model meets difficulty to study heavy ion collisions at low energies near Coulomb barrier since unsuitable dealing with the deformation, such as surface term induced by deformation during approaching projectile and target, which is not important at high energies, and it results in the calculated cross sections with IQMD which are much smaller than the experimental data at low energies. In this report, we propose a new method in which the surface term in the mean field is included in a proper way, the switch function method.
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.
Charge transport network dynamics in molecular aggregates
Energy Technology Data Exchange (ETDEWEB)
Jackson, Nicholas E. [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry; Chen, Lin X. [Argonne National Lab. (ANL), Argonne, IL (United States). Chemical Science and Engineering Division; Ratner, Mark A. [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry
2016-07-20
Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ~100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed.
Molecular-dynamics simulation of two-dimensional thermophoresis
Paredes; Idler; Hasmy; Castells; Botet
2000-11-01
A numerical technique is presented for the thermal force exerted on a solid particle by a gaseous medium between two flat plates at different temperatures, in the free molecular or transition flow. This is a two-dimensional molecular-dynamics simulation of hard disks in a inhomogeneous thermal environment. All steady-state features exhibited by the compressible hard-disk gas are shown to be consistent with the expected behaviors. Moreover the thermal force experienced by a large solid disk is investigated, and compared to the analytical case of cylinders moving perpendicularly to the constant temperature gradient for an infinite Knudsen number and in an infinite medium. We show precise examples of how this technique can be used simply to investigate more difficult practical problems, in particluar the influence of nonlinear gradients for large applied differences of temperature, of proximity of the walls, and of smaller Knudsen numbers.
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).
Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow
Archereau, Aurelien Y M; Willmott, Geoff R
2016-01-01
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; 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 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 (GLE), which can be rigorously derived by means of a linear projection (LP) 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 most 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. Importa...
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations
Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.
2016-10-01
SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
Accelerated molecular dynamics simulations of protein folding.
Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew
2015-07-30
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.
Coarse-grained protein molecular dynamics simulations
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Ito, Hiroaki; Shimokawa, Naofumi
2016-01-01
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the p...
Concise NMR approach for molecular dynamics characterizations in organic solids.
Aliev, Abil E; Courtier-Murias, Denis
2013-08-22
Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics.
Dynamic Wetting on Graphene-Coated Surface: Molecular Dynamics Investigation
Hung, Shih-Wei; Shiomi, Junichiro
2015-11-01
Wettability of graphene-coated surface gained significant attention recently due to discussion on the ``transparency'' (whether the wetting characteristics follow that of graphene or the underlying surface) and practical applications of graphene. In terms of static contact angle, the wettability of graphene-coated surfaces have been widely studied by experiments, simulations, and theory in recent years. However, the studies of dynamic wetting on graphene-coated surfaces are limited. In the present study, molecular dynamics simulation was performed to study the dynamic wetting of water droplet on graphene-coated surfaces from a microscopic point of view. The results show that the degree of similarity between the spreading behavior on graphene-coated surface and that on pure graphene (or that on the underlying surface) depends on time, i.e. how nonequilibrium the interface dynamics is. We also found that this feature can be altered by introducing defects into graphene. The work is partially supported by Grant-in-Aid for JSPS Fellows 26-04364 and JST CREST.
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
Midfrequency band dynamics of large space structures
Coppolino, Robert N.; Adams, Douglas S.; Levine, Marie B.
2004-09-01
High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.
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.
A new formalism for molecular dynamics in internal coordinates
Lee, Sang-Ho; Palmo, Kim; Krimm, Samuel
2001-03-01
Internal coordinate molecular dynamics (ICMD) has been used in the past in simulations for large molecules as an alternative way of increasing step size with a reduced operational dimension that is not achievable by MD in Cartesian coordinates. A new ICMD formalism for flexible molecular systems is presented, which is based on the spectroscopic B-matrix rather than the A-matrix of previous methods. The proposed formalism does not require an inversion of a large matrix as in the recursive formulations based on robot dynamics, and takes advantage of the sparsity of the B-matrix, ensuring computational efficiency for flexible molecules. Each molecule's external rotations about an arbitrary atom center, which may differ from its center of mass, are parameterized by the SU(2) Euler representation, giving singularity free parameterization. Although the formalism is based on the use of nonredundant generalized (internal and external) coordinates, an MD simulation in linearly dependent coordinates can be done by finding a transformation to a new set of independent coordinates. Based on the clear separability in the generalized coordinates between fast varying degrees of freedom and slowly varying ones, a multiple time step algorithm is introduced that avoids the previous nontrivial interaction distance classification. Also presented is a recursive method for computing nonzero A-matrix elements that is much easier to apply to a general molecular structure than the previous method.
Trust Dynamics in a Large System Implementation
DEFF Research Database (Denmark)
Schlichter, Bjarne Rerup; Rose, Jeremy
2013-01-01
A large information systems implementation (such as ERP systems) relies on the trust of its stakeholders to suc-ceed. Such projects impact diverse groups of stakeholders, each with their legitimate interests and expectations. Levels of stakeholder trust can be expected to vary in large scale impl...... and restoration of trust, the role of the information system in restoring trust, and the emergent and reciprocal nature of trust and project outcomes......A large information systems implementation (such as ERP systems) relies on the trust of its stakeholders to suc-ceed. Such projects impact diverse groups of stakeholders, each with their legitimate interests and expectations. Levels of stakeholder trust can be expected to vary in large scale...... implementations (which can take several years), and cannot be taken for granted. Previous studies have largely focused on the taxonomic deconstruction of the trust construct, through point-in-time variance studies. They have identified the relationship between trust and project outcomes, but largely ignored...
Energy Technology Data Exchange (ETDEWEB)
Lahmam-Bennani, A; Naja, A; Staicu Casagrande, E M; Okumus, N [Laboratoire des Collisions Atomiques et Moleculaires (LCAM), Universite Paris-Sud 11, Bat. 351, 91405 Orsay Cedex (France); Dal Cappello, C [Laboratoire de Physique Moleculaire et des Collisions, Institut de Physique, ICPMB (FR 2843), Universite Paul Verlaine-Metz, 1 rue Arago, 57078 Metz Cedex 3 (France); Charpentier, I [Laboratoire de Physique et Mecanique des Materiaux (UMR 7554), Universite Paul Verlaine-Metz, Ile du Saulcy, 57045 Metz Cedex 1 (France); Houamer, S [Laboratoire de Physique Quantique et Systemes Dynamiques, Universite Ferhat Abbas, Setif (Algeria)
2009-08-28
The triply differential cross section has been measured for electron-impact ionization of the outer valence 1t{sub 2} and the inner valence 2a{sub 1} orbitals of methane using the (e,2e) technique with coplanar asymmetric kinematics. The measurements are performed at scattered electron energy of 500 eV, ejected electron energy of 12, 37 and 74 eV and for scattering angle of the fast outgoing electron of 6 deg. This kinematics is characterized by a target ion recoil momentum ranging from moderate (0.25 au) to very large (3.2 au) values. The results are compared with theoretical cross sections calculated using the 1CW and the BBK models recently extended to molecules. The experimental cross sections exhibit a very large recoil scattering, especially for the inner 2a{sub 1} molecular orbital, which is not predicted by the theory. The differences between experiment and theory are attributed to the very strong scattering from the ion, not properly accounted for by theory. This indicates the need for further theoretical developments as well as experimental investigations in order to correctly model the process of molecular ionization.
Molecular Dynamics Simulations of Network Glasses
Drabold, David A.
The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References
Osmosis : a molecular dynamics computer simulation study
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Acceleration of dynamic fluorescence molecular tomography with principal component analysis.
Zhang, Guanglei; He, Wei; Pu, Huangsheng; Liu, Fei; Chen, Maomao; Bai, Jing; Luo, Jianwen
2015-06-01
Dynamic fluorescence molecular tomography (FMT) is an attractive imaging technique for three-dimensionally resolving the metabolic process of fluorescent biomarkers in small animal. When combined with compartmental modeling, dynamic FMT can be used to obtain parametric images which can provide quantitative pharmacokinetic information for drug development and metabolic research. However, the computational burden of dynamic FMT is extremely huge due to its large data sets arising from the long measurement process and the densely sampling device. In this work, we propose to accelerate the reconstruction process of dynamic FMT based on principal component analysis (PCA). Taking advantage of the compression property of PCA, the dimension of the sub weight matrix used for solving the inverse problem is reduced by retaining only a few principal components which can retain most of the effective information of the sub weight matrix. Therefore, the reconstruction process of dynamic FMT can be accelerated by solving the smaller scale inverse problem. Numerical simulation and mouse experiment are performed to validate the performance of the proposed method. Results show that the proposed method can greatly accelerate the reconstruction of parametric images in dynamic FMT almost without degradation in image quality.
Molecular Dynamics Simulations and XAFS (MD-XAFS)
Energy Technology Data Exchange (ETDEWEB)
Schenter, Gregory K.; Fulton, John L.
2017-01-20
MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.
Unusually Large Young's Muduli of Amino Acid Molecular Crystals
Azuri, Ido; Meirzadeh, Elena; Ehre, David; Cohen, Sidney R.; Rappe, Andrew M.; Lahav, Meir; Lubomirsky, Igor; Kronik, Leeor
Young's moduli of selected amino acid molecular crystals were studied both experimentally and computationally using nanoindentation and dispersion-corrected density functional theory. The Young modulus is found to be strongly facet-dependent, with some facets exhibiting exceptionally high values (as large as 44 GPa). The magnitude of Young's modulus is strongly correlated with the relative orientation between the underlying hydrogen-bonding network and the measured facet. Furthermore, we show computationally that the Young modulus can be as large as 70-90 GPa if facets perpendicular to the primary direction of the hydrogen-bonding network can be stabilized. This value is remarkably high for a molecular solid and suggests the design of hydrogen-bond networks as a route for rational design of ultra-stiff molecular solids. Angew. Chem. Int. Ed.. doi: 10.1002/anie.201505813.
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 dissem
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...... 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...
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.
Interaction of collagen with carbon nanotube: a molecular dynamics investigation.
Gopalakrishnan, R; Subramanian, V
2011-02-01
In variety of biological applications carbon nano materials interact with different biological macromolecules, such as proteins, carbohydrates and nucleic acids. In this study carbon nanotube (CNT) has been used as the model for carbon nanomaterials. Since, collagen is a large protein; model collagen like peptide (CPs) has been used to understand the interaction between CNT and collagen. Molecular dynamics (MD) simulation showed that the hydrophobic-hydrophobic interaction of the CNT-CPs play a crucial role in attracting the CPs towards the CNT. No structural aberrations occured in collagen upon interaction with CNT and hence CNT can be employed in the tissue engineering applications.
Molecular dynamical modelling of endohedral fullerenes formation in plasma
Fedorov, A. S.; Kovaleva, E. A.; Lubkova, T. A.; Popov, Z. I.; Kuzubov, A. A.; Visotin, M. A.; Irle, S.
2016-02-01
The initial stages of fullerene and endohedral metallofullerene (EMF) synthesis in carbon-helium plasma at 1500 K and 2500 K have been simulated with quantum chemical molecular dynamics (MD) based on density-functional tight-binding (DFTB). The cases of formation of large (>100 atoms) sp2-carbon clusters with scandium atoms inside were observed. These clusters are considered as precursors of fullerenes or EMFs, and thus it is shown that formation of EMFs can be explained within the framework of "shrinking hot giant" mechanism. Also, the dependence of formation rates on plasma parameters, including temperature, buffer gas and metal atoms concentrations, has been studied.
DMS: A Package for Multiscale Molecular Dynamics
Somogyi, Endre; Ortoleva, Peter J
2013-01-01
Advances in multiscale theory and computation provide a novel paradigm for simulating many-classical particle systems. The Deductive Multiscale Simulator (DMS) is a multiscale molecular dynamics (MD) program built on two of these advances, i.e., multiscale Langevin (ML) and multiscale factorization (MF). Both capture the coevolution of the the coarse-grained (CG) state and the microstate. This provides these methods with great efficiency over conventional MD. Neither involve the introduction of phenomenological governing equations for the CG state with attendant uncertainty in both their form of the governing equations and the data needed to calibrate them. The design and implementation of DMS as an open source computational platform is presented here. DMS is written in Python, uses Gromacs to achieve the microphase, and then advances the microstate via a CG-guided evolution. DMS uses MDAnalysis, a Python library for analyzing MD trajectories, to perform computations required to construct CG-related variables...
Molecular Dynamics Simulations for Predicting Surface Wetting
Directory of Open Access Journals (Sweden)
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
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 dynamics study of ice structural evolution
Institute of Scientific and Technical Information of China (English)
Wang Yan; Dong Shun-Le
2008-01-01
Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of～1.0GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H...O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
王慧; 胡元中; 邹鲲; 冷永胜
2001-01-01
The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.
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.
Molecular-dynamic study of liquid ethylenediamine
Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.
2016-10-01
Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.
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
Dynamic characteristics of large repetitive framelike structures
Nayfeh, A. H.; Hartle, M. S.
1984-01-01
Using a building block approach and starting with a single element, expressions for the energy of various two-dimensional frametype gridwork configurations are derived. These are then used to develop energy equivalent continua for the gridworks. Equations of motion and associated boundary conditions are obtained for the continua. Some dynamic characteristics of these continua are investigated and compared with corresponding results obtained from finite element codes and also with some available theoretical predictions.
Krajewski, Florian R.; Müser, Martin H.
2005-07-01
The spectral density of quantum mechanical Frenkel Kontorova chains moving in disordered, external potentials is investigated by means of path-integral molecular dynamics. If the second moment of the embedding potential is well defined (roughness exponent H=0), there is one regime in which the chain is pinned (large masses m of chain particles) and one in which it is unpinned (small m). If the embedding potential can be classified as a random walk on large length scales ( H=1/2), then the chain is always pinned irrespective of the value of m. For H=1/2, two phonon-like branches appear in the spectra.
Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.
Energy Technology Data Exchange (ETDEWEB)
Ogata, S.
1998-01-27
Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.
Banerjee, Puja; Bagchi, Biman
2016-01-01
Molecular dynamics simulations of aqueous potassium nitrate solution reveal a highly complex rotational dynamics of nitrate ions where, superimposed on the expected continuous Brownian motion, are large amplitude angular jumps that are coupled to and at least partly driven by similar large amplitude jump motions in water molecules which are associated with change in the hydrogen bonded water molecule. These jumps contribute significantly to rotational and translational motions of these ions. We explore the detailed mechanism of these correlated (or, coupled) jumps and introduce a new time correlation function to decompose the coupled orientational- jump dynamics of solvent and solute in the aqueous electrolytic solution. Time correlation function provides for the unequivocal determination of the time constant involved in orientational dynamics originating from making and breaking of hydrogen bonds. We discover two distinct mechanisms-both are coupled to density fluctuation but are of different types.
Molecular Dynamics Simulations of Polyelectrolyte Solutions
Dobrynin, Andrey
2014-03-01
Polyelectrolytes are polymers with ionizable groups. In polar solvents, these groups dissociate releasing counterions into solution and leaving uncompensated charges on the polymer backbone. Examples of polyelectrolytes include biopolymers such as DNA and RNA, and synthetic polymers such as poly(styrene sulfonate) and poly(acrylic acids). In this talk I will discuss recent molecular dynamics simulations of static and dynamic properties of polyelectrolyte solutions. These simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I - 1 / 2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ~ I- 1 / 5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ~ I- 1 / 2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ~ cp-1 / 4 . While at high salt concentrations one observes a weaker dependence of the chain size on the solution ionic strength, R ~ I- 1 / 8. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X (I) in salt solutions and corresponding quantities X (I0) in salt-free solutions, X (I) = X (I0) (I /I0) β . The exponent β = -1/2 for chain persistence length lp , β = 1/4 for solution correlation length, β = -1/5 and β = -1/8 for chain size R in dilute and semidilute solution regimes respectively. Furthermore, the analysis of the spectrum and of the relaxation times of Rouse modes confirms existence of the single length scale (correlation length) that controls both static and dynamic properties of semidilute polyelectrolyte solutions. These findings
Thermal Transport in Carbon Nanotubes using Molecular Dynamics
Moore, Andrew; Khatun, Mahfuza
2011-10-01
We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.
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...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...... efficiency. We also discuss the implementation aspects. Secondly, we explore the final state refinement acceleration by a combination with the conjugate gradient technique, where the key ingredient is an implicit corrector step. Finally, we test the feasibility of passive Hessian matrix accumulation from...
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...
Ice formation on kaolinite: Insights from molecular dynamics simulations
Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos
2016-12-01
The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.
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...... 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...... 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...
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver
2015-06-01
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.
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.
A quantum molecular dynamics study of aqueous solvation dynamics
Videla, Pablo E.; Rossky, Peter J.; Laria, D.
2013-10-01
Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.
Cluster dynamics largely shapes protoplanetary disc sizes
Vincke, Kirsten
2016-01-01
It is still on open question to what degree the cluster environment influences the sizes of protoplanetary discs surrounding young stars. Particularly so for the short-lived clusters typical for the solar neighbourhood in which the stellar density and therefore the influence of the cluster environment changes considerably over the first 10 Myr. In previous studies often the effect of the gas on the cluster dynamics has been neglected, this is remedied here. Using the code NBody6++ we study the stellar dynamics in different developmental phases - embedded, expulsion, expansion - including the gas and quantify the effect of fly-bys on the disc size. We concentrate on massive clusters ($M_{\\text{cl}} \\geq 10^3 - 6 \\cdot 10^4 M_{\\text{Sun}}$), 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...
Hydrotropic Solubilization by Urea Derivatives: A Molecular Dynamics Simulation Study
Directory of Open Access Journals (Sweden)
Yong Cui
2013-01-01
Full Text Available Hydrotropy is a phenomenon where the presence of a large quantity of one solute enhances the solubility of another solute. The mechanism of this phenomenon remains a topic of debate. This study employed molecular dynamics simulation to investigate the hydrotropic mechanism of a series of urea derivatives, that is, urea (UR, methylurea (MU, ethylurea (EU, and butylurea (BU. A poorly water-soluble compound, nifedipine (NF, was used as the model solute that was solubilized. Structural, dynamic, and energetic changes upon equilibration were analyzed to supply insights to the solubilization mechanism. The study demonstrated that NF and urea derivatives underwent significant nonstoichiometric molecular aggregation in the aqueous solution, a result consistent with the self-aggregation of urea derivatives under the same conditions. The analysis of hydrogen bonding and energy changes revealed that the aggregation was driven by the partial restoration of normal water structure. The energetic data also suggested that the promoted solubilization of NF is favored in the presence of urea derivatives. While the solutes aggregated to a varying degree, the systems were still in single-phase liquid state as attested by their active dynamics.
Acoustic properties in glycerol glass-former: Molecular dynamics simulation
Busselez, Remi; Pezeril, Thomas; Institut des Materiaux et Molecules du Mans Team
2013-03-01
Study of high-frequency collective dynamics around TeraHertz region in glass former has been a subject of intense investigations and debates over the past decade. In particular, the presence of the Boson peak characteristic of glassy material and its relation to other glass anomalies. Recently, experiments and simulations have underlined possible relation between Boson peak and transverse acoustic modes in glassy materials. In particular, simulations of simple Lennard Jones glass former have shown a relation between Ioffe-Regel criterion in transverse modes and Boson peak. We present here molecular dynamics simulation on high frequency dynamics of glycerol. In order to study mesoscopic order (0.5-5nm-1), we made use of large simulation box containing 80000 atoms. Analysis of collective longitudinal and transverse acoustic modes shows striking similarities in comparison with simulation of Lennard-Jones particles. In particular, it seems that a connection may exist between Ioffe-Regel criterion for transverse modes and Bose Peak frequency. However,in our case we show that this connection may be related with structural correlation arising from molecular clusters.
Molecular dynamic simulations of the water absorbency of hydrogels.
Ou, Xiang; Han, Qiang; Dai, Hui-Hui; Wang, Jiong
2015-09-01
A polymer gel can imbibe solvent molecules through surface tension effect. When the solvent happens to be water, the gel can swell to a large extent and forms an aggregate called hydrogel. The large deformation caused by such swelling makes it difficult to study the behaviors of hydrogels. Currently, few molecular dynamic simulation works have been reported on the water absorbing mechanism of hydrogels. In this paper, we first use molecular dynamic simulation to study the water absorbing mechanism of hydrogels and propose a hydrogel-water interface model to study the water absorbency of the hydrogel surface. Also, the saturated water content and volume expansion rate of the hydrogel are investigated by building a hydrogel model with different cross-linking degree and by comparing the water absorption curves under different temperatures. The sample hydrogel model used consists of Polyethylene glycol diglycidyl ether (PEGDGE) as epoxy and the Jeffamine, poly-oxy-alkylene-amines, as curing agent. The conclusions obtained are useful for further investigation on PEGDGE/Jeffamine hydrogel. Moreover, the simulation methods, including hydrogel-water interface modeling, we first propose are also suitable to study the water absorbing mechanism of other hydrogels.
Dalby, Andrew; Shamsir, Mohd Shahir
2015-01-01
Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.
Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure
2014-08-30
properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to
Tailoring approach for obtaining molecular orbitals of large systems
Indian Academy of Sciences (India)
Anuja P Rahalkar; Shridhar R Gadre
2012-01-01
Molecular orbitals (MO’s) within Hartree-Fock (HF) theory are of vital importance as they provide preliminary information of bonding and features such as electron localization and chemical reactivity. The contemporary literature treats the Kohn-Sham orbitals within density functional theory (DFT) equivalently to the MO's obtained within HF framework. The high scaling order of ab initio methods is the main hurdle in obtaining the MO's for large molecular systems. With this view, an attempt is made in the present work to employ molecular tailoring approach (MTA) for obtaining the complete set of MO's including occupied and virtual orbitals, for large molecules at HF and B3LYP levels of theory. The energies of highest occupied and lowest unoccupied molecular orbitals, and hence the band gaps, are accurately estimated by MTA for most of the test cases benchmarked in this study, which include -conjugated molecules. Typically, the root mean square errors of valence MO's are in range of 0.001 to 0.010 a.u. for all the test cases examined. MTA shows a time advantage factor of 2 to 3 over the corresponding actual calculation, for many of the systems reported.
Nanoscale deicing by molecular dynamics simulation
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-07-01
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice
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…
Molecular Dynamics Studies of Energy Transfer Processes in Crystal Systems.
1984-11-30
Computer molecular dynamics studies have been carried out on the problem of attaining a fundamental understanding of shock-induced initiation of...intramolecular energy exchange in shock-loaded systems are presented. Originator-supplied keywords include: Molecular dynamics , Energy transfer, Shock front, Shock wave, Explosives, Shock structure.
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…
A Multiscalling Constant Lambda Molecular Dynamic Gromacs Implementation
Goga, Nicolae; Costache, Stefania; Marrink, Siewert
2009-01-01
Molecular dynamics is one of the methods used now-a-days by the scientific community to study the property of polymers. This paper presents a new method for multiscaling molecular dynamics that combines the advantages of fine-grained and coarse grained representations. The new methodology is
Influence of solid-liquid interactions on dynamic wetting: a molecular dynamics study
Bertrand, Emilie; Blake, Terence D.; De Coninck, Joël
2009-11-01
Large-scale molecular dynamics (MD) simulations of liquid drops spreading on a solid substrate have been carried out for a very wide range of solid-liquid interactions and equilibrium contact angles. The results for these systems are shown to be consistent with the molecular-kinetic theory (MKT) of dynamic wetting, which emphasizes the role of contact-line friction as the principal channel of energy dissipation. Several predictions have been confirmed. These include a quantitative link between the dynamics of wetting and the work of adhesion and the existence of an optimum equilibrium contact angle that maximizes the speed of wetting. A feature of the new work is that key parameters (κ0 and λ), normally accessible only by fitting the MKT to dynamic contact angle data, are also obtained directly from the simulations, with good agreement between the two sources. This validates the MKT at some fundamental level. Further verification is provided by contact angle relaxation studies, which also lend support to the interfacial tension relaxation process invoked in Shikhmurzaev's hydrodynamic model of dynamic wetting.
Large deviations for Glauber dynamics of continuous gas
Institute of Scientific and Technical Information of China (English)
2008-01-01
This paper is devoted to the large deviation principles of the Glauber-type dynamics of finite or infinite volume continuous particle systems.We prove that the level-2 empirical process satisfies the large deviation principles in the weak convergence topology,while it does not satisfy the large deviation principles in the T-topology.
Efficient construction of nonorthogonal localized molecular orbitals in large systems.
Cui, Ganglong; Fang, Weihai; Yang, Weitao
2010-08-26
Localized molecular orbitals (LMOs) are much more compact representations of electronic degrees of freedom than canonical molecular orbitals (CMOs). The most compact representation is provided by nonorthogonal localized molecular orbitals (NOLMOs), which are linearly independent but are not orthogonal. Both LMOs and NOLMOs are thus useful for linear-scaling calculations of electronic structures for large systems. Recently, NOLMOs have been successfully applied to linear-scaling calculations with density functional theory (DFT) and to reformulating time-dependent density functional theory (TDDFT) for calculations of excited states and spectroscopy. However, a challenge remains as NOLMO construction from CMOs is still inefficient for large systems. In this work, we develop an efficient method to accelerate the NOLMO construction by using predefined centroids of the NOLMO and thereby removing the nonlinear equality constraints in the original method ( J. Chem. Phys. 2004 , 120 , 9458 and J. Chem. Phys. 2000 , 112 , 4 ). Thus, NOLMO construction becomes an unconstrained optimization. Its efficiency is demonstrated for the selected saturated and conjugated molecules. Our method for fast NOLMO construction should lead to efficient DFT and NOLMO-TDDFT applications to large systems.
A hybrid algorithm for parallel molecular dynamics simulations
Mangiardi, Chris M
2016-01-01
This article describes an algorithm for hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-ranged 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 AVX and AVX-2 processors as well as Xeon-Phi co-processors.
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.
Nanoscale deicing by molecular dynamics simulation.
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-08-14
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.
Molecular Dynamics Study of Helicobacter pylori Urease.
Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M
2014-05-13
Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc.2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.
MOLECULAR DYNAMIC SIMULATION OF PEPTIDE POLYELECTROLYTES
Directory of Open Access Journals (Sweden)
I. M. Neelov
2014-07-01
Full Text Available The paper deals with investigation of the conformational properties of some charged homopolypeptides in dilute aqueous solutions by computer simulation. A method of molecular dynamics for the full-atomic models of polyaspartic acid and polylysine with explicit account of water and counter-ions is used for this purpose. For systems containing these polypeptides we calculated time trajectories and the size, shape, distribution functions and time correlation functions of inertia radius and the distances between the ends of peptide chains. We have also calculated the solvatation characteristics of considered polyelectrolytes. We have found out that polyaspartic acid in dilute aqueous solution has more compact structure and more spherical shape than polylysine. We have shown that these differences are due to different interaction between the polypeptides and water molecules (in particular, the quality and quantity of hydrogen bonds formed by these peptides with water, and the difference in an amount of ion pairs formed by the charged groups of the peptides and counter-ions. The obtained results should be taken into account for elaboration of new products based on the investigated peptides and their usage in various industrial and biomedical applications.
Molecular dynamics simulations of vibrated granular gases.
Barrat, Alain; Trizac, Emmanuel
2002-11-01
We present molecular dynamics simulations of monodisperse or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met experimentally, density and temperature fields display heterogeneous profiles in the direction perpendicular to the walls. A general equation of state for an arbitrary mixture of fluidized inelastic hard spheres is derived and successfully tested against numerical data. Single-particle velocity distribution functions with non-Gaussian features are also obtained, and the influence of various parameters (inelasticity coefficients, density, etc.) are analyzed. The validity of a recently proposed random restitution coefficient model is assessed through the study of projected collisions onto the direction perpendicular to that of energy injection. For the binary mixture, the nonequipartition of translational kinetic energy is studied and compared both to experimental data and to the case of homogeneous energy injection ("stochastic thermostat"). The rescaled velocity distribution functions are found to be very similar for both species.
Molecular dynamics simulation of flow in pores
Blömer, Jan
2001-08-01
The gaseous flow in nano-scale pores is of wide interest for many today's industrial applications, e.g., in microelectronics, nano-mechanical devices (Knudsen compressor) and reaction and adsorption at porous surfaces. This can be seen from a variety of papers of recent RGD Symposia. Furthermore it is possible to separate gases by porous membranes. Although the fundamental problem of all these applications is same, namely the important role of the gas-surface interaction in such small structures, we will primarily concentrate on the separation of different gas species by porous membranes. These membranes are typically very robust (temperature, chemical resistance) because they are made from ceramics which offers new application fields. Porous flow can roughly be divided in several flow regimes by the Knudsen number: From viscous flow to Knudsen diffusion to surface diffusion and up to capillary condensation. A Molecular Dynamics (MD) model for the gas as well as the surface is formulated to investigate the interaction of gas atoms or molecules with internal degrees of freedom and the pore. The MD method seems to be well suited to study these phenomena because it can deal with the high density and the many-body-interactions, which occur during the multilayer adsorption and condensation at the surface, although it is clear that it is limited to a small physical space because of its high computational consumption.
Direct anharmonic correction method by molecular dynamics
Liu, Zhong-Li; Li, Rui; Zhang, Xiu-Lu; Qu, Nuo; Cai, Ling-Cang
2017-04-01
The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties, the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI) method based on the temperature dependent phonon density of states (TD-PDOS) reduced from molecular dynamics simulations. Using the DFEI method, after anharmonic free energy corrections we reproduced the thermal expansion coefficients, the specific heat, the thermal pressure, the isothermal bulk modulus, and the Hugoniot P- V- T relationships of Cu easily and accurately. The extensive tests on other materials including metal, alloy, semiconductor and insulator also manifest that the DFEI method can easily uncover the rest anharmonicity that the quasi-harmonic approximation (QHA) omits. It is thus evidenced that the DFEI method is indeed a very efficient method used to conduct anharmonic effect corrections beyond QHA. More importantly it is much more straightforward and easier compared to previous anharmonic methods.
Efficient compression of molecular dynamics trajectory files.
Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James
2012-10-15
We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases.
Computational Studies on the Anharmonic Dynamics of Molecular Clusters
Mancini, John S.
Molecular nanoclusters present ideal systems to probe the physical forces and dynamics that drive the behavior of larger bulk systems. At the nanocluster limit the first instances of several phenomena can be observed including the breaking of hydrogen and molecular bonds. Advancements in experimental and theoretical techniques have made it possible to explore these phenomena in great detail. The most fruitful of these studies have involved the use of both experimental and theoretical techniques to leverage to strengths of the two approaches. This dissertation seeks to explore several important phenomena of molecular clusters using new and existing theoretical methodologies. Three specific systems are considered, hydrogen chloride clusters, mixed water and hydrogen chloride clusters and the first cluster where hydrogen chloride autoionization occurs. The focus of these studies remain as close as possible to experimentally observable phenomena with the intention of validating, simulating and expanding on experimental work. Specifically, the properties of interested are those related to the vibrational ground and excited state dynamics of these systems. Studies are performed using full and reduced dimensional potential energy surface alongside advanced quantum mechanical methods including diffusion Monte Carlo, vibrational configuration interaction theory and quasi-classical molecular dynamics. The insight gained from these studies are great and varied. A new on-they-fly ab initio method for studying molecular clusters is validated for (HCl)1--6. A landmark study of the dissociation energy and predissociation mechanism of (HCl)3 is reported. The ground states of mixed (HCl)n(H2O)m are found to be highly delocalized across multiple stationary point configurations. Furthermore, it is identified that the consideration of this delocalization is required in vibrational excited state calculations to achieve agreement with experimental measurements. Finally, the theoretical
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Energy Technology Data Exchange (ETDEWEB)
Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy)
2011-01-07
Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
Large N Scalars: From Glueballs to Dynamical Higgs Models
Sannino, Francesco
2015-01-01
We construct effective Lagrangians, and corresponding counting schemes, valid to describe the dynamics of the lowest lying large N stable massive composite state emerging in strongly coupled theories. The large N counting rules can now be employed when computing quantum corrections via an effective Lagrangian description. The framework allows for systematic investigations of composite dynamics of non-Goldstone nature. Relevant examples are the lightest glueball states emerging in any Yang-Mills theory. We further apply the effective approach and associated counting scheme to composite models at the electroweak scale. To illustrate the formalism we consider the possibility that the Higgs emerges as: the lightest glueball of a new composite theory; the large N scalar meson in models of dynamical electroweak symmetry breaking; the large N pseudodilaton useful also for models of near-conformal dynamics. For each of these realisations we determine the leading N corrections to the electroweak precision parameters. ...
Combined molecular dynamics-spin dynamics simulations of bcc iron
Energy Technology Data Exchange (ETDEWEB)
Perera, Meewanage Dilina N [ORNL; Yin, Junqi [ORNL; Landau, David P [University of Georgia, Athens, GA; Nicholson, Don M [ORNL; Stocks, George Malcolm [ORNL; Eisenbach, Markus [ORNL; Brown, Greg [ORNL
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Applications of Langevin and Molecular Dynamics methods
Lomdahl, P. S.
Computer simulation of complex nonlinear and disordered phenomena from materials science is rapidly becoming an active and new area serving as a guide for experiments and for testing of theoretical concepts. This is especially true when novel massively parallel computer systems and techniques are used on these problems. In particular the Langevin dynamics simulation technique has proven useful in situations where the time evolution of a system in contact with a heat bath is to be studied. The traditional way to study systems in contact with a heat bath has been via the Monte Carlo method. While this method has indeed been used successfully in many applications, it has difficulty addressing true dynamical questions. Large systems of coupled stochastic ODE's (or Langevin equations) are commonly the end result of a theoretical description of higher dimensional nonlinear systems in contact with a heat bath. The coupling is often local in nature, because it reflects local interactions formulated on a lattice, the lattice for example represents the underlying discreteness of a substrate of atoms or discrete k-values in Fourier space. The fundamental unit of parallelism thus has a direct analog in the physical system the authors are interested in. In these lecture notes the authors illustrate the use of Langevin stochastic simulation techniques on a number of nonlinear problems from materials science and condensed matter physics that have attracted attention in recent years. First, the authors review the idea behind the fluctuation-dissipation theorem which forms that basis for the numerical Langevin stochastic simulation scheme. The authors then show applications of the technique to various problems from condensed matter and materials science.
Large Scale, High Resolution, Mantle Dynamics Modeling
Geenen, T.; Berg, A. V.; Spakman, W.
2007-12-01
To model the geodynamic evolution of plate convergence, subduction and collision and to allow for a connection to various types of observational data, geophysical, geodetical and geological, we developed a 4D (space-time) numerical mantle convection code. The model is based on a spherical 3D Eulerian fem model, with quadratic elements, on top of which we constructed a 3D Lagrangian particle in cell(PIC) method. We use the PIC method to transport material properties and to incorporate a viscoelastic rheology. Since capturing small scale processes associated with localization phenomena require a high resolution, we spend a considerable effort on implementing solvers suitable to solve for models with over 100 million degrees of freedom. We implemented Additive Schwartz type ILU based methods in combination with a Krylov solver, GMRES. However we found that for problems with over 500 thousend degrees of freedom the convergence of the solver degraded severely. This observation is known from the literature [Saad, 2003] and results from the local character of the ILU preconditioner resulting in a poor approximation of the inverse of A for large A. The size of A for which ILU is no longer usable depends on the condition of A and on the amount of fill in allowed for the ILU preconditioner. We found that for our problems with over 5×105 degrees of freedom convergence became to slow to solve the system within an acceptable amount of walltime, one minute, even when allowing for considerable amount of fill in. We also implemented MUMPS and found good scaling results for problems up to 107 degrees of freedom for up to 32 CPU¡¯s. For problems with over 100 million degrees of freedom we implemented Algebraic Multigrid type methods (AMG) from the ML library [Sala, 2006]. Since multigrid methods are most effective for single parameter problems, we rebuild our model to use the SIMPLE method in the Stokes solver [Patankar, 1980]. We present scaling results from these solvers for 3D
Petascale Molecular Dynamics Simulations of Polymers and Liquid Crystals
Nguyen, Trung Dac; Carrillo, Jan-Michael; Brown, W. Michael
2014-03-01
The availability of faster and larger supercomputers and more efficient parallel algorithms now enable us to perform unprecedented simulations approaching experimental scales. Here we present two examples of our latest large-scale molecular dynamics simulations using the Titan supercomputer in the Oak Ridge Leadership Computing Facility (OLCF). In the first study, we address the rupture origin of liquid crystal thin films wetting a solid substrate. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation. Importantly, we found evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. In the second study, we used coarse-grained molecular dynamics to simulate the thermal annealing of poly(3-hexylthiophene) (P3HT) and Phenyl-C61-butyric acid methyl ester (PCBM) blends in the presence of a silicon substrate found in organic solar cells. Our simulations show different phase segregated morphologies dependent on the P3HT chain length and PCBM volume fraction in the blend. Furthermore, the ternary blend of short and long P3HT chains with PCBM affects the vertical phase segregation of PCBM decreasing its concentration in the vicinity of the substrate. U.S. DOE Contract No. DE-AC05-00OR22725.
Explicit inclusion of electronic correlation effects in molecular dynamics
Julien, Jean-Pierre; Kress, Joel D.; Zhu, Jian-Xin
2017-07-01
We design a quantum molecular dynamics method for strongly correlated electron metals. The strong electronic correlation effects are treated within a real-space version of the Gutzwiller variational approximation (GA), which is suitable for the inhomogeneity inherent in the process of quantum molecular dynamics (MD) simulations. We also propose an efficient algorithm based on the second-moment approximation to the electronic density of states for the search of the optimal variation parameters, from which the renormalized interatomic MD potentials are fully determined. By considering a minimal one-correlated-orbital Anderson model with parameterized spatial dependence of tight-binding hopping integrals, this fast GA-MD method is benchmarked with that using exact diagonalization to solve the GA variational parameters. The efficiency and accuracy are illustrated. We have demonstrated the effect of temperature coupled with electronic correlation on structural properties simulated with MD. This method will open up an unprecedented opportunity enabling large-scale quantum MD simulations of strongly correlated electronic materials.
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.
Fast paths in large-scale dynamic road networks
Nannicini, Giacomo; Barbier, Gilles; Krob, Daniel; Liberti, Leo
2007-01-01
Efficiently computing fast paths in large scale dynamic road networks (where dynamic traffic information is known over a part of the network) is a practical problem faced by several traffic information service providers who wish to offer a realistic fast path computation to GPS terminal enabled vehicles. The heuristic solution method we propose is based on a highway hierarchy-based shortest path algorithm for static large-scale networks; we maintain a static highway hierarchy and perform each query on the dynamically evaluated network.
Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure
Garcia-Garibay, Miguel A.
2005-01-01
Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the...
Thermophoresis in liquids: a molecular dynamics simulation study.
Han, Minsub
2005-04-01
Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.
Petascale computations for Large-scale Atomic and Molecular collisions
McLaughlin, Brendan M
2014-01-01
Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schroedinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. Various examples are shown of our theoretical results compared with those obtained from Synchrotron Radiation facilities and from Satellite observations. We also indicate future directions and implementation of the R-matrix codes on emerging GPU architectures.
Molecular Dynamics of Materials Possessing High Energy Content.
1988-01-26
I -RI90 634 MOLECULAR DYNAMICS OF MATERIALS POSSESSING HIGH ENERGY 1/1 r CONTENTCU) COLUMBIA UNIV MENd YORK N J TURRO 26 JAN GO I RFOSR-TR-88-0168...Bolling Air Force Base, D.C. 2 61102F_ 2303 I B2 11 T,TL.E (Inciuoe Security Classification) Molecular Dynamics of Materials Possessing High Energy...York 10027 (212) 280-2175 TITLE: MOLECULAR DYNAMICS OF MATERIALS POSSESSING HIGH ENERGY CONTENT .. 0 0 88 2 ... "" ’% ,i u , . .. .. ....... ŝ" ;! ,i
Dynamic Mode Decomposition for Large and Streaming Datasets
Hemati, Maziar S; Rowley, Clarence W
2014-01-01
We formulate a low-storage method for performing dynamic mode decomposition that can be updated inexpensively as new data become available; this formulation allows dynamical information to be extracted from large datasets and data streams. We present two algorithms: the first is mathematically equivalent to a standard "batch-processed" formulation; the second introduces a compression step that maintains computational efficiency, while enhancing the ability to isolate pertinent dynamical information from noisy measurements. Both algorithms reliably capture dominant fluid dynamic behaviors, as demonstrated on cylinder wake data collected from both direct numerical simulations and particle image velocimetry experiments
Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics
Vila Verde, A.; Beltramo, Peter J.; Maranas, Janna K.
2011-01-01
We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala 10 , Ser 10 , Thr 10 , Arg 10 , Lys 10 , and Gln 10 ], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movemen...
Visualization and orchestration of the dynamic molecular society in cells
Institute of Scientific and Technical Information of China (English)
Xuebiao Yao; Guowei Fang
2009-01-01
@@ Visualization of specific molecules and their interactions in real space and time is essential to delineate how cellular plasticity and dynamics are achieved and orchestrated as perturbation of cellular plasticity and dynamics is detrimental to health. Elucidation of cellular dynamics requires molecular imaging at nanometer scale at millisecond resolution. The 1st International Conference on Cellular Dynamics and Chemical Biology held in Hefei, China (from 12 September to 15 September,2008) launched the quest by bringing synergism among photonics, chemistry and biology.
Molecular Dynamics study on the Micellization of Rhamnolipids.
Munusamy, Elango; Schwartz, Steven D.
2015-03-01
Oil spills have become one of the most serious environmental and ecological problems owing to the growth of oil exploration, production and transportation. Millions of gallons of crude oil and refined products are spilled into marine waters worldwide each year. Large volumes of surfactants are applied to the ocean as a remediation strategy. Environmental and toxicity issues arise when such a voluminous amounts of chemical surfactants are applied. One prospective solution to this problem is to use greener surfactants that possess excellent biodegradation and toxicity characteristics relative to existing classes of commonly used surfactants. In this context, we are interested in designing and developing greener surfactants that are patterned after naturally occurring glycolipids. In the present work, we concentrate on one of the more commonly studied glycolipid, rhamnolipid (Rha1C10C10) . Despite the available experimental data, the molecular structure, shape and geometry of micelles formed by rhamnolipid is unknown. Molecular Dynamics (MD) simulations were performed to understand the aggregation behavior of rhamnolipids in aqueous solution and at air-water interface. All calculations were performed in NPT ensembles at 300 K using NAMD 2.8, a parallel code designed for high-performance simulation of large biological macromolecule using the CHARMM force field. The results obtained from MD simulations on the aggregation of rhamnolipids in water and at air-water interface will be presented.
Molecular transport through large-diameter DNA nanopores
Krishnan, Swati; Ziegler, Daniela; Arnaut, Vera; Martin, Thomas G.; Kapsner, Korbinian; Henneberg, Katharina; Bausch, Andreas R.; Dietz, Hendrik; Simmel, Friedrich C.
2016-01-01
DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ≈4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ≈3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration. PMID:27658960
Molecular transport through large-diameter DNA nanopores
Krishnan, Swati; Ziegler, Daniela; Arnaut, Vera; Martin, Thomas G.; Kapsner, Korbinian; Henneberg, Katharina; Bausch, Andreas R.; Dietz, Hendrik; Simmel, Friedrich C.
2016-09-01
DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ~4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ~3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration.
A molecular theory of large-solute diffusion
Directory of Open Access Journals (Sweden)
A.Yoshimori
2007-12-01
Full Text Available The limit of a large solute in the molecular theory of diffusion developed by Yamaguchi et al. [Yamaguchi T. et al., J. Chem. Phys., 2005, 123, 034504] is studied. By the limit, the Stokes approximation to the hydrodynamic equations is derived in the outside region of a diffusing solute. The limit of a large solute also leads to equations in the inside region of the solute. The analytical solution of the inside equation allows one to derive the boundary condition, which is needed on the surface of the solute when the hydrodynamic equations are calculated. The boundary condition includes stick and slip boundary conditions employed by the Stokes law, in the special case. Besides stick and slip conditions, other conditions can be expressed. The boundary condition depends on properties of a solvent.
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)
Capillary dynamics driven by molecular self-layering.
Wu, Pingkeng; Nikolov, Alex; Wasan, Darsh
2017-02-10
Capillary dynamics is a ubiquitous everyday phenomenon. It has practical applications in diverse fields, including ink-jet printing, lab-on-a-chip, biotechnology, and coating. Understanding capillary dynamics requires essential knowledge on the molecular level of how fluid molecules interact with a solid substrate (the wall). Recent studies conducted with the surface force apparatus (SFA), atomic force microscope (AFM), and statistical mechanics simulation revealed that molecules/nanoparticles confined into the film/wall surfaces tend to self-layer into 2D layer/s and even 2D in-layer with increased confinement and fluid volume fraction. Here, the capillary rise dynamics of simple molecular fluids in cylindrical capillary is explained by the molecular self-layering model. The proposed model considers the role of the molecular shape on self-layering and its effect on the molecularly thin film viscosity in regards to the advancing (dynamic) contact angle. The model was tested to explain the capillary rise dynamics of fluids of spherical, cylindrical, and disk shape molecules in borosilicate glass capillaries. The good agreement between the capillary rise data and SFA data from the literature for simple fluid self-layering shows the validity of the present model. The present model provides new insights into the design of many applications where dynamic wetting is important because it reveals the significant impact of molecular self-layering close to the wall on dynamic wetting.
Molecular dynamics simulations of thermal effects in nanometric cutting process
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
Understanding the basic action of how material removing in nanoscale is a critical issue of producing well-formed components.In order to clarify thermal effects on material removal at atomic level,molecular dynamics(MD)simulations of nanometric cutting of mono-crystalline copper are performed with Morse,EAM and Tersoff potential.The effects of cutting speed on temperature distribution are investigated.The simulation results demonstrate that the temperature distribution shows a roughly concentric shape around shear zone and a steep temperature gradient lies in diamond tool,a relative high temperature is located in shear zone and machined surface,but the highest temperature is found in chip.At a high cutting speed mode,the atoms in shear zone with high temperature implies a large stress is built up in a local region.
Molecular dynamics simulations of bubble nucleation in dark matter detectors
Denzel, Philipp; 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)], 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 di...
Molecular-dynamics simulation of a ceramide bilayer
Pandit, Sagar A.; Scott, H. Larry
2006-01-01
Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368K (5° above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall "dipole potential," when ceramide is compared to sphingomyelin.
Pasta Elasticity: Molecular dynamics simulations of nuclear pasta deformations
Caplan, M. E.; Horowitz, C. J.; Berry, D. K.
2015-04-01
Nuclear pasta is expected in the inner crust of neutron stars at densities near the nuclear saturation density. In this work, the elastic properties of pasta are calculated from large scale molecular dynamics simulations by deforming the simulation volume. Our model uses a semi-classical two-nucleon potential that reproduces nuclear saturation. We report the shear modulus and breaking strain of a variety of pasta phases for different temperatures, densities, and proton fractions. The presence of pasta in neutron stars could have significant effects on crustal oscillations and could be inferred from observations of soft-gamma repeaters. Additionally, these elastic parameters will enable us to improve estimates of the maximum size and lifetime of ``mountains'' on the crust, which could efficiently radiate gravitational waves.
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.
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).
Molecular Dynamic Screening Sesquiterpenoid Pogostemon Herba as Suggested Cyclooxygenase Inhibitor.
Raharjo, Sentot Joko; Kikuchi, Takeshi
2016-10-01
Virtual molecular dynamic sesquiterpenoid Pogostemon Herba (CID56928117, CID94275, CID107152, and CID519743) have screening as cyclooxygenase (COX-1/COX-2) selective inhibitor. Molecular interaction studies sesquiterpenoid compounds with COX-1 and COX-2 were using the molecular docking tools by Hex 8.0 and interactions were further visualized using by Discovery Studio Client 3.5 software tool and Virtual Molecular Dynamic 1.9.1 software. The binding energy calculation of molecular dynamic interaction was calculated by AMBER12 software. The analysis of the sesquiterpenoid compounds showed that CID56928117, CID94275, CID107152, and CID519743 have suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor.
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.
Dynamical Systems and Control Theory Inspired by Molecular Biology
2014-10-02
in both bacterial and eukaryotic signaling pathways. A common theme in the systems biology literature is that certain systems whose output variables...AFRL-OSR-VA-TR-2014-0282 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY Eduardo Sontag RUTGERS THE STATE UNIVERSITY OF NEW JERSEY...Standard Form 298 (Re . 8-98) v Prescribed by ANSI Std. Z39.18 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY AFOSR FA9550-11-1-0247
First principles molecular dynamics without self-consistent field optimization
Souvatzis, Petros
2013-01-01
We present a first principles molecular dynamics approach that is based on time-reversible ex- tended Lagrangian Born-Oppenheimer molecular dynamics [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) costruction are required in each integration time step. The proposed dy- namics 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 an ideal starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents ...
Martí, J; Nagy, G; Guàrdia, E; Gordillo, M C
2006-11-30
Electric and dielectric properties and microscopic dynamics of liquid water confined between graphite slabs are analyzed by means of molecular dynamics simulations for several graphite-graphite separations at ambient conditions. The electric potential across the interface shows oscillations due to water layering, and the overall potential drop is about -0.28 V. The total dielectric constant is larger than the corresponding value for the bulklike internal region of the system. This is mainly due to the preferential orientations of water nearest the graphite walls. Estimation of the capacitance of the system is reported, indicating large variations for the different adsorption layers. The main trend observed concerning water diffusion is 2-fold: on one hand, the overall diffusion of water is markedly smaller for the closest graphite-graphite separations, and on the other hand, water molecules diffuse in interfaces slightly slower than those in the bulklike internal areas. Molecular reorientational times are generally larger than those corresponding to those of unconstrained bulk water. The analysis of spectral densities revealed significant spectral shifts, compared to the bands in unconstrained water, in different frequency regions, and associated to confinement effects. These findings are important because of the scarce information available from experimental, theoretical, and computer simulation research into the dielectric and dynamical properties of confined water.
Institute of Scientific and Technical Information of China (English)
Bing XIONG; Xiao-qin HUANG; Ling-ling SHEN; Jian-hua SHEN; Xiao-min LUO; Xu SHEN; Hua-liang JIANG; Kai-xian CHEN
2004-01-01
AIM: Based on the structural analysis to reveal the mechanism of ligand binding to β-secretase and the specificity of each binding sub-site. METHODS: Molecular dynamics was used to simulate on the ligand free β-secretase and ligand bound β-secretase. The trajectories were analyzed using the essential dynamics, and the significant conformational change was illustrated employing the DynDom program. RESULTS: The essential dynamics and DynDom analyses clearly showed that the β-secretase experienced a large conformational change upon the substrate or inhibitor binding. The flap structure adopted a swing motion, gradually covering the active site to facilitate the ligand binding process. Residues Ser86 and Ile87 served as the hinge point. Inhibitor-enzyme interaction analysis revealed that residues at P2, Pl, and P1' positions of the inhibitor were very important for the binding, and residues at P2' and P3' positions may be modified to improve the binding specificity. S3 subsite of the enzyme still had space to modify the inhibitors in increasing the binding affinity. CONCLUSION: The information presented here is valuable and could be used to identify small molecular inhibitors of β-secretase.
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.
Elucidation of molecular dynamics of invasive species of rice
Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...
Unified rotational dynamics of molecular crystals with orientational phase transition
Michel, K.H.; Raedt, H. De
1976-01-01
A unified theory for the rotational dynamics of molecular crystals with orientational phase transitions is given. As basic secular variables one takes symmetry adapted functions, which describe the molecular orientations, and the angular momenta of the molecules. Using Mori’s projection operator tec
What is a Multiscale Problem in Molecular Dynamics?
Directory of Open Access Journals (Sweden)
Luigi Delle Site
2013-12-01
Full Text Available In this work, we make an attempt to answer the question of what a multiscale problem is in Molecular Dynamics (MD, or, more in general, in Molecular Simulation (MS. By introducing the criterion of separability of scales, we identify three major (reference categories of multiscale problems and discuss their corresponding computational strategies by making explicit examples of applications.
HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.
Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G
2016-04-12
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features.
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
Volkovich, Roie
2010-01-01
The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor molecular junction model yields currents which transfer charge (electron and holes) unevenly to the two leads in the absence of a bias potential. The utility of this mechanism for charge pumping in steady state conditions is proposed.
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
2010-01-01
The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor ...
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.
Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics
Sanz-Navarro, C 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...
National Research Council Canada - National Science Library
Yang, Chao-Yie; Wang, Shaomeng
2011-01-01
.... Molecular dynamics simulation in the isopropanol/water cosolvent environment and in water was employed to investigate Bcl-xL protein, which has a highly flexible, large, and primarily hydrophobic binding site...
Prasad, Manish; Sinno, Talid
2004-11-01
An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.
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
The Computer Simulation of Liquids by Molecular Dynamics.
Smith, W.
1987-01-01
Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)
Molecular dynamics simulation of a polysorbate 80 micelle in water
Amani, Amir; York, Peter; de Waard, Hans; Anwar, Jamshed
2011-01-01
The structure and dynamics of a single molecule of the nonionic surfactant polysorbate 80 (POE (20) sorbitan monooleate; Tween 80 (R)) as well as a micelle comprising sixty molecules of polysorbate 80 in water have been investigated by molecular dynamics simulation. In its free state in water the po
Interfacial Properties of an Ionic Liquid by Molecular Dynamics
Heggen, B.; Zhao, W.; Leroy, F.; Dammers, A.T.; Müller-Plathe, F.
2010-01-01
We studied the influence of a liquid-vapor interface on dynamic properties like reorientation and diffusion as well as the surface tension of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) by molecular dynamics simulations. In the interfacial region, reorientation of
Interfacial Properties of an Ionic Liquid by Molecular Dynamics
Heggen, B.; Zhao, W.; Leroy, F.; Dammers, A.T.; Müller-Plathe, F.
2010-01-01
We studied the influence of a liquid-vapor interface on dynamic properties like reorientation and diffusion as well as the surface tension of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) by molecular dynamics simulations. In the interfacial region, reorientation of
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...
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
Energy Technology Data Exchange (ETDEWEB)
Lau, E Y; Krishnan, V V
2007-07-18
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
Quantum dynamics of bio-molecular systems in noisy environments
Huelga S.F.; Plenio M.B.
2012-01-01
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical descripti...
Virtual-Wall Model for Molecular Dynamics Simulation
Directory of Open Access Journals (Sweden)
Lijuan Qian
2016-12-01
Full Text Available A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed.
Multiscale molecular dynamics using the matched interface and boundary method
Geng, Weihua; Wei, G.W.
2010-01-01
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. PMID:21088761
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.
Molecular Dynamics Simulation of Amyloid Beta Dimer Formation
Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V
2004-01-01
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...
Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions
Zobač, Vladmír; Lewis, James P.; Jelínek, Pavel
2016-07-01
We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.
Molecular dynamics for irradiation driven chemistry
DEFF Research Database (Denmark)
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-01-01
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....
Effect of solvent model when probing protein dynamics with molecular dynamics.
Genheden, Samuel
2017-01-01
We probe the dynamics of the Bpti and Galectin-3 proteins using molecular dynamics simulations employing three water models at different levels of resolution, viz. the atomistic TIP4P-Ewald, the coarse-grained Elba and an implicit generalised Born model. The dynamics are quantified indirectly by model-free order parameters, S(2) of the backbone NH and selected side-chain bond vectors, which also have been determined experimentally through NMR relaxation measurements. For the backbone, the order parameters produced with the three solvent models agree to a large extent with experiments, giving average unsigned deviations between 0.03 and 0.06. For the side-chains, for which the experimental data is incomplete, the deviations are considerably larger with mean deviations between 0.13 and 0.17. However, for both backbone and side-chains, it is difficult to pick a winner, as all models perform equally well overall. For a more complete set of side-chain vectors, we resort to analysing the variation among the estimates from different solvent models. Unfortunately, the variations are found to be sizeable with mean deviations between 0.11 and 0.15. Implications for computational assessment of protein dynamics are discussed.
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...
Vector dissipativity theory for large-scale impulsive dynamical systems
Directory of Open Access Journals (Sweden)
Haddad Wassim M.
2004-01-01
Full Text Available Modern complex large-scale impulsive systems involve multiple modes of operation placing stringent demands on controller analysis of increasing complexity. In analyzing these large-scale systems, it is often desirable to treat the overall impulsive system as a collection of interconnected impulsive subsystems. Solution properties of the large-scale impulsive system are then deduced from the solution properties of the individual impulsive subsystems and the nature of the impulsive system interconnections. In this paper, we develop vector dissipativity theory for large-scale impulsive dynamical systems. Specifically, using vector storage functions and vector hybrid supply rates, dissipativity properties of the composite large-scale impulsive systems are shown to be determined from the dissipativity properties of the impulsive subsystems and their interconnections. Furthermore, extended Kalman-Yakubovich-Popov conditions, in terms of the impulsive subsystem dynamics and interconnection constraints, characterizing vector dissipativeness via vector system storage functions, are derived. Finally, these results are used to develop feedback interconnection stability results for large-scale impulsive dynamical systems using vector Lyapunov functions.
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.
Size effects in molecular dynamics thermal conductivity predictions
Sellan, D. P.; Landry, E. S.; Turney, J. E.; McGaughey, A. J. H.; Amon, C. H.
2010-06-01
We predict the bulk thermal conductivity of Lennard-Jones argon and Stillinger-Weber silicon using the Green-Kubo (GK) and direct methods in classical molecular dynamics simulations. While system-size-independent thermal conductivities can be obtained with less than 1000 atoms for both materials using the GK method, the linear extrapolation procedure [Schelling , Phys. Rev. B 65, 144306 (2002)] must be applied to direct method results for multiple system sizes. We find that applying the linear extrapolation procedure in a manner consistent with previous researchers can lead to an underprediction of the GK thermal conductivity (e.g., by a factor of 2.5 for Stillinger-Weber silicon at a temperature of 500 K). To understand this discrepancy, we perform lattice dynamics calculations to predict phonon properties and from these, length-dependent thermal conductivities. From these results, we find that the linear extrapolation procedure is only accurate when the minimum system size used in the direct method simulations is comparable to the largest mean-free paths of the phonons that dominate the thermal transport. This condition has not typically been satisfied in previous works. To aid in future studies, we present a simple metric for determining if the system sizes used in direct method simulations are sufficiently large so that the linear extrapolation procedure can accurately predict the bulk thermal conductivity.
Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions.
Directory of Open Access Journals (Sweden)
Natalie S Scholes
2016-05-01
Full Text Available Transcriptional activation domains (ADs are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators.
How to identify dislocations in molecular dynamics simulations?
Li, Duo; Wang, FengChao; Yang, ZhenYu; Zhao, YaPu
2014-12-01
Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals. With the development of computational facilities and technologies, the observations of dislocations at atomic level through numerical simulations are permitted. Molecular dynamics (MD) simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects. However, the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures. Thus, it is a big challenge for the beginners in this community to choose a proper method to start their investigations. In this review, we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids. A comprehensive comparison was made between the advantages and disadvantages of these typical techniques. We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing. It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.
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.
2016-12-01
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 than He diffusion through fuzz nanorods. Instead of trying to grow a fuzz layer starting from a flat piece of bulk W, a new approach of creating a fully formed fuzz structure 0.43 µm thick out of ellipsoidal pieces of W is employed. Lack of detailed experimental knowledge of the 3D structure of fuzz is dealt with by simulating He bombardment on five different structures of 15 vol% W and determining the variation in He penetration for each case. The results show that by far the most important factor determining He penetration is the amount of open channels through which He ions can travel unimpeded. For a more or less even W density distribution He penetration into fuzz falls off exponentially with distance and can thus be described by a ‘half depth’. In a 15 vol% fuzz structure, the half depth can reach 0.18 µm. In the far sparser fuzz structures that were recently reported, the half depth might be 1 µm or more. This means that ballistic He penetration offers a more likely scenario than He diffusion through nanorods for how He moves through fuzz and may provide an adequate explanation for how He penetrates through the thickest fuzz layers reported so far. Furthermore, the exponential decrease in penetration with depth would follow a logarithmic dependence on fluence which is compatible with experiments. A comparison of these results and molecular dynamics calculations carried out in the recoil interaction approximation shows that results for W fuzz are qualitatively very different from conventional stopping power calculations on W with a similarly low but homogeneous density distribution.
Dynamics of molecular superrotors in external magnetic field
Korobenko, Aleksey
2015-01-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of 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 the 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 in 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.
First principles molecular dynamics without self-consistent field optimization
Energy Technology Data Exchange (ETDEWEB)
Souvatzis, Petros, E-mail: petros.souvatsiz@fysik.uu.se [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); Niklasson, Anders M. N., E-mail: amn@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)
2014-01-28
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.
First principles molecular dynamics without self-consistent field optimization.
Souvatzis, Petros; Niklasson, Anders M N
2014-01-28
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.
Dynamics Studies on Molecular Diffusion in Zeolites
Institute of Scientific and Technical Information of China (English)
王秋霞; 樊建芬; 肖鹤鸣
2003-01-01
A review about the applications of molecular dynamics（MD）simulation in zeolites is presented. MD simulation has been proved to be a useful tool due to its applications in this field for the recent two decades. The fundamental theory of MD is introduced and the hydrocarbon diffusion in zeolites is mainly focused on in this paper.
Development of models and methods for the molecular simulation of large systems and molecules
Walter, Jonathan; Horsch, Martin; Vrabec, Jadran; Hasse, Hans
2010-01-01
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new models for carbon dioxide and cyclohexanolare discussed and a new method for the model development is introduced. Force fields and models for the simulation of PNIPAAm hydrogel in pure water and sodium chloride solution are tested and verified and applied to the simulation of nucleation processes.
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...
Study of the Dynamics of Large Reflector Antennas with Accelerometers
Snel, R C; Baars, J W M
2007-01-01
The Atacama Large Millimeter Array (ALMA) will consist of up to 64 state-of-the-art sub-mm telescopes, subject to stringent performance specifications which will push the boundaries of the technology, and makes testing of antenna performance a likewise challenging task. Two antenna prototypes were evaluated at the ALMA Test Facility at the Very Large Array site in New Mexico, USA. The dynamic behaviour of the antennas under operational conditions was investigated with the help of an accelerometer system capable of measuring rigid body motion of the elevation structure of the antenna, as well as a few low-order deformation modes, resulting in dynamic performance numbers for pointing stability, reflector surface stability, path length stability, and structure flexure. Special emphasis was given to wind effects, one of the major factors affecting performance on timescales of seconds to tens of minutes. This paper describes the accelerometer system, its capabilities and limitations, and presents the dynamic perfo...
The dynamics of large-scale arrays of coupled resonators
Borra, Chaitanya; Pyles, Conor S.; Wetherton, Blake A.; Quinn, D. Dane; Rhoads, Jeffrey F.
2017-03-01
This work describes an analytical framework suitable for the analysis of large-scale arrays of coupled resonators, including those which feature amplitude and phase dynamics, inherent element-level parameter variation, nonlinearity, and/or noise. In particular, this analysis allows for the consideration of coupled systems in which the number of individual resonators is large, extending as far as the continuum limit corresponding to an infinite number of resonators. Moreover, this framework permits analytical predictions for the amplitude and phase dynamics of such systems. The utility of this analytical methodology is explored through the analysis of a system of N non-identical resonators with global coupling, including both reactive and dissipative components, physically motivated by an electromagnetically-transduced microresonator array. In addition to the amplitude and phase dynamics, the behavior of the system as the number of resonators varies is investigated and the convergence of the discrete system to the infinite-N limit is characterized.
Parallel Molecular Dynamics Simulations of Ejection from the Metal Cu and Al Under Shock Loading
Institute of Scientific and Technical Information of China (English)
CHEN Qi-Feng; CAO Xiao-Lin; ZHANG Ying; CAI Ling-Cang; CHEN Dong-Quan
2005-01-01
@@ Large-scale non-equilibrium molecular dynamics simulations are used to investigate the ejection of the metal under a shock loading. The present work focus on the dynamic process of ejection from the metal Cu and Al surface groove under shock loading, using parallel MD implementation and the Morse potential. The ejected mass coefficient and the size distribution of ejected particles (cluster for atoms) are investigated with changes of the half-angle or the depth of groove and shock strength.
Understanding ion association states and molecular dynamics using infrared spectroscopy
Masser, Hanqing
microphase separates from the PEO-rich microphase, and ionic groups are preferentially solvated by PEO chains and reside in the PEO-rich microphase. As the ratio of PTMO increases, the fraction of aggregates increases, resulting in more highly coordinated aggregation states. Results on ion association states are in good agreement with previous results on ion conductivity, polymer dynamics and morphology. The effects of ion content, cation type and ionic side chain structure on ion association states are systemically studied in a series of ionomers with short ethylene oxide and ionic sulfonated styrene side chains, and then correlated to the ion and polymer dynamic characterization. It is found that ionomers with modest ion content, large cation and styrene ionic side chain have the most "free ions" and ion pairs, and highest ion conductivity. Ion conduction in ionomers is optimized by systematically changing their chemical structures. In addition to knowledge of ion association states, a IR band shape also contains information on molecular dynamics. In companion investigation, the vibrational relaxation and dynamic transitions of conformationally insensitive normal modes in two different polymer systems (atactic polystyrene and deuterated poly(methyl methacrylate)) are studied. The information on vibrational relaxations is resolved by conducting precisely controlled FTIR experiments, applying specialized curve resolving data analysis, and calculating time correlation functions through numerical Fourier transformation. The vibrational relaxations of these modes can be described by a two process model: a fast process on the time scale of 0.01 ps, which is inhomogeneously broadened by a slow process on the time scale of picoseconds.
MOLECULAR-DYNAMICS SIMULATION ON AN I860 BASED RING ARCHITECTURE
BEKKER, H; DIJKSTRA, EJ; BERENDSEN, HJC
1993-01-01
Molecular Dynamics (M.D.) simulation is a widely used computational technique to study the properties of many-body (atom) systems. Because the number or particles in these simulations is large, and many time steps are required to cover the minimal time span on which biomolecular processes take place
Weijs, J.H.; Snoeijer, J.H.; Lohse, D.
2012-01-01
We study surface nanobubbles using molecular dynamics simulation of ternary (gas, liquid, solid) systems of Lennard-Jones fluids. They form for a sufficiently low gas solubility in the liquid, i.e., for a large relative gas concentration. For a strong enough gas-solid attraction, the surface nanobub
VUV studies of molecular photofragmentation dynamics
Energy Technology Data Exchange (ETDEWEB)
White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)
1993-12-01
State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.
Rotor dynamic considerations for large wind power generator systems
Ormiston, R. A.
1973-01-01
Successful large, reliable, low maintenance wind turbines must be designed with full consideration for minimizing dynamic response to aerodynamic, inertial, and gravitational forces. Much of existing helicopter rotor technology is applicable to this problem. Compared with helicopter rotors, large wind turbines are likely to be relatively less flexible with higher dimensionless natural frequencies. For very large wind turbines, low power output per unit weight and stresses due to gravitational forces are limiting factors. The need to reduce rotor complexity to a minimum favors the use of cantilevered (hingeless) rotor configurations where stresses are relieved by elastic deformations.
Relativistic corrections to molecular dynamic dipole polarizabilities
DEFF Research Database (Denmark)
Kirpekar, Sheela; Oddershede, Jens; Jensen, Hans Jørgen Aagaard
1995-01-01
Using response function methods we report calculations of the dynamic isotropic polarizability of SnH4 and PbH4 and of the relativistic corrections to it in the random phase approximation and at the correlated multiconfigurational linear response level of approximation. All relativistic corrections...
Simplistic Coulomb Forces in Molecular Dynamics
DEFF Research Database (Denmark)
Hansen, Jesper Schmidt; Schrøder, Thomas; Dyre, J. C.
2012-01-01
salt model the SF approximation overall reproduces the structural and dynamical properties as accurately as does the Wolf method. It is shown that the optimal Wolf damping parameter depends on the property in focus and that neither the potential energy nor the radial distribution function are useful...
Dune-like dynamic of Martian Aeolian large ripples
Silvestro, S.; Vaz, D. A.; Yizhaq, H.; Esposito, F.
2016-08-01
Martian dunes are sculpted by meter-scale bed forms, which have been interpreted as wind ripples based on orbital data. Because aeolian ripples tend to orient and migrate transversely to the last sand-moving wind, they have been widely used as wind vanes on Earth and Mars. In this report we show that Martian large ripples are dynamically different from Earth's ripples. By remotely monitoring their evolution within the Mars Science Laboratory landing site, we show that these bed forms evolve longitudinally with minimal lateral migration in a time-span of ~ six terrestrial years. Our observations suggest that the large Martian ripples can record more than one wind direction and that in certain cases they are more similar to linear dunes from a dynamic point of view. Consequently, the assumption of the transverse nature of the large Martian ripples must be used with caution when using these features to derive wind directions.
Low thermal conductivity of graphyne nanotubes from molecular dynamics study
Hu, Ming; Jing, Yuhang; Zhang, Xiaoliang
2015-04-01
It is well known that carbon nanotubes (CNTs) possess ultrahigh thermal conductivity that is comparable to bulk diamond. However, no research has studied the possible low thermal conductivity of different CNTs so far. By performing nonequilibrium molecular dynamic simulations, we reveal that the perfect graphyne nanotube (GNT) exhibits an unprecedentedly low thermal conductivity (below 10 W/mK at room temperature), which is generally two orders of magnitude lower than that of ordinary CNTs and even lower than the values reported for defected, doped, and chemically functionalized CNTs. By performing phonon polarization and spectral energy density analysis, we observe that the ultralow thermal conductivity stems from the unique atomic structure of the GNT, consisting of the weak acetylenic linkage (s p C-C bonds) and the strong hexagonal ring (s p2 C-C bonds), which results in a large vibrational mismatch between these two components, and thus induces significantly inefficient heat transfer. Moreover, the thermal transport in GNT with a large number of acetylenic linkages is dominated by the low frequency longitudinal modes in the linkage. Such strong confinement of the low frequency thermal energy results in the extremely low thermal conductivity due to the flattened phonon dispersion curves (low phonon group velocities). The exploration of the abnormal thermal transport of GNTs paves the way for design and application of the relevant devices that could benefit from the ultralow thermal conductivity, such as thermoelectrics for energy conversion.
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
Corticomuscular synchronization with small and large dynamic force output.
Andrykiewicz, Agnieszka; Patino, Luis; Naranjo, Jose Raul; Witte, Matthias; Hepp-Reymond, Marie-Claude; Kristeva, Rumyana
2007-11-27
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. 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. 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 in the low force range investigated
Tunneling Dynamics Between Atomic and Molecular Bose-Einstein Condensates
Institute of Scientific and Technical Information of China (English)
CHEN Chang-Yong
2004-01-01
Tunneling dynamics of multi-atomic molecules between atomic and multi-atomic molecular Bose-Einstein condensates with Feshbach resonance is investigated.It is indicated that the tunneling in the two Bose-Einstein condensates depends on not only the inter-atomic-molecular nonlinear interactions and the initial number of atoms in these condensates,but also the tunneling coupling between the atomic condensate and the multi-atomic molecular condensate.It is discovered that besides oscillating tunneling current between the atomic condensate and the multi-atomic molecular condensate,the nonlinear multi-atomic molecular tunneling dynamics sustains a self-locked population imbalance:a macroscopic quantum self-trapping effect.The influence of de-coherence caused by non-condensate atoms on the tunneling dynamics is studied.It is shown that de-coherence suppresses the multi-atomic molecular tunneling.Moreover,the conception of the molecular Bose-Einstein condensate,which is different from the conventional single-atomic Bose-Einstein condensate,is specially emphasized in this paper.
Static and dynamic properties of large polymer melts in equilibrium
Hsu, Hsiao-Ping; Kremer, Kurt
2016-04-01
We present a detailed study of the static and dynamic behaviors of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [G. Zhang et al., ACS Macro Lett. 3, 198 (2014)], we investigate their static and dynamic scaling behaviors as predicted by theory. We find that for semiflexible chains in a melt, results of the mean square internal distance, the probability distributions of the end-to-end distance, and the chain structure factor are well described by theoretical predictions for ideal chains. We examine the motion of monomers and chains by molecular dynamics simulations using the ESPResSo++ package. The scaling predictions of the mean squared displacement of inner monomers, center of mass, and relations between them based on the Rouse and the reptation theory are verified, and related characteristic relaxation times are determined. Finally, we give evidence that the entanglement length Ne,PPA as determined by a primitive path analysis (PPA) predicts a plateau modulus, GN 0 = /4 5 ( ρ k B T / N e ) , consistent with stresses obtained from the Green-Kubo relation. These comprehensively characterized equilibrium structures, which offer a good compromise between flexibility, small Ne, computational efficiency, and small deviations from ideality, provide ideal starting states for future non-equilibrium studies.
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.
High resolution, large dynamic range field map estimation
Dagher, Joseph; Reese, Timothy; Bilgin, Ali
2013-01-01
Purpose We present a theory and a corresponding method to compute high resolution field maps over a large dynamic range. Theory and Methods We derive a closed-form expression for the error in the field map value when computed from two echoes. We formulate an optimization problem to choose three echo times which result in a pair of maximally distinct error distributions. We use standard field mapping sequences at the prescribed echo times. We then design a corresponding estimation algorithm which takes advantage of the optimized echo times to disambiguate the field offset value. Results We validate our method using high resolution images of a phantom at 7T. The resulting field maps demonstrate robust mapping over both a large dynamic range, and in low SNR regions. We also present high resolution offset maps in vivo using both, GRE and MEGE sequences. Even though the proposed echo time spacings are larger than the well known phase aliasing cutoff, the resulting field maps exhibit a large dynamic range without the use of phase unwrapping or spatial regularization techniques. Conclusion We demonstrate a novel 3-echo field map estimation method which overcomes the traditional noise-dynamic range trade-off. PMID:23401245
Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs
Institute of Scientific and Technical Information of China (English)
CHEN Fei-Guo; GE Wei; LI Jing-Hai
2009-01-01
Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20-60 fold speedup over that of one core of the Intel Xeon 5430 CPU was achieved, reaching up to 150 Gflopa. MD simulation of cavity flow and particle-bubble interaction in liquid was implemented on multiple GPUs using a message passing interface (MPI). Up to 200 GPUs were tested on a special network topology, which achieves good scalability. The capability of GPU clusters for large-scale molecular dynamics simulation of meso-scale flow behavior was, therefore, uncovered.
Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20-60 fold speedup over that of one core of the Intel Xeon 5430 CPU was achieved, reaching up to 150 Gflops. MD simulation of cavity flow and particle-bubble interaction in liquid was implemented on multiple GPUs using a message passing interface (MPI). Up to 200 GPUs were tested on a special network topology, which achieves good scalability. The capability of GPU clusters for large-scale molecular dynamics simulation of meso-scale flow behavior was, therefore, uncovered.
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.
Methods for molecular dynamics with nonadiabatic transitions
Coker, D F
1994-01-01
We show how the dynamically nonlocal formulation of classical nuclear motion in the presence of quantal electronic transitions presented many years ago by Pechukas can be localized in time using time dependent perturbation theory to give an impulsive force which acts when trajectories hop between electronic surfaces. The action of this impulsive force is completely equivalent to adjusting the nuclear velocities in the direction of the nonadiabatic coupling vector so as to conserve energy, a procedure which is widely used in surface hopping trajectory methods. This is the first time the precise connection between these two formulations of the nonadiabatic dynamics problem has been considered. We also demonstrate that the stationary phase approximation to the reduced propagator at the heart of Pechukas' theory is not unitary due to its neglect of nonstationary paths. As such mixed quantum-classical evolution schemes based on this approximation are not norm conserving and in general must fail to give the correct...
On the stochastic dynamics of molecular conformation
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamiltonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.
Combining Molecular Dynamics and Density Functional Theory
Kaxiras, Efthimios
2015-03-01
The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.
Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.
Teimouri, Hamid; Kolomeisky, Anatoly B; Mehrabiani, Kareem
2015-02-13
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.
Molecular dynamics insights into human aquaporin 2 water channel.
Binesh, A R; Kamali, R
2015-12-01
In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney.
Hub, Jochen S; Grubmüller, Helmut; de Groot, Bert L
2009-01-01
Aquaporins (AQPs) are a family of integral membrane proteins, which facilitate the rapid and yet highly selective flux of water and other small solutes across biological membranes. Molecular dynamics (MD) simulations contributed substantially to the understanding of the molecular mechanisms that underlie this remarkable efficiency and selectivity of aquaporin channels. This chapter reviews the current state of MD simulations of aquaporins and related aquaglyceroporins as well as the insights these simulations have provided. The mechanism of water permeation through AQPs and methods to determine channel permeabilities from simulations are described. Protons are strictly excluded from AQPs by a large electrostatic barrier and not by an interruption of the Grotthuss mechanism inside the pore. Both the protein's electric field and desolvation effects contribute to this barrier. Permeation of apolar gas molecules such as CO(2) through AQPs is accompanied by a large energetic barrier and thus can only be expected in membranes with a low intrinsic gas permeability. Additionally, the insights from simulations into the mechanism of glycerol permeation through the glycerol facilitator GlpF from E. coli are summarized. Finally, MD simulations are discussed that revealed that the aro-matic/arginine constriction region is generally the filter for uncharged solutes, and that AQP selectivity is controlled by a hydrophobic effect and steric restraints.
DynamO: a free O(N) general event-driven molecular dynamics simulator.
Bannerman, M N; Sargant, R; Lue, L
2011-11-30
Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo.
Prototyping Bio-Nanorobots using Molecular Dynamics Simulation
Hamdi, Mustapha; Sharma, Gaurav; Ferreira, A.; Mavroidis, Constantinos
2005-01-01
Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920); International audience; This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The mai...
Prototyping Bio-Nanorobots using Molecular Dynamics Simulation
Hamdi, Mustapha; Sharma, Gaurav; Ferreira, A.; Mavroidis, Constantinos
2005-01-01
Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920); International audience; This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The mai...
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.
Charge and Energy Transfer Dynamics in Molecular Systems
May, Volkhard
2004-01-01
This second edition is based on the successful concept of the first edition in presenting a unified perspective on molecular charge and energy transfer processes. The authors bridge the regimes of coherent and dissipative dynamics, thus establishing the connection between classic rate theories and modern treatments of ultrafast phenomena. The book serves as an introduction for graduate students and researchers. Among the new topics of this second edition are. - semiclassical and quantum-classical hybrid formulations of molecular dynamics. - the basics of femtosecond nonlinear spectroscopy. - e
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
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...... an improved stability with a factor of , but the overhead of computer time is a factor of at least two. The conclusion is that the second-order “Verlet”-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated...
Molecular Dynamics Simulation on thermodynamic Properties and Transport Coefficients
Institute of Scientific and Technical Information of China (English)
D.X.Xiong
1996-01-01
Moecular dynamics simulation (MDS) is used to study the thermodynamic properties and transport coefficients of an argon system with Lennend-Jones potential.The results on the velocity distribution,mean free path,mean collison time,specific heat and self0diffusion coefficient agree well with the existing theoretical /experimental data,It shows that molecular dynamics method is another bridge to connect microworld and macreoworld.
Molecular dynamics simulations of peptides on calcite surface
Yang, Mingjun; Rodger, Mark; Harding, John; Stipp, Susan S.L.
2009-01-01
Abstract A series of Molecular Dynamics (MD) simulations has been carried out to investigate the interaction between peptides and a calcite (1 0 -1 4) surface in water. A 16-amino acid and a 17-amino acid peptide have been built and three different configurations for each peptide are used as starting configurations. The dynamic behaviour of these peptides has been investigated by calculating their radii of gyration and distribution of dihedral angles. For comparison, the simulatio...
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.
AN INVARIANCE PRINCIPLE IN LARGE POPULATION STOCHASTIC DYNAMIC GAMES
Institute of Scientific and Technical Information of China (English)
Minyi HUANG; Peter E. CAINES; Roland P. MALHAM(E)
2007-01-01
We study large population stochastic dynamic games where the so-called Nash certainty equivalence based control laws are implemented by the individual players. We first show a martingale property for the limiting control problem of a single agent and then perform averaging across the population; this procedure leads to a constant value for the martingale which shows an invariance property of the population behavior induced by the Nash strategies.
Highly accurate fiber transfer delay measurement with large dynamic range
Dong, J W; Gao, C; Guo, Y C; Wang, L J
2015-01-01
A novel and efficient method for fiber transfer delay measurement is demonstrated. Fiber transfer delay measurement in time domain is converted into the frequency measurement of the modulation signal in frequency domain, accompany with a coarse and easy ambiguity resolving process. This method achieves a sub-picosecond resolution, with an accuracy of 1 picosecond, and a large dynamic range up to 50 km as well as no measurement dead zone.
Mesoscopic Dynamics of Biopolymers and Protein Molecular Machines
Kapral, Raymond
2013-03-01
The dynamics of biopolymers in solution and in crowded molecular environments, which mimic some features of the interior of a biochemical cell, will be discussed. In particular, the dynamics of protein machines that utilize chemical energy to effect cyclic conformational changes to carry out their catalytic functions will be described. The investigation of the dynamics of such complex systems requires knowledge of the time evolution on physically relevant long distance and time scales. This often necessitates a coarse grained or mesoscopic treatment of the dynamics. A hybrid particle-based mesoscopic dynamical method, which combines molecular dynamics for a coarse-grain model of the proteins with multiparticle collision dynamics for the solvent, will be described and utilized to study the dynamics of such systems. See, C. Echeverria, Y. Togashi, A. S. Mikhailov, and R. Kapral, Phys. Chem. Chem. Phys 13, 10527 (2011); C. Echeverria and R. Kapral, Phys. Chem. Chem. Phys., 14, 6755 (2012); J. M. Schofield, P. Inder and R. Kapral, J. Chem. Phys. 136, 205101 (2012). Work was supported in part by a grant from the Natural Sciences and Engineering Research Council of Canada.
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.
Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations
Nguyen, Trung Dac; Carrillo, Jan-Michael Y.; Matheson, Michael A.; Brown, W. Michael
2014-02-01
The ability of liquid crystal (LC) molecules to respond to changes in their environment makes them an interesting candidate for thin film applications, particularly in bio-sensing, bio-mimicking devices, and optics. Yet the understanding of the (in)stability of this family of thin films has been limited by the inherent challenges encountered by experiment and continuum models. Using unprecedented large-scale molecular dynamics (MD) simulations, we address the rupture origin of LC thin films wetting a solid substrate at length scales similar to those in experiment. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation, and importantly, for the first time, evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. We further demonstrate that the primary driving force for rupture is closely related to the tendency of the LC mesogens to recover their local environment in the bulk state. Our study not only provides new insights into the rupture mechanism of liquid crystal films, but also sets the stage for future investigations of thin film systems using peta-scale molecular dynamics simulations.The ability of liquid crystal (LC) molecules to respond to changes in their environment makes them an interesting candidate for thin film applications, particularly in bio-sensing, bio-mimicking devices, and optics. Yet the understanding of the (in)stability of this family of thin films has been limited by the inherent challenges encountered by experiment and continuum models. Using unprecedented large-scale molecular dynamics (MD) simulations, we address the rupture origin of LC thin films wetting a solid substrate at length scales similar to those in experiment. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation, and importantly, for the first time, evidence of a common rupture mechanism
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.
Chignola, R; Chignola, Roberto; Milotti, Edoardo
2005-01-01
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a simplified model of cell metabolism, growth and proliferation, suitable for inclusion in a multicell simulator, now under development (Chignola R and Milotti E 2004 Physica A 338 261-6). Nutrients regulate the proliferation dynamics of tumor cells which adapt their behaviour to respond to changes in the biochemical composition of the environment. This modeling of nutrient metabolism and cell cycle at a mesoscopic scale level leads to a continuous flow of information between the two disparate spatiotemporal scales of molecular and cellular dynamics that can be simulated with modern computers and tested experimentally.
Single polymer dynamics under large amplitude oscillatory extension
Zhou, Yuecheng; Schroeder, Charles M.
2016-09-01
Understanding the conformational dynamics of polymers in time-dependent flows is of key importance for controlling materials properties during processing. Despite this importance, however, it has been challenging to study polymer dynamics in controlled time-dependent or oscillatory extensional flows. In this work, we study the dynamics of single polymers in large-amplitude oscillatory extension (LAOE) using a combination of experiments and Brownian dynamics (BD) simulations. Two-dimensional LAOE flow is generated using a feedback-controlled stagnation point device known as the Stokes trap, thereby generating an oscillatory planar extensional flow with alternating principal axes of extension and compression. Our results show that polymers experience periodic cycles of compression, reorientation, and extension in LAOE, and dynamics are generally governed by a dimensionless flow strength (Weissenberg number Wi) and dimensionless frequency (Deborah number De). Single molecule experiments are compared to BD simulations with and without intramolecular hydrodynamic interactions (HI) and excluded volume (EV) interactions, and good agreement is obtained across a range of parameters. Moreover, transient bulk stress in LAOE is determined from simulations using the Kramers relation, which reveals interesting and unique rheological signatures for this time-dependent flow. We further construct a series of single polymer stretch-flow rate curves (defined as single molecule Lissajous curves) as a function of Wi and De, and we observe qualitatively different dynamic signatures (butterfly, bow tie, arch, and line shapes) across the two-dimensional Pipkin space defined by Wi and De. Finally, polymer dynamics spanning from the linear to nonlinear response regimes are interpreted in the context of accumulated fluid strain in LAOE.
Superspreading: molecular dynamics simulations and experimental results
Theodorakis, Panagiotis; Kovalchuk, Nina; Starov, Victor; Muller, Erich; Craster, Richard; Matar, Omar
2015-11-01
The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Recently, we have observed that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. Here, we present the structural characteristics and kinetics of the droplet spreading during the different stages of this process, and we compare our results with experimental data for trisiloxane and poly oxy ethylene surfactants. In this way, we highlight and explore the differences between surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting. EPSRC Platform Grant MACIPh (EP/L020564/).
Seveno, D; Dinter, N; De Coninck, J
2010-09-21
We study the spontaneous wetting of liquid drops on FCC solid substrates using large-scale molecular dynamics simulations. By varying the solid lattice parameter, five different drop/solid dynamic systems are investigated. It is shown that the results are in agreement with the molecular-kinetic theory (MKT) describing the dynamics of wetting. Moreover, it is established that the microscopic parameters resulting from fits using the MKT, the so-called molecular jump frequency at equilibrium and the jump length, correspond to the values that can be estimated directly from the simulations. This agreement strongly supports the validity of the MKT at the microscopic scale.
A computational toy model for shallow landslides: Molecular dynamics approach
Martelloni, Gianluca; Bagnoli, Franco; Massaro, Emanuele
2013-09-01
The aim of this paper is to propose a 2D computational algorithm for modeling the triggering and propagation of shallow landslides caused by rainfall. We used a molecular dynamics (MD) approach, similar to the discrete element method (DEM), that is suitable to model granular material and to observe the trajectory of a single particle, so to possibly identify its dynamical properties. We consider that the triggering of shallow landslides is caused by the decrease of the static friction along the sliding surface due to water infiltration by rainfall. Thence the triggering is caused by the two following conditions: (a) a threshold speed of the particles and (b) a condition on the static friction, between the particles and the slope surface, based on the Mohr-Coulomb failure criterion. The latter static condition is used in the geotechnical model to estimate the possibility of landslide triggering. The interaction force between particles is modeled, in the absence of experimental data, by means of a potential similar to the Lennard-Jones one. The viscosity is also introduced in the model and for a large range of values of the model's parameters, we observe a characteristic velocity pattern, with acceleration increments, typical of real landslides. The results of simulations are quite promising: the energy and time triggering distribution of local avalanches show a power law distribution, analogous to the observed Gutenberg-Richter and Omori power law distributions for earthquakes. Finally, it is possible to apply the method of the inverse surface displacement velocity [4] for predicting the failure time.
Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations
Radak, Brian K.; Roux, Benoît
2016-10-01
Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Finally, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.
Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.
Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C; Roux, Benoît
2013-10-01
A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific β-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26-27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K(+) channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K(+) and Na(+) concentration gradients and the electrostatic potential difference of living cells.
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.
Pasta nucleosynthesis: Molecular dynamics simulations of nuclear statistical equilibrium
Caplan, M. E.; Schneider, A. S.; Horowitz, C. J.; Berry, D. K.
2015-06-01
Background: Exotic nonspherical nuclear pasta shapes are expected in nuclear matter at just below saturation density because of competition between short-range nuclear attraction and long-range Coulomb repulsion. Purpose: We explore the impact nuclear pasta may have on nucleosynthesis during neutron star mergers when cold dense nuclear matter is ejected and decompressed. Methods: We use a hybrid CPU/GPU molecular dynamics (MD) code to perform decompression simulations of cold dense matter with 51 200 and 409 600 nucleons from 0.080 fm-3 down to 0.00125 fm-3 . Simulations are run for proton fractions YP= 0.05, 0.10, 0.20, 0.30, and 0.40 at temperatures T = 0.5, 0.75, and 1.0 MeV. The final composition of each simulation is obtained using a cluster algorithm and compared to a constant density run. Results: Size of nuclei in the final state of decompression runs are in good agreement with nuclear statistical equilibrium (NSE) models for temperatures of 1 MeV while constant density runs produce nuclei smaller than the ones obtained with NSE. Our MD simulations produces unphysical results with large rod-like nuclei in the final state of T =0.5 MeV runs. Conclusions: Our MD model is valid at higher densities than simple nuclear statistical equilibrium models and may help determine the initial temperatures and proton fractions of matter ejected in mergers.
Nonequilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition
Alavi, Saman; Ripmeester, J. A.
2010-04-01
Nonequilibrium, constant energy, constant volume (NVE) molecular dynamics simulations are used to study the decomposition of methane clathrate hydrate in contact with water. Under adiabatic conditions, the rate of methane clathrate decomposition is affected by heat and mass transfer arising from the breakup of the clathrate hydrate framework and release of the methane gas at the solid-liquid interface and diffusion of methane through water. We observe that temperature gradients are established between the clathrate and solution phases as a result of the endothermic clathrate decomposition process and this factor must be considered when modeling the decomposition process. Additionally we observe that clathrate decomposition does not occur gradually with breakup of individual cages, but rather in a concerted fashion with rows of structure I cages parallel to the interface decomposing simultaneously. Due to the concerted breakup of layers of the hydrate, large amounts of methane gas are released near the surface which can form bubbles that will greatly affect the rate of mass transfer near the surface of the clathrate phase. The effects of these phenomena on the rate of methane hydrate decomposition are determined and implications on hydrate dissociation in natural methane hydrate reservoirs are discussed.
Stresses and elastic constants of crystalline sodium, from molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
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.
Orbital-Free Molecular Dynamics Simulations at Extreme Conditions
Kress, J. D.; Collins, L. A.; Ticknor, C.
2015-06-01
Large-scale molecular dynamics (MD) simulations in an orbital-free (OF) density-functional theory (DFT) formulation have been performed for pure and mixed species over a broad range of temperatures (T) and densities (ρ) that includes the warm, dense matter and high-energy density physics regimes. A finite-temperature Thomas-Fermi-Dirac form with a local-density exchange-correlation potential and a regularized electron-ion interaction represents the quantum nature of the electrons. In particular, we examine the efficacy of the OFMD approach as an effective bridge between Kohn-Sham DFT MD at low temperatures and simple, fully-ionized plasma models at high temperatures. Comparisons against intermediate-range constructions such as the Yukawa and one-component plasmas are also made. We examine the mass transport (diffusion, viscosity) properties of various systems, ranging from light to heavy elements, including lithium hydride (LiH), mixtures of LiH with uranium, mixtures of deuterium-tritium (DT) with plutonium and mixtures of DT with plastic (CH). The OFMD mass transport results have been fitted to simple functions of ρ and T suitable for use in hydrodynamics simulation codes.
Indole Localization in an Explicit Bilayer Revealed via Molecular Dynamics
Norman, Kristen
2005-11-01
It is well known that the amino-acid tryptophan is particularly stable in the interfacial region of biological membranes, and this preference is a property of the tryptophan side-chain. Analogues of this side-chain, such as indole, strongly localize in the interfacial region, especially near the glycerol moiety of the lipids in the bilayer. Using molecular dynamics calculations, we determine the potential of mean force (PMF) for indoles in the bilayer. We compare the calculated PMF for indole with that of benzene to show that exclusion from the center of the lipid bilayer does not occur in all aromatics, but is strong in indoles. We find three minima in the PMF. Indole is most stabilized near the glycerol moiety. A weaker binding location is found near the choline groups of the lipid molecules. An even weaker binding side is found near the center of the lipid hydrocarbon core. Comparisions between uncharged, weakly charged, and highly charged indoles demonstrate that the exclusion is caused by the charge distribution on the indole rather than the ``lipo-phobic'' effect. High temperature simulations are used to determine the relative contribution of enthalpy and entropy to indole localization. The orientation of indole is found to be largely charge independent and is a strong function of depth within the bilayer. We find good agreement between simulated SCD order parameters for indole and experimentally determined order parameters.
A Formulation of the Ring Polymer Molecular Dynamics
Horikoshi, Atsushi
2014-01-01
The exact formulation of the path integral centroid dynamics is extended to include composites of the position and momentum operators. We present the generalized centroid dynamics (GCD), which provides a basis to calculate Kubo-transformed correlation functions by means of classical averages. We define various types of approximate GCD, one of which is equivalent to the ring polymer molecular dynamics (RPMD). The RPMD and another approximate GCD are tested in one-dimensional harmonic system, and it is shown that the RPMD works better in the short time region.
Nonlocalized cluster dynamics and nuclear molecular structure
Zhou, Bo; Horiuchi, Hisashi; Ren, Zhongzhou; Röpke, Gerd; Schuck, Peter; Tohsaki, Akihiro; Xu, Chang; Yamada, Taiichi
2013-01-01
A container picture is proposed for understanding cluster dynamics where the clusters make nonlocalized motion occupying the lowest orbit of the cluster mean-field potential characterized by the size parameter $``B"$ in the THSR (Tohsaki-Horiuchi-Schuck-R\\"{o}pke) wave function. The nonlocalized cluster aspects of the inversion-doublet bands in $^{20}$Ne which have been considered as a typical manifestation of localized clustering are discussed. So far unexplained puzzling features of the THSR wave function, namely that after angular-momentum projection for two cluster systems the prolate THSR wave function is almost 100$\\%$ equivalent to an oblate THSR wave function is clarified. It is shown that the true intrinsic two-cluster THSR configuration is nonetheless prolate. The proposal of the container picture is based on the fact that typical cluster systems, 2$\\alpha$, 3$\\alpha$, and $\\alpha$+$^{16}$O, are all well described by a single THSR wave function. It will be shown for the case of linear-chain states w...
Molecular dynamics simulations on PGLa using NMR orientational constraints.
Sternberg, Ulrich; Witter, Raiker
2015-11-01
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.
Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations
Bulacu, Monica; Goga, Nicolae; Zhao, Wei; Rossi, Giulia; Monticelli, Luca; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.
2013-01-01
Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules.
Calcium binding to the purple membrane : A molecular dynamics study
Wassenaar, Tsjerk A.; Daura, Xavier; Padros, Esteve; Mark, Alan E.
2009-01-01
The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highl
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.
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_18^2+ ...
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 tr
Active site modeling in copper azurin molecular dynamics simulations
Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R
2004-01-01
Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po
Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations
2008-07-17
Medical Research and Materiel Command, Fort Detrick, Maryland #Department of Cell Biology and Biochemistry , U.S. Army Medical Research Institute of...Molecular dynamics of n- alkanes ," J. Comput. Phys., vol. 23, pp. 327-341, 1977. [24] S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-10-01
Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.
Simulations of boundary migration during recrystallization using molecular dynamics
DEFF Research Database (Denmark)
Godiksen, Rasmus Brauner; Trautt, Z.T.; Upmanyu, M.
2007-01-01
We have applied an atomistic simulation methodology based on molecular dynamics to study grain boundary migration in crystalline materials, driven by the excess energy of dislocation arrangements. This method is used to simulate recrystallization in metals. The simulations reveal that the migration...
Nonlinear dynamics of zigzag molecular chains (in Russian)
DEFF Research Database (Denmark)
Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth;
1999-01-01
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-dependent...
Benchmark of Schemes for Multiscale Molecular Dynamics Simulations
Goga, N.; Melo, M. N.; Rzepiela, A. J.; de Vries, Alex; Hadar, A.; Marrink, S. J.; Berendsen, Herman
2015-01-01
In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hy
Molecular dynamics simulations of barrier crossings in the condensed phase
den Otter, Wouter K.
1998-01-01
The isomerisation rates of a calix[4]arene in vacuo and in two solvents have been computed by means of molecular dynamics simulations (MD). In MD the equations of classical mechanics are used to calculate the motion of the reacting molecule and the surrounding solvent molecules. Thus, the intricate
Reasoning with Atomic-Scale Molecular Dynamic Models
Pallant, Amy; Tinker, Robert F.
2004-01-01
The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…
Stability of Surface Nanobubbles: A Molecular Dynamics Study
Maheshwari, Shantanu; Hoef, van der Martin; Zhang, Xuehua; Lohse, Detlef
2016-01-01
The stability and growth or dissolution of a single surface nanobubble on a chemically patterned surface are studied by molecular dynamics simulations of binary mixtures consisting of Lennard-Jones (LJ) particles. Our simulations reveal how pinning of the three-phase contact line on the surface can
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...
Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations
De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut
2011-01-01
With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices c
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
Ab initio molecular dynamics study of Fe-containing smectites
Liu, X.; Meijer, E.J.; Lu, X.; Wang, R.
2010-01-01
In order to identify the influences imposed by Fe substitution, density functional theory-based Car-Parrinello molecular dynamics simulations were employed to study both oxidized and reduced Fe-bearing smectites. The following basic properties were investigated: local structures in the clay layer, h
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)
A Molecular Dynamics Approach to Grain Boundary Structure and Migration
DEFF Research Database (Denmark)
Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans
1974-01-01
It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...
Molecular Dynamic Screening Sesquiterpenoid Pogostemon Herba as Suggested Cyclooxygenase Inhibitor
Raharjo, Sentot Joko; Kikuchi, Takeshi
2016-01-01
Objective: Virtual molecular dynamic sesquiterpenoid Pogostemon Herba (CID56928117, CID94275, CID107152, and CID519743) have screening as cyclooxygenase (COX-1/COX-2) selective inhibitor. Methods: Molecular interaction studies sesquiterpenoid compounds with COX-1 and COX-2 were using the molecular docking tools by Hex 8.0 and interactions were further visualized using by Discovery Studio Client 3.5 software tool and Virtual Molecular Dynamic 1.9.1 software. The binding energy calculation of molecular dynamic interaction was calculated by AMBER12 software. Result: The analysis of the sesquiterpenoid compounds showed that CID56928117, CID94275, CID107152, and CID519743 have suggested as inhibitor of COX-1 and COX-2. Conclusion: Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor. PMID:28077888
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...... to wakes in the large Danish offshore wind farms at Horns Rev and Nysted indicated that losses were larger than expected. Temporary solutions have been found to account for this in wind farm models including use of an ‘added roughness’ block around the offshore wind farm. In the long-term however physical...
Molecular dynamics simulation of biomembranes in aqueous solution
Bostick, David Lee
In recent years, the developments in classical molecular dynamics simulation have allowed for an atomistic depiction of mesoscopic biological systems. With the awareness of such developments, the natural strive of the scientific community has been to increase the size of such simulated systems [70]. Nonetheless, the subtleties in the properties of biomembranes require an unusually thoughtful approach [70, 203]. In this work, a hierarchical approach is taken, with respect to system complexity, in the classical molecular dynamics simulation of biomembrane systems in aqueous solution. A progression of simulation studies is presented that begins with the analysis of the interfacial properties of neat bilayers composed of zwitterionic (phosphatidylcholine) lipids in both pure water and in electrolyte. We move on to study mixed bilayers containing zwitterionic (phosphatidylcholine) and acidic (phosphatidylserine) lipids with counterions immersed in electrolyte. Yet another layer of complexity is added to the problem by studying hydrated bilayers containing phosphatidylcholine lipids and cholesterol. Finally, we address the semipermeable nature of biomembranes by studying two membrane-channel systems. We start with a simple model membrane-channel consisting of a six-helix alamethicin bundle embedded in a hydrated phosphatidylcholine bilayer. The knowledge gained from this study is then carried over to the simulation of a large membrane-embedded prokaryotic ClC Cl-/H + antiporter, utilizing a free-energetic analysis to reveal the role of protons in the Cl- transport mechanism. Throughout the progression, methods are developed and used in the analysis of interfacial aqueous solution structure, ion-membrane binding, lipid structural properties, inter-lipid hydrogen bonded complexation, and electrostatics at the membrane interface. The developments reveal the layered nature of water near the rugged, molecularscale aqueous solution/membrane interface and its electrostatic
STRUCTURE AND DYNAMICS OF ALKALI BORATE GLASSES - A MOLECULAR-DYNAMICS STUDY
VERHOEF, AH; DENHARTOG, HW
1995-01-01
Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at all
Watching coherent molecular structural dynamics during photoreaction: beyond kinetic description
Lemke, Henrik T; Hartsock, Robert; van Driel, Tim Brandt; Chollet, Matthieu; Glownia, J M; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Nielsen, Martin M; Benfatto, Maurizio; Gaffney, Kelly J; Collet, Eric; Cammarata, Marco
2015-01-01
A deep understanding of molecular photo-transformations occurring is challenging because of the complex interaction between electronic and nuclear structure. The initially excited electronic energy dissipates into electronic and structural reconfigurations often in less than a billionth of a second. Molecular dynamics induced by photoexcitation have been very successfully studied with femtosecond optical spectroscopies, but electronic and nuclear dynamics are often very difficult to disentangle. X-ray based spectroscopies can reduce the ambiguity between theoretical models and experimental data, but it is only with the recent development of bright ultrafast X-ray sources, that key information during transient molecular processes can be obtained on their intrinsic timescale. We use Free Electron Laser (FEL) based time-resolved X-ray Absorption Near Edge Structure (XANES) measurements around the Iron K-edge of a spin crossover prototypical compound. We reveal its transformation from the ligand-located electroni...
Coarse-grained molecular dynamics simulations of biomolecules
Directory of Open Access Journals (Sweden)
Ken Takahashi
2014-03-01
Full Text Available Coarse-grained molecular dynamics (CGMD simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.
Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.
Tavernelli, Ivano
2015-03-17
Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular
Shock waves simulated using the dual domain material point method combined with molecular dynamics
Zhang, Duan Z.; Dhakal, Tilak R.
2017-04-01
In this work we combine the dual domain material point method with molecular dynamics in an attempt to create a multiscale numerical method to simulate materials undergoing large deformations with high strain rates. In these types of problems, the material is often in a thermodynamically nonequilibrium state, and conventional constitutive relations or equations of state are often not available. In this method, the closure quantities, such as stress, at each material point are calculated from a molecular dynamics simulation of a group of atoms surrounding the material point. Rather than restricting the multiscale simulation in a small spatial region, such as phase interfaces, or crack tips, this multiscale method can be used to consider nonequilibrium thermodynamic effects in a macroscopic domain. This method takes the advantage that the material points only communicate with mesh nodes, not among themselves; therefore molecular dynamics simulations for material points can be performed independently in parallel. The dual domain material point method is chosen for this multiscale method because it can be used in history dependent problems with large deformation without generating numerical noise as material points move across cells, and also because of its convergence and conservation properties. To demonstrate the feasibility and accuracy of this method, we compare the results of a shock wave propagation in a cerium crystal calculated using the direct molecular dynamics simulation with the results from this combined multiscale calculation.
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.
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.
Combining docking and molecular dynamic simulations in drug design.
Alonso, Hernán; Bliznyuk, Andrey A; Gready, Jill E
2006-09-01
A rational approach is needed to maximize the chances of finding new drugs, and to exploit the opportunities of potential new drug targets emerging from genomic and proteomic initiatives, and from the large libraries of small compounds now readily available through combinatorial chemistry. Despite a shaky early history, computer-aided drug design techniques can now be effective in reducing costs and speeding up drug discovery. This happy outcome results from development of more accurate and reliable algorithms, use of more thoughtfully planned strategies to apply them, and greatly increased computer power to allow studies with the necessary reliability to be performed. Our review focuses on applications and protocols, with the main emphasis on critical analysis of recent studies where docking calculations and molecular dynamics (MD) simulations were combined to dock small molecules into protein receptors. We highlight successes to demonstrate what is possible now, but also point out drawbacks and future directions. The review is structured to lead the reader from the simpler to more compute-intensive methods. Thus, while inexpensive and fast docking algorithms can be used to scan large compound libraries and reduce their size, more accurate but expensive MD simulations can be applied when a few selected ligand candidates remain. MD simulations can be used: during the preparation of the protein receptor before docking, to optimize its structure and account for protein flexibility; for the refinement of docked complexes, to include solvent effects and account for induced fit; to calculate binding free energies, to provide an accurate ranking of the potential ligands; and in the latest developments, during the docking process itself to find the binding site and correctly dock the ligand a priori.
Influence of conformational molecular dynamics on matter wave interferometry
Gring, Michael; Eibenberger, Sandra; Nimmrichter, Stefan; Berrada, Tarik; Arndt, Markus; Ulbricht, Hendrik; Hornberger, Klaus; Müri, Marcel; Mayor, Marcel; Böckmann, Marcus; Doltsinis, Nikos
2014-01-01
We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum object, our experiment demonstrates that the translational quantum phase is sensitive to dynamic conformational state changes inside the diffracted molecules. The structural flexibility of tailor-made hot organic particles is sufficient to admit a mixture of strongly fluctuating dipole moments. These modify the electric susceptibility and through this the quantum interference pattern in the presence of an external electric field. Detailed molecular dynamics simulations combined with density functional theory allow us to quantify the time-dependent structural reconfigurations and to predict the ensemble-averaged square of the dipole moment which is found to be in good agreement with the interferometric result. The experiment thus opens a new perspective on matter wave interfe...
Reaction dynamics of molecular hydrogen on silicon surfaces
DEFF Research Database (Denmark)
Bratu, P.; Brenig, W.; Gross, A.
1996-01-01
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...... 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......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...
GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.
Energy Technology Data Exchange (ETDEWEB)
HALL, G.E.
2006-05-30
This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.
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...... the temporal correlation function and dynamical friction within density functional theory....
A family of dynamic models for large-eddy simulation
Carati, D.; Jansen, K.; Lund, T.
1995-01-01
Since its first application, the dynamic procedure has been recognized as an effective means to compute rather than prescribe the unknown coefficients that appear in a subgrid-scale model for Large-Eddy Simulation (LES). The dynamic procedure is usually used to determine the nondimensional coefficient in the Smagorinsky (1963) model. In reality the procedure is quite general and it is not limited to the Smagorinsky model by any theoretical or practical constraints. The purpose of this note is to consider a generalized family of dynamic eddy viscosity models that do not necessarily rely on the local equilibrium assumption built into the Smagorinsky model. By invoking an inertial range assumption, it will be shown that the coefficients in the new models need not be nondimensional. This additional degree of freedom allows the use of models that are scaled on traditionally unknown quantities such as the dissipation rate. In certain cases, the dynamic models with dimensional coefficients are simpler to implement, and allow for a 30% reduction in the number of required filtering operations.
Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart
2015-01-22
Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the
Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.
Fogarty, Aoife C; Laage, Damien
2014-07-17
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.
Local near instantaneously dynamically triggered aftershocks of large earthquakes
Fan, Wenyuan; Shearer, Peter M.
2016-09-01
Aftershocks are often triggered by static- and/or dynamic-stress changes caused by mainshocks. The relative importance of the two triggering mechanisms is controversial at near-to-intermediate distances. We detected and located 48 previously unidentified large early aftershocks triggered by earthquakes with magnitudes between ≥7 and 8 within a few fault lengths (approximately 300 kilometers), during times that high-amplitude surface waves arrive from the mainshock (less than 200 seconds). The observations indicate that near-to-intermediate-field dynamic triggering commonly exists and fundamentally promotes aftershock occurrence. The mainshocks and their nearby early aftershocks are located at major subduction zones and continental boundaries, and mainshocks with all types of faulting-mechanisms (normal, reverse, and strike-slip) can trigger early aftershocks.
Large N classical dynamics of holographic matrix models
Asplund, Curtis T; Dzienkowski, Eric
2014-01-01
Using a numerical simulation of the classical dynamics of the plane-wave and flat space matrix models of M-theory, we study the thermalization, equilibrium thermodynamics and fluctuations of these models as we vary the temperature and the size of the matrices, N. We present our numerical implementation in detail and several checks of its precision and consistency. We show evidence for thermalization by matching the time-averaged distributions of the matrix eigenvalues to the distributions of the appropriate Traceless Gaussian Unitary Ensemble of random matrices. We study the autocorrelations and power spectra for various fluctuating observables and observe evidence of the expected chaotic dynamics as well as a hydrodynamic type limit at large N, including near-equilibrium dissipation processes. These configurations are holographically dual to black holes in the dual string theory or M-theory and we discuss how our results could be related to the corresponding supergravity black hole solutions.
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.
Dynamic characteristics of nanoindentation in Ni:A molecular dynamics simulation study
Institute of Scientific and Technical Information of China (English)
Muhammad Imran; Fayyaz Hussain; Muhammad Rashid; S.A.Ahmad
2012-01-01
In this work,three-dimensional molecular dynamics simulation is carried out to elucidate the nanoindentation behaviour of single crystal Ni.The substrate indenter system is modelled using hybrid interatomic potentials including the manybody potential (embedded atom method) and two-body Morse potential.The spherical indenter is chosen,and the simulation is performed for different loading rates from 10 m/s to 200 m/s.Results show that the maximum indentation load and hardness of the system increase with the increase of velocity.The effect of indenter size on the nanoindentation response is also analysed.It is found that the maximum indentation load is higher for the large indenter whereas the hardness is higher for the smaller indenter.Dynamic nanoindentation is carried out to investigate the behaviour of Ni substrate to multiple loading-unloading cycles.It is observed from the results that the increase in the number of loading unloading cycles reduces the maximum load and hardness of the Ni substrate.This is attributed to the decrease in recovery force due to defects and dislocations produced after each indentation cycle.
Dynamical modeling and analysis of large cellular regulatory networks
Bérenguier, D.; Chaouiya, C.; Monteiro, P. T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L.
2013-06-01
The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.
Markov State Models for Rare Events in Molecular Dynamics
Directory of Open Access Journals (Sweden)
Marco Sarich
2013-12-01
Full Text Available Rare, but important, transition events between long-lived states are a key feature of many molecular systems. In many cases, the computation of rare event statistics by direct molecular dynamics (MD simulations is infeasible, even on the most powerful computers, because of the immensely long simulation timescales needed. Recently, a technique for spatial discretization of the molecular state space designed to help overcome such problems, so-called Markov State Models (MSMs, has attracted a lot of attention. We review the theoretical background and algorithmic realization of MSMs and illustrate their use by some numerical examples. Furthermore, we introduce a novel approach to using MSMs for the efficient solution of optimal control problems that appear in applications where one desires to optimize molecular properties by means of external controls.
Molecular dynamics computer simulation of permeation in solids
Energy Technology Data Exchange (ETDEWEB)
Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M. [Sandia National Labs., Albuquerque, NM (United States)
1997-12-31
In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.
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.
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.
Xia, Junchao; Flynn, William F; Gallicchio, Emilio; Zhang, Bin W; He, Peng; Tan, Zhiqiang; Levy, Ronald M
2015-09-05
We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta-cyclodextrin-heptanoate host-guest system in the context of one- and two-dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (>picoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle.
Molecular dynamics analysis on impact behavior of carbon nanotubes
Energy Technology Data Exchange (ETDEWEB)
Seifoori, Sajjad, E-mail: sajjad.seifoori@vru.ac.ir
2015-01-30
Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler–Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation.
Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water.
Comez, L; Paolantoni, M; Sassi, P; Corezzi, S; Morresi, A; Fioretto, D
2016-07-07
When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.
Asymptotic dynamics, large gauge transformations and infrared symmetries
Gomez, Cesar
2016-01-01
Infrared finite S matrices enjoy an infinite family of symmetries, namely decoupling of asymptotic soft modes with arbitrary direction. The infrared structure of the theory manifests itself in the form of vacuum degeneracy and in nontrivial asymptotic dynamics. These two ingredients are unified in the infrared finite S matrix symmetries and can be disentangled as soft and hard components of corresponding charges. When these two components are disentangled, the nontrivial role of large gauge transformations becomes manifest. The soft decoupling symmetry of the physical S matrix leads to relations between the corresponding soft/hard decompositions for the in and out states that can encode crucial nontrivial information about the scattering process.
Adiabatic hyperspherical approach to large-scale nuclear dynamics
Suzuki, Yasuyuki
2015-01-01
We formulate a fully microscopic approach to large-scale nuclear dynamics using a hyperradius as a collective coordinate. An adiabatic potential is defined by taking account of all possible configurations at a fixed hyperradius, and its hyperradius dependence plays a key role in governing the global nuclear motion. In order to go to larger systems beyond few-body systems, we suggest basis functions of a microscopic multicluster model, propose a method for calculating matrix elements of an adiabatic Hamiltonian with use of Fourier transforms, and test its effectiveness.
The dynamics and control of large flexible space structures
Bainum, P. M.; Krishna, R.; Kumar, V. K.; Reddy, A. S. S. R.
1981-01-01
The dynamics and attitude and shape control of very large, inherently flexible spacecraft systems were investigated. Increasingly more complex examples were examined, beginning with a uniform free-free beam, next a free-free uniform plate/platform and finally by considering a thin shallow spherical shell structure in orbit. The effects devices were modeled. For given sets of assumed actuator locations, the controllability of these systems was first established. Control laws for each of the actuators were developed based on decoupling techniques (including distributed modal control) pole placement algorithms and a application of the linear regulator problem for optical control theory.
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)
Ab initio molecular dynamics using hybrid density functionals
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Koehl, Patrice; Poitevin, Frédéric; Navaza, Rafael; Delarue, Marc
2017-03-14
Understanding the dynamics of biomolecules is the key to understanding their biological activities. Computational methods ranging from all-atom molecular dynamics simulations to coarse-grained normal-mode analyses based on simplified elastic networks provide a general framework to studying these dynamics. Despite recent successes in studying very large systems with up to a 100,000,000 atoms, those methods are currently limited to studying small- to medium-sized molecular systems due to computational limitations. One solution to circumvent these limitations is to reduce the size of the system under study. In this paper, we argue that coarse-graining, the standard approach to such size reduction, must define a hierarchy of models of decreasing sizes that are consistent with each other, i.e., that each model contains the information of the dynamics of its predecessor. We propose a new method, Decimate, for generating such a hierarchy within the context of elastic networks for normal-mode analysis. This method is based on the concept of the renormalization group developed in statistical physics. We highlight the details of its implementation, with a special focus on its scalability to large systems of up to millions of atoms. We illustrate its application on two large systems, the capsid of a virus and the ribosome translation complex. We show that highly decimated representations of those systems, containing down to 1% of their original number of atoms, still capture qualitatively and quantitatively their dynamics. Decimate is available as an OpenSource resource.
Large-deformation modal coordinates for nonrigid vehicle dynamics
Likins, P. W.; Fleischer, G. E.
1972-01-01
The derivation of minimum-dimension sets of discrete-coordinate and hybrid-coordinate equations of motion of a system consisting of an arbitrary number of hinge-connected rigid bodies assembled in tree topology is presented. These equations are useful for the simulation of dynamical systems that can be idealized as tree-like arrangements of substructures, with each substructure consisting of either a rigid body or a collection of elastically interconnected rigid bodies restricted to small relative rotations at each connection. Thus, some of the substructures represent elastic bodies subjected to small strains or local deformations, but possibly large gross deformations, in the hybrid formulation, distributed coordinates referred to herein as large-deformation modal coordinates, are used for the deformations of these substructures. The equations are in a form suitable for incorporation into one or more computer programs to be used as multipurpose tools in the simulation of spacecraft and other complex electromechanical systems.
THE LARGE SCALE MOLECULAR ENVIRONMENT TOWARDS WESTERLUND 1
Directory of Open Access Journals (Sweden)
A. Luna
2009-01-01
Full Text Available We report the discovery of an out ow and a molecular cavity at the Norma near-arm around the young Super Star Cluster (SSC Westerlund 1 (Wd1. Association of the SSC Wd1 with the cavity and the molecular out- ow is discussed based on the observed kinematics from CO and HI emission, and also in the observed HI absorptions. We conclude that the possibility of association of Wd1 with the cavity is high if both are located at a distance of 5.0=0.5Kpc, which is a factor 1.4 farther than the most recent distance estimation to Wd1. The shell surrounding the cavity has a molecular mass of 1 x 106 M and is expanding at a velocity of 8 km s-1. The corresponding kinetic energy of expansion is 1 x 1051 erg. The magnetar associated with Wd1 could be the source of this energy.
Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach.
Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano
2017-03-10
Peptides have gained increased interest as therapeutic agents during recent years. The high specificity and relatively low toxicity of peptide drugs derive from their extremely tight binding to their targets. Indeed, understanding the molecular mechanism of protein-peptide recognition has important implications in the fields of biology, medicine, and pharmaceutical sciences. Even if crystallography and nuclear magnetic resonance are offering valuable atomic insights into the assembling of the protein-peptide complexes, the mechanism of their recognition and binding events remains largely unclear. In this work we report, for the first time, the use of a supervised molecular dynamics approach to explore the possible protein-peptide binding pathways within a timescale reduced up to three orders of magnitude compared with classical molecular dynamics. The better and faster understating of the protein-peptide recognition pathways could be very beneficial in enlarging the applicability of peptide-based drug design approaches in several biotechnological and pharmaceutical fields.
Correlations and Symmetry of Interactions Influence Collective Dynamics of Molecular Motors
Celis-Garza, Daniel; 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 ad...
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.
Large-Scale Filaments: Newtonian versus Modified Dynamics
Milgrom, Mordehai
1997-03-01
Eisenstein, Loeb, & Turner (ELT) have recently proposed a method for estimating the dynamical masses of large-scale filaments, whereby the filament is modeled by an infinite, axisymmetric, isothermal, self-gravitating, radially virialized cylinder, for which ELT derive a global relation between the (constant) velocity dispersion and the total line density. We show that the model assumptions of ELT can be relaxed materially: an exact relation between the rms velocity and the line density can be derived for any infinite cylinder (not necessarily axisymmetric) with an arbitrary constituent distribution function (so isothermality need not be assumed). We also consider the same problem in the context of the modified Newtonian dynamics (MOND). After we compare the scaling properties in the two theories, we study two idealized MOND model filaments, one with assumptions similar to those of ELT, which we can only solve numerically, and another, which we solve in closed form. A preliminary application to the same segment of the Perseus-Pisces filament treated by ELT gives MOND M/L estimates of order 10(M/L)⊙, compared with the Newtonian value M/L ~ 450(H0/100 km s-1 Mpc-1)(M/L)⊙ that ELT find. In spite of the large uncertainties still besetting the analysis, this instance of MOND application is of particular interest because (1) objects of this geometry have not been dealt with before; (2) it pertains to large-scale structure; and (3) the typical accelerations involved are the lowest so far encountered in a semivirialized system--only a few percent of the critical MOND acceleration--leading to a large predicted mass discrepancy.
Lahnsteiner, Jonathan; Kresse, Georg; Kumar, Abhinav; Sarma, D. D.; Franchini, Cesare; Bokdam, Menno
2016-12-01
The high efficiency of lead organo-metal-halide perovskite solar cells has raised many questions about the role of the methylammonium (MA) molecules in the Pb-I framework. Experiments indicate that the MA molecules are able to "freely" spin around at room temperature even though they carry an intrinsic dipole moment. We have performed large supercell (2592 atoms) finite-temperature ab initio molecular dynamics calculations to study the correlation between the molecules in the framework. An underlying long-range antiferroelectric ordering of the molecular dipoles is observed. The dynamical correlation between neighboring molecules shows a maximum around room temperature in the mid-temperature phase. In this phase, the rotations are slow enough to (partially) couple to neighbors via the Pb-I cage. This results in a collective motion of neighboring molecules in which the cage acts as the mediator. At lower and higher temperatures, the motions are less correlated.
Quantum dynamics of bio-molecular systems in noisy environments
Plenio, M B
2012-01-01
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.
Molecular dynamics simulation of liquid-vapor surface tension
Institute of Scientific and Technical Information of China (English)
王德; ZENG; Danling; 等
2002-01-01
A molecular dynamics simulation model is established based on the well-known Lennard-Jones 12-6 potential function to determine the surface tension of a Lennard-Jones liquid-vapor interface.The simulation is carried out with argon as the working fluid of a given molecular number at different temperature and different truncated radius.It is found that the surface tension of a Lennard-Jones fluid is likely to be bigger for a bigger truncated radius,and tends to be constant after the truncated radius increased to a certain value.It is also found that the surface tension becomes smaller as the temperature increases.
A molecular dynamics study of polymer/graphene interfacial systems
Energy Technology Data Exchange (ETDEWEB)
Rissanou, Anastassia N.; Harmandaris, Vagelis [Department of Mathematics and Applied Mathematics, University of Crete, GR-71409, Heraklion, Crete, Greece and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-71110, Heraklion, Cret (Greece)
2014-05-15
Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.
Anomalous flow behavior in nanochannels: A molecular dynamics study
Murad, Sohail; Luo, Lin; Chu, Liang-Yin
2010-06-01
We report molecular dynamics simulations of flow of water in nanochannels with a range of surface wettability characteristics (hydrophobic to strongly hydrophilic) and driving forces (pressures). Our results show apparently anomalous behavior. At low pressures, the rate is higher in nanochannels with hydrophilic surfaces than that with hydrophobic surfaces; however, with high pressure driven flow we observe opposite trends. This apparently anomalous behavior can be explained on the basis of molecular thermodynamics and fluid mechanics considerations. Understanding such behavior is important in many nanofluidic devices such as nanoreactors, nanosensors, and nanochips that are increasingly being designed and used.
Molecular dynamics simulations of diffusion mechanisms in NiAl
Energy Technology Data Exchange (ETDEWEB)
Soule De Bas, B.; Farkas, D
2003-03-14
Molecular dynamics simulations of the diffusion process in ordered B2 NiAl at high temperature were performed using an embedded atom interatomic potential. Diffusion occurs through a variety of cyclic mechanisms that accomplish the motion of the vacancy through nearest neighbor jumps restoring order to the alloy at the end of the cycle. The traditionally postulated six-jump cycle is only one of the various cycles observed and some of these are quite complex. A detailed sequential analysis of the observed six-jump cycles was performed and the results are analyzed in terms of the activation energies for individual jumps calculated using molecular statics simulations.
Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ
DEFF Research Database (Denmark)
Euro, Liliya; Haapanen, Outi; Róg, Tomasz
2017-01-01
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...... 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...
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.
Two years ago, when we first proposed to organize a Workship on Molecular Dynamics of Proteins. We desired a format that combined elements of these...students of the field. Molecular Dynamics of Biomolecules; Methods in Molecular Dynamics ; Potential Functions for Simulations of Biomolecules...Statistical Mechanics and Molecular Dynamics ; Molecular Dynamics and Structure Refinement; Simulation of Activated Processes and Reactions; Graphics; Computer
Large mass hierarchies from strongly-coupled dynamics
Athenodorou, Andreas; Bergner, Georg; Elander, Daniel; Lin, C -J David; Lucini, Biagio; Piai, Maurizio
2016-01-01
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 ...
Large-scale filaments-newtonian vs. modified dynamics
Milgrom, M
1996-01-01
Eisenstein Loeb and Turner (ELT) have recently proposed a method for estimating the dynamical masses of large-scale filaments, whereby the filament is modeled by an axisymmetric, isothermal cylinder, for which ELT derive a global relation between the (constant) velocity dispersion and the total line density. We first show that the model assumptions of ELT can be relaxed materially: an exact relation between the velocity and line density is derived for any cylinder (not necessarily axisymmetric), with an arbitrary constituent distribution function (so isothermality need not be assumed). We then consider the same problem in the context of the modified dynamics (MOND). After a brief comparison between scaling properties in the two theories, we study idealized MOND model filaments. A preliminary application to the segment of the Perseus-Pisces filament treated by ELT, gives MOND M/L estimates of order 10 s.u., compared with the Newtonian value of about 450, which ELT find. In spite of the large uncertainties stil...
Illig, Steffen; Eggeman, Alexander S; Troisi, Alessandro; Jiang, Lang; Warwick, Chris; Nikolka, Mark; Schweicher, Guillaume; Yeates, Stephen G; Henri Geerts, Yves; Anthony, John E; Sirringhaus, Henning
2016-02-22
Thermal vibrations and the dynamic disorder they create can detrimentally affect the transport properties of van der Waals bonded molecular semiconductors. The low-energy nature of these vibrations makes it difficult to access them experimentally, which is why we still lack clear molecular design rules to control and reduce dynamic disorder. In this study we discuss the promising organic semiconductors rubrene, 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothio-phene and 2,9-di-decyl-dinaphtho-[2,3-b:20,30-f]-thieno-[3,2-b]-thiophene in terms of an exceptionally low degree of dynamic disorder. In particular, we analyse diffuse scattering in transmission electron microscopy, to show that small molecules that have their side chains attached along the long axis of their conjugated core are better encapsulated in their crystal structure, which helps reduce large-amplitude thermal motions. Our work provides a general strategy for the design of new classes of very high mobility organic semiconductors with a low degree of dynamic disorder.
Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.
2010-01-01
As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…
Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.
2010-01-01
As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…
Large dynamic range diagnostics for high current electron LINACs
Energy Technology Data Exchange (ETDEWEB)
Evtushenko, Pavel [JLAB
2013-11-01
The Jefferson Lab FEL driver accelerator - Energy Recovery Linac has provided a beam with average current of up to 9 mA and beam energy of 135 MeV. The high power beam operations have allowed developing and testing methods and approaches required to set up and tune such a facility simultaneously for the high beam power and high beam quality required for high performance FEL operations. In this contribution we briefly review this experience and outline problems that are specific to high current - high power non-equilibrium linac beams. While the original strategy for beam diagnostics and tuning have proven to be quite successful, some shortcomings and unresolved issues were also observed. The most important issues are the non-equilibrium (non-Gaussian) nature of the linac beam and the presence of small intensity - large amplitude fraction of the beam a.k.a. beam halo. Thus we also present a list of the possible beam halo sources and discuss possible mitigations means. We argue that for proper understanding and management of the beam halo large dynamic range (>10{sup 6}) transverse and longitudinal beam diagnostics can be used. We also present results of transverse beam profile measurements with the dynamic range approaching 10{sup 5} and demonstrate the effect the increased dynamic range has on the beam characterization, i.e., emittance and Twiss parameters measurements. We also discuss near future work planned in this field and where the JLab FEL facility will be used for beam tests of the developed of new diagnostics.
Large dynamic range diagnostics for high current electron LINACs
Energy Technology Data Exchange (ETDEWEB)
Evtushenko, P., E-mail: Pavel.Evtushenko@jlab.org [Thomas Jefferson National Accelerator Facility 12000 Jefferson Avenue, Newport News, VA 23606 (United States)
2013-11-07
The Jefferson Lab FEL driver accelerator - Energy Recovery Linac has provided a beam with average current of up to 9 mA and beam energy of 135 MeV. The high power beam operations have allowed developing and testing methods and approaches required to set up and tune such a facility simultaneously for the high beam power and high beam quality required for high performance FEL operations. In this contribution we briefly review this experience and outline problems that are specific to high current - high power non-equilibrium linac beams. While the original strategy for beam diagnostics and tuning have proven to be quite successful, some shortcomings and unresolved issues were also observed. The most important issues are the non-equilibrium (non-Gaussian) nature of the linac beam and the presence of small intensity - large amplitude fraction of the beam a.k.a. beam halo. Thus we also present a list of the possible beam halo sources and discuss possible mitigations means. We argue that for proper understanding and management of the beam halo large dynamic range (>10{sup 6}) transverse and longitudinal beam diagnostics can be used. We also present results of transverse beam profile measurements with the dynamic range approaching 10{sup 5} and demonstrate the effect the increased dynamic range has on the beam characterization, i.e., emittance and Twiss parameters measurements. We also discuss near future work planned in this field and where the JLab FEL facility will be used for beam tests of the developed of new diagnostics.
Ab initio molecular dynamics study of liquid methanol
Handgraaf, J W; Meijer, E J; Handgraaf, Jan-Willem; Erp, Titus S. van; Meijer, Evert Jan
2003-01-01
We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.
Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms
Energy Technology Data Exchange (ETDEWEB)
Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R
2005-02-02
Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.
Molecular dynamical simulations of melting behaviors of metal clusters
Directory of Open Access Journals (Sweden)
Ilyar Hamid
2015-04-01
Full Text Available The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002] for the statically stable structures.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
Surprising Existence of Massive and Large Molecular Gas Reservoirs in A Distant Protocluster
Dannerbauer, Helmut
2017-07-01
We know that environment has a critical impact on galaxy growth and evolution. What we do not know is when it starts to have an impact and how it does it. I present results of our on-going survey of low surface brightness emission of cold molecular gas in protoclusters galaxies and their halos with the Australian Telescope Compact Array (ATCA). These findings alter our view of the important topics of the development and gas phase distribution of the "proto-intracluster medium": how ram pressure stripping may operate in protoclusters, how the galaxies may contribute to the proto-intracluster medium and how their star formation may be limited by dynamics. Finally, I present our new ATCA Large Program, COALAS (CO ATCA Legacy Archive of Star-Forming Galaxies), which will extend significantly our study of environmental effects on cluster and field galaxies.
Kobayashi, Fumiharu
2015-01-01
We extend the method of antisymmetrized molecular dynamics to investigate dineutron correlation. We apply this method to $^{10}$Be as an example and investigate the motion of two neutrons around a largely deformed $^8$Be core by analyzing the two-neutron overlap function around the core. We show that the core structure plays an important role in dineutron formation and expansion from the core and that the present framework is effective for the studies of dineutron correlation.
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.
Molecular dynamics simulation of phosphorylated KID post-translational modification.
Directory of Open Access Journals (Sweden)
Hai-Feng Chen
Full Text Available BACKGROUND: 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. METHODOLOGY: 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. CONCLUSIONS: 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.
Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems.
Nemec, Mike; Hoffmann, Daniel
2017-02-14
Molecular dynamics (MD) simulation is a natural method for the study of flexible molecules but at the same time is limited by the large size of the conformational space of these molecules. We ask by how much the MD sampling quality for flexible molecules can be improved by two means: the use of diverse sets of trajectories starting from different initial conformations to detect deviations between samples and sampling with enhanced methods such as accelerated MD (aMD) or scaled MD (sMD) that distort the energy landscape in controlled ways. To this end, we test the effects of these approaches on MD simulations of two flexible biomolecules in aqueous solution, Met-Enkephalin (5 amino acids) and HIV-1 gp120 V3 (a cycle of 35 amino acids). We assess the convergence of the sampling quantitatively with known, extensive measures of cluster number Nc and cluster distribution entropy Sc and with two new quantities, conformational overlap Oconf and density overlap Odens, both conveniently ranging from 0 to 1. These new overlap measures quantify self-consistency of sampling in multitrajectory MD experiments, a necessary condition for converged sampling. A comprehensive assessment of sampling quality of MD experiments identifies the combination of diverse trajectory sets and aMD as the most efficient approach among those tested. However, analysis of Odens between conventional and aMD trajectories also reveals that we have not completely corrected aMD sampling for the distorted energy landscape. Moreover, for V3, the courses of Nc and Odens indicate that much higher resources than those generally invested today will probably be needed to achieve convergence. The comparative analysis also shows that conventional MD simulations with insufficient sampling can be easily misinterpreted as being converged.
Amorphous silicene—a view from molecular dynamics simulation
Van Hoang, Vo; Long, N. T.
2016-05-01
Models of amorphous silicene (a-silicene) containing 104 atoms are obtained by cooling from the melt via molecular dynamics (MD) simulation. The evolution of various kinds of structural and thermodynamic behavior in models upon cooling from the melt is found, including total energy, radial distribution function (RDF), interatomic distance, coordination number, and ring and bond-angle distributions. We also show the buckling distribution and a 2D visualization of the atomic configurations. The diffraction pattern shows that a glass state is indeed formed in the system. The glass transition temperature of 2D silicon ({{T}\\text{g}}=1350 K) has a reasonable value compared to that of its 3D counterpart. Calculations show that although most atoms in a-silicene obtained at 300 K have a three-fold coordination and mainly evolve into six-fold rings, a-silicene also contains various structural defects including those not found in crystalline silicene (c-silicene) such as adatoms, clusters of small-membered rings, large-membered rings and local linear defects. The concentration of defects in a-silicene is much higher than that of the crystalline version. We find that buckling is not unique for all the atoms in the model. The strong distorted structure of a-silicene compared to that of the crystalline version may lead to physico-chemical properties, including the possibility of opening the band gap in the former compared to the zero band gap of the latter. Note that due to the fixed length being equal to buckling of 0.44 Å in the z direction with the elastic reflection behavior boundary, our models are relevant for a-silicene formed in confinement between two planar simple hard walls.
Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan
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
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
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.
Kinetic distance and kinetic maps from molecular dynamics simulation
Noe, Frank
2015-01-01
Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine...
Serine Proteases an Ab Initio Molecular Dynamics Study
De Santis, L
1999-01-01
In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.
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.
Excitation Dynamics and Relaxation in a Molecular Heterodimer
Balevicius, V; Abramavicius, D; Mancal, T; Valkunas, L
2011-01-01
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 energy gap of the molecular excitation, 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.
Surface hopping in laser-driven molecular dynamics
Fiedlschuster, T.; Handt, J.; Gross, E. K. U.; Schmidt, R.
2017-06-01
A theoretical justification of the empirical surface hopping method for the laser-driven molecular dynamics is given by utilizing the formalism of the exact factorization of the molecular wave function [Abedi et al., Phys. Rev. Lett. 105, 123002 (2010), 10.1103/PhysRevLett.105.123002] in its quantum-classical limit. Employing an exactly solvable H2+-like model system, it is shown that the deterministic classical nuclear motion on a single time-dependent surface in this approach describes the same physics as stochastic (hopping-induced) motion on several surfaces, provided Floquet surfaces are applied. Both quantum-classical methods do describe reasonably well the exact nuclear wave-packet dynamics for extremely different dissociation scenarios. Hopping schemes using Born-Oppenheimer surfaces or instantaneous Born-Oppenheimer surfaces fail completely.
Surface hopping methodology in laser-driven molecular dynamics
Fiedlschuster, T; Gross, E K U; Schmidt, R
2016-01-01
A theoretical justification of the empirical surface hopping method for the laser-driven molecular dynamics is given utilizing the formalism of the exact factorization of the molecular wavefunction [Abedi et al., PRL $\\textbf{105}$, 123002 (2010)] in its quantum-classical limit. Employing an exactly solvable $\\textrm H_2^{\\;+}$-like model system, it is shown that the deterministic classical nuclear motion on a single time-dependent surface in this approach describes the same physics as stochastic (hopping-induced) motion on several surfaces, provided Floquet surfaces are applied. Both quantum-classical methods do describe reasonably well the exact nuclear wavepacket dynamics for extremely different dissociation scenarios. Hopping schemes using Born-Oppenheimer surfaces or instantaneous Born-Oppenheimer surfaces fail completely.
Tensor-optimized antisymmetrized molecular dynamics in nuclear physics
Myo, Takayuki; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro
2015-01-01
We develop a new formalism to treat nuclear many-body systems using bare nucleon-nucleon interaction. It has become evident that the tensor interaction plays important role in nuclear many-body systems due to the role of the pion in strongly interacting system. We take the antisymmetrized molecular dynamics (AMD) as a basic framework and add a tensor correlation operator acting on the AMD wave function using the concept of the tensor-optimized shell model (TOSM). We demonstrate a systematical and straightforward formulation utilizing the Gaussian integration and differentiation method and the antisymmetrization technique to calculate all the matrix elements of the many-body Hamiltonian. We can include the three-body interaction naturally and calculate the matrix elements systematically in the progressive order of the tensor correlation operator. We call the new formalism "tensor-optimized antisymmetrized molecular dynamics".
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...... 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......), BMC Struct. Biol., 8) and the approach to fix the water activity which often is used in experimental studies. The water activity is shown to have a profound effect on the structure and dynamics of CALB. Conformational flexibility, for instance, increases with increasing hydration in acetone, t...
Visual verification and analysis of cluster detection for molecular dynamics.
Grottel, Sebastian; Reina, Guido; Vrabec, Jadran; Ertl, Thomas
2007-01-01
A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented.
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...
Molecular dynamics investigation of radiation damage in semiconductors
Good, Brian S.
1991-01-01
Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.
Molecular Dynamics study of Pb overlayer on Cu(100)
Karimi, M.; Tibbits, P.; Ila, D.; Dalins, I.; Vidali, G.
1991-01-01
Isothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2x2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.
Simulation of a flowing snow avalanche using molecular dynamics
2010-01-01
Ankara : The Department of Computer Engineering and the Institute of Engineering and Science of Bilkent University, 2010. Thesis (Master's) -- Bilkent University, 2010. Includes bibliographical references leaves 45-50. This thesis presents an approach for modeling and simulation of a flowing snow avalanche, which is formed of dry and liquefied snow that slides down a slope, by using molecular dynamics and discrete element method. A particle system is utilized as a base method for th...
Caloric Effects in Methylammonium Lead Iodide from Molecular Dynamics Simulations
Liu, Shi; Cohen, Ronald E.
2016-01-01
Organic-inorganic hybrid perovskite architecture could serve as a robust platform for materials design to realize functionalities beyond photovoltaic applications. We explore caloric effects in organometal halide perovskites, taking methylammonium lead iodide (MAPbI$_3$) as an example, using all-atom molecular dynamics simulations with a first-principles based interatomic potential. The adiabatic thermal change is estimated directly by introducing different driving fields in the simulations. ...
Molecular Dynamics Simulation of Shear Moduli for Coulomb Crystals
Horowitz, C J
2008-01-01
Torsional (shear) oscillations of neutron stars may have been observed in quasiperiodic oscillations of Magnetar Giant Flares. The frequencies of these modes depend on the shear modulus of neutron star crust. We calculate the shear modulus of Coulomb crystals from molecular dynamics simulations. We find that electron screening reduces the shear modulus by about 10% compared to previous Ogata et al. results. Our MD simulations can be extended to calculate the effects of impurities and or polycrystalline structures on the shear modulus.
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.
Quantum tunneling splittings from path-integral molecular dynamics
Mátyus, Edit; Wales, David J.; Althorpe, Stuart C.
2016-03-01
We illustrate how path-integral molecular dynamics can be used to calculate ground-state tunnelling splittings in molecules or clusters. The method obtains the splittings from ratios of density matrix elements between the degenerate wells connected by the tunnelling. We propose a simple thermodynamic integration scheme for evaluating these elements. Numerical tests on fully dimensional malonaldehyde yield tunnelling splittings in good overall agreement with the results of diffusion Monte Carlo calculations.
Variational path integral molecular dynamics study of a water molecule
Miura, Shinichi
2013-08-01
In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.
Mechanical characterization of nanoindented graphene via molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Wang Tong
2011-01-01
Full Text Available Abstract The mechanical behavior of graphene under various indentation depths, velocities, and temperatures is studied using molecular dynamics analysis. The results show that the load, elastic and plastic energies, and relaxation force increased with increasing indentation depth and velocity. Nanoindentation induced pile ups and corrugations of the graphene. Resistance to deformation decreased at higher temperature. Strong adhesion caused topological defects and vacancies during the unloading process.
Spin dynamics of an ultra-small nanoscale molecular magnet
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Ciftja Orion
2007-01-01
Full Text Available AbstractWe present mathematical transformations which allow us to calculate the spin dynamics of an ultra-small nanoscale molecular magnet consisting of a dimer system of classical (high Heisenberg spins. We derive exact analytic expressions (in integral form for the time-dependent spin autocorrelation function and several other quantities. The properties of the time-dependent spin autocorrelation function in terms of various coupling parameters and temperature are discussed in detail.
Molecular Dynamics Simulations of DNA Translocation through a biological Nanopore
Barder, Simen Eidsmo
2012-01-01
Experimental and simulation studies of nucleic acid transport through nanosized channels, both biological and synthetic, has become a rapidly growing research area over the last decade. While the utilization of the alpha-hemolysin channel as a sequencing device is soon to be realized, other biological nanochannels may hold advantages that are yet unknown. Motivated by this, the first reported molecular dynamics simulations of DNA translocation through a connexon 26 channel were accomplished, ...
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
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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.
Molecular dynamics modeling of a nanomaterials-water surface interaction
Nejat Pishkenari, Hossein; Keramati, Ramtin; Abdi, Ahmad; Minary-Jolandan, Majid
2016-04-01
In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements.
Molecular dynamics investigation of radiation damage in semiconductors
Good, Brian S.
1991-01-01
Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.
Molecular Dynamics study of Pb overlayer on Cu(100)
Karimi, M.; Tibbits, P.; Ila, D.; Dalins, I.; Vidali, G.
1991-01-01
Isothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2x2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.
Dynamic covalent chemistry approaches toward macrocycles, molecular cages, and polymers.
Jin, Yinghua; Wang, Qi; Taynton, Philip; Zhang, Wei
2014-05-20
The current research in the field of dynamic covalent chemistry includes the study of dynamic covalent reactions, catalysts, and their applications. Unlike noncovalent interactions utilized in supramolecular chemistry, the formation/breakage of covalent bonding has slower kinetics and usually requires the aid of a catalyst. Catalytic systems that enable efficient thermodynamic equilibrium are thus essential. In this Account, we describe the development of efficient catalysts for alkyne metathesis, and discuss the application of dynamic covalent reactions (mainly imine, olefin, and alkyne metathesis) in the development of organic functional materials. Alkyne metathesis is an emerging dynamic covalent reaction that offers robust and linear acetylene linkages. By introducing a podand motif into the catalyst ligand design, we have developed a series of highly active and robust alkyne metathesis catalysts, which, for the first time, enabled the one-step covalent assembly of ethynylene-linked functional molecular cages. Imine chemistry and olefin metathesis are among the most well-established reversible reactions, and have also been our main synthetic tools. Various shape-persistent macrocycles and covalent organic polyhedrons have been efficiently constructed in one-step through dynamic imine chemistry and olefin metathesis. The geometrical features and solubilizing groups of the building blocks as well as the reaction kinetics have significant effect on the outcome of a covalent assembly process. More recently, we explored the orthogonality of imine and olefin metatheses, and successfully synthesized heterosequenced macrocycles and molecular cages through one-pot orthogonal dynamic covalent chemistry. In addition to discrete molecular architectures, functional polymeric materials can also be accessed through dynamic covalent reactions. Defect-free solution-processable conjugated polyaryleneethynylenes and polydiacetylenes have been prepared through alkyne metathesis
Insights from molecular dynamics simulations for computational protein design.
Childers, Matthew Carter; Daggett, Valerie
2017-02-01
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
Excitation dynamics and relaxation in a molecular heterodimer
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Balevicius, V.; Gelzinis, A. [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Avenue 9, build. 3, LT-10222 Vilnius (Lithuania); Center for Physical Sciences and Technology, Institute of Physics, Savanoriu Avenue 231, LT-02300 Vilnius (Lithuania); Abramavicius, D. [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Avenue 9, build. 3, LT-10222 Vilnius (Lithuania); State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Street, Changchun 130012 (China); Mancal, T. [Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2 (Czech Republic); Valkunas, L., E-mail: leonas.valkunas@ff.vu.lt [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Avenue 9, build. 3, LT-10222 Vilnius (Lithuania); Center for Physical Sciences and Technology, Institute of Physics, Savanoriu Avenue 231, LT-02300 Vilnius (Lithuania)
2012-08-24
Highlights: Black-Right-Pointing-Pointer Dynamics of excitation within a heterogenous molecular dimer. Black-Right-Pointing-Pointer Excited states can be swapped due to different reorganization energies of monomers. Black-Right-Pointing-Pointer Conventional excitonic basis becomes renormalized due to interaction with the bath. Black-Right-Pointing-Pointer 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.
Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics
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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.
Molecular Dynamics Studies on the Buffalo Prion Protein
Zhang, Jiapu
2015-01-01
It was reported that buffalo is a low susceptibility species resisting to TSEs (Transmissible Spongiform Encephalopathies) (same as rabbits, horses and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (in humans prion diseases are (v)CJDs, GSS, FFI, and kulu etc). It was reported that buffalo is a low susceptibility species resisting to prion diseases (as rabbits, dogs, horses). In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to find out the reason why buffaloes are resistant to prion diseases. We first did molecular modeling a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonanc...