Simple posterior frequency correction for vibrational spectra from molecular dynamics
NASA Astrophysics Data System (ADS)
Tikhonov, Denis S.
2016-05-01
Vibrational spectra computed from molecular dynamics simulations with large integration time steps suffer from nonphysical frequency shifts of signals [M. Praprotnik and D. Janežič, J. Chem. Phys. 122, 174103 (2005)]. A simple posterior correction technique was developed for compensation of this behavior. It performs through replacement of abscissa in the calculated spectra using following formula: ν corrected = /√{ 2 ṡ (" separators=" 1 - cos ( 2 π ṡ Δ t ṡ ν initial ) ) } 2 π ṡ Δ t , where ν are initial and corrected frequencies and Δt is the MD simulation time step. Applicability of this method was tested on gaseous infrared spectra of hydrogen fluoride and formic acid.
Simple posterior frequency correction for vibrational spectra from molecular dynamics.
Tikhonov, Denis S
2016-05-01
Vibrational spectra computed from molecular dynamics simulations with large integration time steps suffer from nonphysical frequency shifts of signals [M. Praprotnik and D. Janežič, J. Chem. Phys. 122, 174103 (2005)]. A simple posterior correction technique was developed for compensation of this behavior. It performs through replacement of abscissa in the calculated spectra using following formula: νcorrected=2⋅1-cos(2π⋅Δt⋅νinitial)2π⋅Δt, where ν are initial and corrected frequencies and Δt is the MD simulation time step. Applicability of this method was tested on gaseous infrared spectra of hydrogen fluoride and formic acid. PMID:27155626
NASA Astrophysics Data System (ADS)
Costandy, Joseph; Michalis, Vasileios K.; Tsimpanogiannis, Ioannis N.; Stubos, Athanassios K.; Economou, Ioannis G.
2016-03-01
We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies.
Costandy, Joseph; Michalis, Vasileios K; Tsimpanogiannis, Ioannis N; Stubos, Athanassios K; Economou, Ioannis G
2016-03-28
We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies. PMID:27036466
NASA Astrophysics Data System (ADS)
Ma, Zhonghua; Zhang, Yanli; Tuckerman, Mark E.
2012-07-01
It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the isothermal-isobaric ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)], 10.1002/jcc.20495. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm3 while that obtained with dispersion corrections is 1.07 g/cm3, indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical correction suggests the cause of the discrepancy: the Grimme dispersion correction is parameterized for use with a particular basis set; this parameterization is sensitive to this choice and, therefore, is not transferable to other basis sets.
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.
Molecular dynamics of large systems with quantum corrections for the nuclei
NASA Astrophysics Data System (ADS)
Gu, Bing; Garashchuk, Sophya
2015-12-01
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, C37H15 and a calculation of the ground state of solid 4He simulated by a cell 180-atoms.
Molecular dynamics of large systems with quantum corrections for the nuclei
Gu, Bing; Garashchuk, Sophya
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.
VandeVondele, Joost; Sprik, Michiel
2005-04-01
We have performed density functional theory based molecular dynamics (MD) simulations of the *OH radical in solution using self-interaction corrected (SIC) methods. We use a scheme recently proposed by M. d'Avezac, M. Calandra and F. Mauri [arXiv:cond-mat/0407750] in which a correction is only applied to the spin density within a restricted open shell formulation. In addition to two correction formulas employed within this scheme by M. d'Avezac, M. Calandra and F. Mauri, we propose and test an new empirical form which only introduces a scaled Coulomb term. This new functional leads to good agreement with reference calculations on radical cation dimers and on the hydroxyl water dimer in the gas phase. Applied in ab initio MD simulations, these three SIC methods provide a picture of the *OH solvation that differs qualitatively from the one obtained using the standard generalised gradient approximation (GGA). Hemibonded water, observed in GGA simulations and believed to be an artefact due to self-interaction error, is not present. We find that the *OH acts as a good hydrogen bond donor, but accepts less than two hydrogen bonds on average. These hydrogen bonds are part of a mobile, otherwise quasi-hydrophobic solvation cage. Our results show the potential of this computationally expedient scheme, which might extend the range of problems that can be modelled adequately with density functional theory. PMID:19787955
Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations
König, Gerhard; Brooks, Bernard R.
2014-01-01
Background Free energy simulations are an important tool in the arsenal of computational biophysics, allowing the calculation of thermodynamic properties of binding or enzymatic reactions. This paper introduces methods to increase the accuracy and precision of free energy calculations by calculating the free energy costs of constraints during post-processing. The primary purpose of employing constraints for these free energy methods is to increase the phase space overlap between ensembles, which is required for accuracy and convergence. Methods The free energy costs of applying or removing constraints are calculated as additional explicit steps in the free energy cycle. The new techniques focus on hard degrees of freedom and use both gradients and Hessian estimation. Enthalpy, vibrational entropy, and Jacobian free energy terms are considered. Results We demonstrate the utility of this method with simple classical systems involving harmonic and anharmonic oscillators, four-atomic benchmark systems, an alchemical mutation of ethane to methanol, and free energy simulations between alanine and serine. The errors for the analytical test cases are all below 0.0007 kcal/mol, and the accuracy of the free energy results of ethane to methanol is improved from 0.15 to 0.04 kcal/mol. For the alanine to serine case, the phase space overlaps of the unconstrained simulations range between 0.15 and 0.9%. The introduction of constraints increases the overlap up to 2.05%. On average, the overlap increases by 94% relative to the unconstrained value and precision is doubled. Conclusions The approach reduces errors arising from constraints by about an order of magnitude. Free energy simulations benefit from the use of constraints through enhanced convergence and higher precision. General Significance The primary utility of this approach is to calculate free energies for systems with disparate energy surfaces and bonded terms, especially in multi-scale molecular mechanics
Accelerated molecular dynamics methods
Perez, Danny
2011-01-04
The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.
Nonequilibrium molecular dynamics
Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )
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.
Substructured multibody molecular dynamics.
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.
Superposition State Molecular Dynamics.
Venkatnathan, Arun; Voth, Gregory A
2005-01-01
The ergodic sampling of rough energy landscapes is crucial for understanding phenomena like protein folding, peptide aggregation, polymer dynamics, and the glass transition. These rough energy landscapes are characterized by the presence of many local minima separated by high energy barriers, where Molecular Dynamics (MD) fails to satisfy ergodicity. To enhance ergodic behavior, we have developed the Superposition State Molecular Dynamics (SSMD) method, which uses a superposition of energy states to obtain an effective potential for the MD simulation. In turn, the dynamics on this effective potential can be used to sample the configurational free energy of the real potential. The effectiveness of the SSMD method for a one-dimensional rough potential energy landscape is presented as a test case. PMID:26641113
Open boundary molecular dynamics
NASA Astrophysics Data System (ADS)
Delgado-Buscalioni, R.; Sablić, J.; Praprotnik, M.
2015-09-01
This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.
Molecular Dynamics of Acetylcholinesterase
Shen, T Y.; Tai, Kaihsu; Henchman, Richard H.; Mccammon, Andy
2002-06-01
Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.
Multiscale reactive molecular dynamics
NASA Astrophysics Data System (ADS)
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-12-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
Interactive molecular dynamics
NASA Astrophysics Data System (ADS)
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.
Molecular dynamics simulation of benzene
NASA Astrophysics Data System (ADS)
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.
Quantum corrections to inflaton and curvaton dynamics
Markkanen, Tommi; Tranberg, Anders E-mail: anders.tranberg@nbi.dk
2012-11-01
We compute the fully renormalized one-loop effective action for two interacting and self-interacting scalar fields in FRW space-time. We then derive and solve the quantum corrected equations of motion both for fields that dominate the energy density (such as an inflaton) and fields that do not (such as a subdominant curvaton). In particular, we introduce quantum corrected Friedmann equations that determine the evolution of the scale factor. We find that in general, gravitational corrections are negligible for the field dynamics. For the curvaton-type fields this leaves only the effect of the flat-space Coleman-Weinberg-type effective potential, and we find that these can be significant. For the inflaton case, both the corrections to the potential and the Friedmann equations can lead to behaviour very different from the classical evolution. Even to the point that inflation, although present at tree level, can be absent at one-loop order.
Introduction to Accelerated Molecular Dynamics
Perez, Danny
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
Molecular Dynamics Calculations
NASA Technical Reports Server (NTRS)
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
Molecular dynamics simulations
Alder, B.J.
1985-07-01
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs.
VMD: visual molecular dynamics.
Humphrey, W; Dalke, A; Schulten, K
1996-02-01
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web. PMID:8744570
Floating orbital molecular dynamics simulations.
Perlt, Eva; Brüssel, Marc; Kirchner, Barbara
2014-04-21
We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated. PMID:24600690
Nonadiabatic Molecular Dynamics with Trajectories
NASA Astrophysics Data System (ADS)
Tavernelli, Ivano
2012-02-01
In the mixed quantum-classical description of molecular systems, only the quantum character of the electronic degrees of freedom is considered while the nuclear motion is treated at a classical level. In the adiabatic case, this picture corresponds to the Born-Oppenheimer limit where the nuclei move as point charges on the potential energy surface (PES) associated with a given electronic state. Despite the success of this approximation, many physical and chemical processes do not fall in the regime where nuclei and electrons can be considered decoupled. In particular, most photoreactions pass through regions of the PES in which electron-nuclear quantum interference effects are sizeable and often crucial for a correct description of the phenomena. Recently, we have developed a trajectory-based nonadiabatic molecular dynamics scheme that describes the nuclear wavepacket as an ensemble of particles following classical trajectories on PESs derived from time-dependent density functional theory (TDDFT) [1]. The method is based on Tully's fewest switches trajectories surface hopping (TSH) where the nonadiabatic coupling elements between the different potential energy surfaces are computed on-the-fly as functionals of the ground state electron density or, equivalently, of the corresponding Kohn-Sham orbitals [2]. Here, we present the theoretical fundamentals of our approach together with an extension that allows for the direct coupling of the dynamics to an external electromagnetic field [3] as well as to the external potential generated by the environment (solvent effects) [4]. The method is applied to the study of the photodissociation dynamics of simple molecules in gas phase and to the description of the fast excited state dynamics of molecules in solution (in particular Ruthenium (II) tris(bipyridine) in water). [4pt] [1] E. Tapavicza, I. Tavernelli, U. Rothlisberger, Phys. Rev. Lett., 98, (2007) 023001. [0pt] [2] Tavernelli I.; Tapavicza E.; Rothlisberger U., J. Chem
Molecular photoionization dynamics
Dehmer, Joseph L.
1982-05-01
This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed. (WHK)
Self-correcting maps of molecular pathways.
Rzhetsky, Andrey; Zheng, Tian; Weinreb, Chani
2006-01-01
Reliable and comprehensive maps of molecular pathways are indispensable for guiding complex biomedical experiments. Such maps are typically assembled from myriads of disparate research reports and are replete with inconsistencies due to variations in experimental conditions and/or errors. It is often an intractable task to manually verify internal consistency over a large collection of experimental statements. To automate large-scale reconciliation efforts, we propose a random-arcs-and-nodes model where both nodes (tissue-specific states of biological molecules) and arcs (interactions between them) are represented with random variables. We show how to obtain a non-contradictory model of a molecular network by computing the joint distribution for arc and node variables, and then apply our methodology to a realistic network, generating a set of experimentally testable hypotheses. This network, derived from an automated analysis of over 3,000 full-text research articles, includes genes that have been hypothetically linked to four neurological disorders: Alzheimer's disease, autism, bipolar disorder, and schizophrenia. We estimated that approximately 10% of the published molecular interactions are logically incompatible. Our approach can be directly applied to an array of diverse problems including those encountered in molecular biology, ecology, economics, politics, and sociology. PMID:17183692
Dynamic-domain-decomposition parallel molecular dynamics
NASA Astrophysics Data System (ADS)
Srinivasan, S. G.; Ashok, I.; Jônsson, Hannes; Kalonji, Gretchen; Zahorjan, John
1997-05-01
Parallel molecular dynamics with short-range forces can suffer from load-imbalance problems and attendant performance degradation due to density variations in the simulated system. In this paper, we describe an approach to dynamical load balancing, enabled by the Ādhāra runtime system. The domain assigned to each processor is automatically and dynamically resized so as to evenly distribute the molecular dynamics computations across all the processors. The algorithm was tested on an Intel Paragon parallel computer for two and three-dimensional Lennard-Jones systems containing 99 458 and 256000 atoms, respectively, and using up to 256 processors. In these benchmarks, the overhead for carrying out the load-balancing operations was found to be small and the total computation time was reduced by as much as 50%.
Stochastic Dynamics with Correct Sampling for Constrained Systems.
Peters, E A J F; Goga, N; Berendsen, H J C
2014-10-14
In this paper we discuss thermostatting using stochastic methods for molecular simulations where constraints are present. For so-called impulsive thermostats, like the Andersen thermostat, the equilibrium temperature will differ significantly from the imposed temperature when a limited number of particles are picked and constraints are applied. We analyze this problem and give two rigorous solutions for it. A correct general treatment of impulsive stochastic thermostatting, including pairwise dissipative particle dynamics and stochastic forcing in the presence of constraints, is given and it is shown that the constrained canonical distribution is sampled rigorously. We discuss implementation issues such as second order Trotter expansions. The method is shown to rigorously maintain the correct temperature for the case of extended simple point charge (SPC/E) water simulations. PMID:26588119
Molecular dynamics and protein function
Karplus, M.; Kuriyan, J.
2005-01-01
A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. 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 with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F1 ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems. PMID:15870208
A sampling of molecular dynamics
NASA Astrophysics Data System (ADS)
Sindhikara, Daniel Jon
The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: increasing efficiency, measuring convergence, avoiding pitfalls, and an application and analysis of a biological system. Chapters 3 and 4 deal with an enhanced sampling algorithm called "replica exchange molecular dynamics" which is designed to speed-up molecular dynamics simulations. The optimization of a key parameter of these simulations is analyzed. In these successive projects, it was found conclusively that maximizing "exchange attempt frequency" is the most efficient way to run a replica exchange molecular dynamics simulation. Chapter 5 describes an enhanced metric for convergence in parallel simulations called the normalized ergodic measure. The metric is applied to several properties for several replica exchange simulations. Advantages of this metric over other methods are described. Chapter 6 describes the implementation and optimization of an enhanced sampling algorithm similar to replica exchange molecular dynamics called multicanonical algorithm replica exchange molecular dynamics. The algorithm was implemented into a biomolecular simulation suite called AMBER. Additionally several parameters were analyzed and optimized. In Chapter 7, a pitfall in molecular dynamics is observed in biological systems that is caused by negligent use of a simulation's "thermostat". It was found that if the same pseudorandom number seed were used for multiple systems, they eventually synchronize. In this project, synchronization was observed in biological molecules. Various negative effects including corruption of data are pointed out. Chapter 8 describes molecular dynamics simulation of NikR, a homotetrameric nickel
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.
Integration methods for molecular dynamics
Leimkuhler, B.J.; Reich, S.; Skeel, R.D.
1996-12-31
Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplecticness, can be imposed on the discretization which tend to imply good long term behavior. The presence of a variety of types and strengths of interatom potentials in standard molecular models places severe restrictions on the timestep for numerical integration used in explicit integration schemes, so much recent research has concentrated on the search for alternatives that possess (1) proper dynamical properties, and (2) a relative insensitivity to the fastest components of the dynamics. We survey several recent approaches. 48 refs., 2 figs.
Small, Matthew W; Sanchez, Sergio I; Menard, Laurent D; Kang, Joo H; Frenkel, Anatoly I; Nuzzo, Ralph G
2011-03-16
This study describes a prototypical, bimetallic heterogeneous catalyst: compositionally well-defined Ir-Pt nanoclusters with sizes in the range of 1-2 nm supported on γ-Al(2)O(3). Deposition of the molecular bimetallic cluster [Ir(3)Pt(3)(μ-CO)(3)(CO)(3)(η-C(5)Me(5))(3)] on γ-Al(2)O(3), and its subsequent reduction with hydrogen, provides highly dispersed supported bimetallic Ir-Pt nanoparticles. Using spherical aberration-corrected scanning transmission electron microscopy (C(s)-STEM) and theoretical modeling of synchrotron-based X-ray absorption spectroscopy (XAS) measurements, our studies provide unambiguous structural assignments for this model catalytic system. The atomic resolution C(s)-STEM images reveal strong and specific lattice-directed strains in the clusters that follow local bonding configurations of the γ-Al(2)O(3) support. Combined nanobeam diffraction (NBD) and high-resolution transmission electron microscopy (HRTEM) data suggest the polycrystalline γ-Al(2)O(3) support material predominantly exposes (001) and (011) surface planes (ones commensurate with the zone axis orientations frequently exhibited by the bimetallic clusters). The data reveal that the supported bimetallic clusters exhibit complex patterns of structural dynamics, ones evidencing perturbations of an underlying oblate/hemispherical cuboctahedral cluster-core geometry with cores that are enriched in Ir (a result consistent with models based on surface energetics, which favor an ambient cluster termination by Pt) due to the dynamical responses of the M-M bonding to the specifics of the adsorbate and metal-support interactions. Taken together, the data demonstrate that strong temperature-dependent charge-transfer effects occur that are likely mediated variably by the cluster-support, cluster-adsorbate, and intermetallic bonding interactions. PMID:21341654
Molecular dynamics investigation of nanoscale cavitation dynamics
NASA Astrophysics Data System (ADS)
Sasikumar, Kiran; Keblinski, Pawel
2014-12-01
We use molecular dynamics simulations to investigate the cavitation dynamics around intensely heated solid nanoparticles immersed in a model Lennard-Jones fluid. Specifically, we study the temporal evolution of vapor nanobubbles that form around the solid nanoparticles heated over ps time scale and provide a detail description of the following vapor formation and collapse. For 8 nm diameter nanoparticles we observe the formation of vapor bubbles when the liquid temperature 0.5-1 nm away from the nanoparticle surface reaches ˜90% of the critical temperature, which is consistent with the onset of spinodal decomposition. The peak heat flux from the hot solid to the surrounding liquid at the bubble formation threshold is ˜20 times higher than the corresponding steady state critical heat flux. Detailed analysis of the bubble dynamics indicates adiabatic formation followed by an isothermal final stage of growth and isothermal collapse.
Dynamic fracture toughness determined using molecular dynamics
Swadener, J. G.; Baskes, M. I.; Nastasi, Michael Anthony,
2004-01-01
Molecular dynamics (MD) simulations of fracture in crystalline silicon are conducted in order to determine the dynamic fracture toughness. The MD simulations show how the potential energy released during fracture is partitioned into surface energy, energy stored in defects and kinetic energy. First, the MD fracture simulations are shown to produce brittle fracture and be in reasonable agreement with experimental results. Then dynamic hcture toughness is calculated as the sum of the surface energy and the energy stored as defects directly from the MD models. Models oriented to produce fracture on either (111) or (101) planes are used. For the (101) fracture orientation, equilibrium crack speeds of greater than 80% of the Rayleigh wave speed are obtained. Crack speeds initially show a steep increase with increasing energy release rate followed by a much more gradual increase. No plateau in crack speed is observed for static energy release rates up to 20 J/m{sup 2}. At the point where the change in crack speed behavior occur, the dynamic fracture toughness (J{sub d}) is still within 10% of two times the surface energy (2{gamma}{sub 0}) and changing very slowly. From these MD simulations, it appears that the change in crack speed behavior is due to a change in the kinetic energy generation during dynamic fracture. In addition, MD simulations of facture in silicon with defects were conducted. The addition of defects increases the inelastic dissipation and the energy stored in defects.
Fiftieth anniversary of molecular dynamics
NASA Astrophysics Data System (ADS)
Melker, Alexander I.
2007-04-01
The history of computer application in physics for solving nonlinear problems is considered. Examples from different branches of condensed matter physics (nonlinear vibrations of anharmonic chains of atoms, dynamics of radiation damage of crystals, deformation and fracture of crystals) are given. A new line of investigation and the results obtained in the field of computer simulation of physical processes realized in the department of metal physics and computer technologies in materials science are considered. This line incorporates both a study of self-organization and properties of new materials (fullerenes, carbon nanotubes) and biological objects by molecular dynamics technique as well as the development of new computer simulation methods.
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. PMID:27053964
Molecular dynamics on vector computers
NASA Astrophysics Data System (ADS)
Sullivan, F.; Mountain, R. D.; Oconnell, J.
1985-10-01
An algorithm called the method of lights (MOL) has been developed for the computerized simulation of molecular dynamics. The MOL, implemented on the CYBER 205 computer, is based on sorting and reformulating the manner in which neighbor lists are compiled, and it uses data structures compatible with specialized vector statements that perform parallel computations. The MOL is found to reduce running time over standard methods in scalar form, and vectorization is shown to produce an order-of-magnitude reduction in execution time.
Molecular dynamics at constant temperature and pressure
NASA Astrophysics Data System (ADS)
Toxvaerd, S.
1993-01-01
Algorithms for molecular dynamics (MD) at constant temperature and pressure are investigated. The ability to remain in a regular orbit in an intermittent chaotic regime is used as a criterion for long-time stability. A simple time-centered algorithm (leap frog) is found to be the most stable of the commonly used algorithms in MD. A model of N one-dimensional dimers with a double-well intermolecular potential, for which the distribution functions at constant temperature T and pressure P can be calculated, is used to investigate MD-NPT dynamics. A time-centered NPT algorithm is found to sample correctly and to be very robust with respect to volume scaling.
Molecular dynamics for dense matter
NASA Astrophysics Data System (ADS)
Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi
2012-08-01
We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.
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
2008-01-01
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 paper, 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. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper 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. PMID:16222654
Application of optimal prediction to molecular dynamics
Barber IV, John Letherman
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 {delta}-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.
Multisurface Adiabatic Reactive Molecular Dynamics.
Nagy, Tibor; Yosa Reyes, Juvenal; Meuwly, Markus
2014-04-01
Adiabatic reactive molecular dynamics (ARMD) simulation method is a surface-crossing algorithm for modeling chemical reactions in classical molecular dynamics simulations using empirical force fields. As the ARMD Hamiltonian is time dependent during crossing, it allows only approximate energy conservation. In the current work, the range of applicability of conventional ARMD is explored, and a new multisurface ARMD (MS-ARMD) method is presented, implemented in CHARMM and applied to the vibrationally induced photodissociation of sulfuric acid (H2SO4) in the gas phase. For this, an accurate global potential energy surface (PES) involving 12 H2SO4 and 4 H2O + SO3 force fields fitted to MP2/6-311G++(2d,2p) reference energies is employed. The MS-ARMD simulations conserve total energy and feature both intramolecular H-transfer reactions and water elimination. An analytical treatment of the dynamics in the crossing region finds that conventional ARMD can approximately conserve total energy for limiting cases. In one of them, the reduced mass of the system is large, which often occurs for simulations of solvated biomolecular systems. On the other hand, MS-ARMD is a general approach for modeling chemical reactions including gas-phase, homogeneous, heterogeneous, and enzymatic catalytic reactions while conserving total energy in atomistic simulations. PMID:26580356
Better, Cheaper, Faster Molecular Dynamics
NASA Technical Reports Server (NTRS)
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.
Molecular Dynamics Simulations of Polymers
NASA Astrophysics Data System (ADS)
Han, Jie
1995-01-01
Molecular dynamics (MD) simulations have been undertaken in this work to explore structures and properties of polyethylene (PE), polyisobutylene (PIB), atactic polypropylene (aPP) and atactic polystyrene (aPS). This work has not only demonstrated the reliability of MD simulations by comparing results with available experiments, but more importantly has revealed structure-property relationships on a molecular level for these selected polymers. Structures of these amorphous polymers were characterized by radial distribution functions (RDFs) or scattering profiles, and properties of the polymers studied were pressure-volume -temperature (PVT) equation of state, enthalpy, cohesive energy, the diffusion coefficient of methane in the polymer, and glass transition temperature. Good agreement was found for these structures and properties between simulation and experiment. More importantly, the scientific understanding of structure-property relationships was established on a molecular level. In the order of aPP (PE), PIB and aPS, with the chain surface separation or free volume decreasing, the density increases and the diffusion coefficient decreases. Therefore, the effects of changes or modifications in the chemical structure of monomer molecules (substituting pendent hydrogen with methyl or phenyl) on polymeric materials performance were attributed to the effects of molecular chain structure on packing structure, which, in turn, affects the properties of these polymers. Local chain dynamics and relaxation have been studied for bulk PE and aPS. Cooperative transitions occur at second-neighbor bonds for PE, and first-neighbor bonds for aPS due to the role of side groups. The activation energy is a single torsional barrier for overall conformational transitions, and is single torsional barrier plus locally "trapped" barrier for relaxation. Temperature dependence is Arrhenius for transition time, and is WLF for relaxation time. The mean correlation times derived from
Spectroscopy and molecular dynamics in nonpolar fluids
NASA Astrophysics Data System (ADS)
Everitt, Karl Frederick
This thesis considers the mechanisms by which molecular dynamics in nonpolar liquids influences solvation dynamics and vibrational energy relaxation. We use semiclassical molecular dynamics simulations to calculate photon echo signals for two simple fluids. We demonstrate that two new observables are directly related to the relevant molecular quantity, the frequency- frequency time correlation function (TCF), in contrast to the commonly measured 3PEPS, which cannot be simply related to this TCF at short times. We also present a semianalytic photon echo theory, based on an ansatz which determines the full time dependence from the short time expansion coefficients of the TCF. We demonstrate that this theory accurately predicts most photon echo observables, even when the theory's gaussian approximation is not accurate. We also consider vibrational energy relaxation (VER) in liquid oxygen. Using semiclassical molecular dynamics simulations and an intermolecular potential from the literature, we evaluate the required quantity (the spectral density of a certain force-force TCF) using the same ansatz described above. We demonstrate numerically that this procedure is accurate. Approximately relating this semiclassical rate to the fully quantum mechanical VER rate, using one of the more accurate ``quantum corrections'' available in the literature, yields a result which is in order-of-magnitude agreement with the experimental VER rate. We also calculate the VER rate for liquid oxygen/argon mixtures. The rotations of the solvent near a vibrationally excited molecule, and of that molecule itself, have important consequences for the short-time dynamics of the force-force TCF. We propose a simple statistical model which quantitatively explains the mole- fraction dependence of the observed VER rate. Next, we demonstrate that a newly-developed model for oxygen very accurately describes the liquid, by comparing to experimental measures of microscopic structure and dynamics. We also
Proposal on dynamic correction method for resonance ionization mass spectrometry
NASA Astrophysics Data System (ADS)
Noto, Takuma; Tomita, Hideki; Richter, Sven; Schneider, Fabian; Wendt, Klaus; Iguchi, Tetsuo; Kawarabayashi, Jun
2013-04-01
For high precision and accuracy in isotopic ratio measurement of transuranic elements using laser ablation assisted resonance ionization mass spectrometry, a dynamic correction method based on correlation of ion signals with energy and timing of each laser pulse was proposed. The feasibility of this dynamic correction method was investigated through the use of a programmable electronics device for fast acquisition of the energy and timing of each laser pulse.
Radiation in molecular dynamic simulations
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M
2008-10-13
Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.
The "Collisions Cube" Molecular Dynamics Simulator.
ERIC Educational Resources Information Center
Nash, John J.; Smith, Paul E.
1995-01-01
Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)
A concurrent multiscale micromorphic molecular dynamics
Li, Shaofan Tong, Qi
2015-04-21
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.
Buckybomb: Reactive Molecular Dynamics Simulation.
Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V
2015-03-01
Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672
Software for Correcting the Dynamic Error of Force Transducers
Miyashita, Naoki; Watanabe, Kazuhide; Irisa, Kyouhei; Iwashita, Hiroshi; Araki, Ryosuke; Takita, Akihiro; Yamaguchi, Takao; Fujii, Yusaku
2014-01-01
Software which corrects the dynamic error of force transducers in impact force measurements using their own output signal has been developed. The software corrects the output waveform of the transducers using the output waveform itself, estimates its uncertainty and displays the results. In the experiment, the dynamic error of three transducers of the same model are evaluated using the Levitation Mass Method (LMM), in which the impact forces applied to the transducers are accurately determined as the inertial force of the moving part of the aerostatic linear bearing. The parameters for correcting the dynamic error are determined from the results of one set of impact measurements of one transducer. Then, the validity of the obtained parameters is evaluated using the results of the other sets of measurements of all the three transducers. The uncertainties in the uncorrected force and those in the corrected force are also estimated. If manufacturers determine the correction parameters for each model using the proposed method, and provide the software with the parameters corresponding to each model, then users can obtain the waveform corrected against dynamic error and its uncertainty. The present status and the future prospects of the developed software are discussed in this paper. PMID:25004158
Software for correcting the dynamic error of force transducers.
Miyashita, Naoki; Watanabe, Kazuhide; Irisa, Kyouhei; Iwashita, Hiroshi; Araki, Ryosuke; Takita, Akihiro; Yamaguchi, Takao; Fujii, Yusaku
2014-01-01
Software which corrects the dynamic error of force transducers in impact force measurements using their own output signal has been developed. The software corrects the output waveform of the transducers using the output waveform itself, estimates its uncertainty and displays the results. In the experiment, the dynamic error of three transducers of the same model are evaluated using the Levitation Mass Method (LMM), in which the impact forces applied to the transducers are accurately determined as the inertial force of the moving part of the aerostatic linear bearing. The parameters for correcting the dynamic error are determined from the results of one set of impact measurements of one transducer. Then, the validity of the obtained parameters is evaluated using the results of the other sets of measurements of all the three transducers. The uncertainties in the uncorrected force and those in the corrected force are also estimated. If manufacturers determine the correction parameters for each model using the proposed method, and provide the software with the parameters corresponding to each model, then users can obtain the waveform corrected against dynamic error and its uncertainty. The present status and the future prospects of the developed software are discussed in this paper. PMID:25004158
Coulomb-corrected molecular orbital tomography of nitrogen
NASA Astrophysics Data System (ADS)
Zhai, Chunyang; He, Lixin; Lan, Pengfei; Zhu, Xiaosong; Li, Yang; Wang, Feng; Shi, Wenjing; Zhang, Qingbin; Lu, Peixiang
2016-03-01
High-order harmonic generation (HHG) from aligned molecules has provided a promising way to probe the molecular orbital with an Ångström resolution. This method, usually called molecular orbital tomography (MOT) replies on a simple assumption of the plane-wave approximation (PW), which has long been questioned due to that PW approximation is known to be valid in the keV energy region. However, the photon energy is usually no more than 100 eV in HHG. In this work, we experimentally reconstruct the highest occupied molecular orbital (HOMO) of nitrogen (N2) by using a Coulomb-corrected MOT (CCMOT) method. In our scheme, the molecular continuum states are described by a Coulomb wave function instead of the PW approximation. With CCMOT, the reconstructed orbital is demonstrated to agree well with the theoretical prediction and retain the main features of the HOMO of N2. Compared to the PW approximation method, the CCMOT shows a significant improvement in eliminating the artificial structures caused by PW approximation.
Coulomb-corrected molecular orbital tomography of nitrogen.
Zhai, Chunyang; He, Lixin; Lan, Pengfei; Zhu, Xiaosong; Li, Yang; Wang, Feng; Shi, Wenjing; Zhang, Qingbin; Lu, Peixiang
2016-01-01
High-order harmonic generation (HHG) from aligned molecules has provided a promising way to probe the molecular orbital with an Ångström resolution. This method, usually called molecular orbital tomography (MOT) replies on a simple assumption of the plane-wave approximation (PW), which has long been questioned due to that PW approximation is known to be valid in the keV energy region. However, the photon energy is usually no more than 100 eV in HHG. In this work, we experimentally reconstruct the highest occupied molecular orbital (HOMO) of nitrogen (N2) by using a Coulomb-corrected MOT (CCMOT) method. In our scheme, the molecular continuum states are described by a Coulomb wave function instead of the PW approximation. With CCMOT, the reconstructed orbital is demonstrated to agree well with the theoretical prediction and retain the main features of the HOMO of N2. Compared to the PW approximation method, the CCMOT shows a significant improvement in eliminating the artificial structures caused by PW approximation. PMID:27000666
Coulomb-corrected molecular orbital tomography of nitrogen
Zhai, Chunyang; He, Lixin; Lan, Pengfei; Zhu, Xiaosong; Li, Yang; Wang, Feng; Shi, Wenjing; Zhang, Qingbin; Lu, Peixiang
2016-01-01
High-order harmonic generation (HHG) from aligned molecules has provided a promising way to probe the molecular orbital with an Ångström resolution. This method, usually called molecular orbital tomography (MOT) replies on a simple assumption of the plane-wave approximation (PW), which has long been questioned due to that PW approximation is known to be valid in the keV energy region. However, the photon energy is usually no more than 100 eV in HHG. In this work, we experimentally reconstruct the highest occupied molecular orbital (HOMO) of nitrogen (N2) by using a Coulomb-corrected MOT (CCMOT) method. In our scheme, the molecular continuum states are described by a Coulomb wave function instead of the PW approximation. With CCMOT, the reconstructed orbital is demonstrated to agree well with the theoretical prediction and retain the main features of the HOMO of N2. Compared to the PW approximation method, the CCMOT shows a significant improvement in eliminating the artificial structures caused by PW approximation. PMID:27000666
Molecular dynamics of membrane proteins.
Woolf, Thomas B.; 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.
Langevin stabilization of molecular dynamics
NASA Astrophysics Data System (ADS)
Izaguirre, Jesús A.; Catarello, Daniel P.; Wozniak, Justin M.; Skeel, Robert D.
2001-02-01
In this paper we show the possibility of using very mild stochastic damping to stabilize long time step integrators for Newtonian molecular dynamics. More specifically, stable and accurate integrations are obtained for damping coefficients that are only a few percent of the natural decay rate of processes of interest, such as the velocity autocorrelation function. Two new multiple time stepping integrators, Langevin Molly (LM) and Brünger-Brooks-Karplus-Molly (BBK-M), are introduced in this paper. Both use the mollified impulse method for the Newtonian term. LM uses a discretization of the Langevin equation that is exact for the constant force, and BBK-M uses the popular Brünger-Brooks-Karplus integrator (BBK). These integrators, along with an extrapolative method called LN, are evaluated across a wide range of damping coefficient values. When large damping coefficients are used, as one would for the implicit modeling of solvent molecules, the method LN is superior, with LM closely following. However, with mild damping of 0.2 ps-1, LM produces the best results, allowing long time steps of 14 fs in simulations containing explicitly modeled flexible water. With BBK-M and the same damping coefficient, time steps of 12 fs are possible for the same system. Similar results are obtained for a solvated protein-DNA simulation of estrogen receptor ER with estrogen response element ERE. A parallel version of BBK-M runs nearly three times faster than the Verlet-I/r-RESPA (reversible reference system propagator algorithm) when using the largest stable time step on each one, and it also parallelizes well. The computation of diffusion coefficients for flexible water and ER/ERE shows that when mild damping of up to 0.2 ps-1 is used the dynamics are not significantly distorted.
Dynamical Localization in Molecular Systems.
NASA Astrophysics Data System (ADS)
Wang, Xidi
In the first four chapters of this thesis we concentrate on the Davydov model which describes the vibrational energy quanta of Amide I bonds (C=O bonds on the alpha -helix) coupled to the acoustic phonon modes of the alpha-helix backbone in the form of a Frohlich Hamiltonian. Following a brief introduction in chapter one, in chapter two we formulate the dynamics of vibrational quanta at finite temperature by using coherent state products. The fluctuation-dissipation relation is derived. At zero temperature, in the continuum limit, we recover the original results of Davydov. We also achieve good agreement with numerical simulations. In chapter three, the net contraction of the lattice is calculated exactly at any temperature, and its relation to the so -call "topological stability" of the Davydov soliton is discussed. In the second section of the chapter three we calculate the overtone spectra of crystalline acetanilide (according to some opinions ACN provides experimental evidence for the existence of Davydov solitons). Good agreement with experimental data has been obtained. In chapter four we study the self-trapped vibrational excitations by the Quantum Monte Carlo technique. For a single excitation, the temperature dependence of different physical observables is calculated. The quasi-particle which resembles the Davydov soliton has been found to be fairly narrow using the most commonly used data for the alpha -helix; at temperatures above a few Kelvin, the quasi-particle reaches its smallest limit (extends over three sites), which implies diffusive motion of the small polaron-like quasi-particle at high temperatures. For the multi-excitation case, bound pairs and clusters of excitations are found at low temperatures; they gradually dissociate when the temperature of the system is increased as calculated from the density-density correlation function. In the last chapter of this thesis, we study a more general model of dynamical local modes in molecular systems
NASA Astrophysics Data System (ADS)
Barone, Luciano Maria; Simonazzi, Riccardo; Tenenbaum, Alexander
1995-09-01
We have studied portability, efficiency and accuracy of a standard Molecular Dynamics simulation on the SIMD parallel computer APE100. Computing speed performance and physical system size range have been analyzed and compared with those of a conventional computer. Short range and long range potentials have been considered, and the comparative advantage of different simulation approaches has been assessed. For long range potentials, APE turns out to be faster than a conventional computer; large systems can be conveniently simulated using either the cloning approach (up to ˜ 10 5 particles) or a domain decomposition with the systolic method. In the case of short range potentials and systems with diffusion (like a liquid), APE is convenient only when using a large number of processors. In a special case (a crystal without diffusion), a specific domain decomposition technique with frames makes APE advantageous for intermediate and large systems. Using the latter technique we have studied in detail the effect of different numerical error sources, and compared the accuracy of APE with that of a conventional computer.
Dynamics of riboswitches: Molecular simulations.
Sanbonmatsu, Karissa Y
2014-10-01
Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail. Molecular dynamics simulations are useful for interpreting existing experimental data and producing predictions for new experiments. Here, a wide range of computational studies on riboswitches is reviewed. By elucidating the key principles of riboswitch operation, computation may aid in the effort to design more specific antibiotics with affinities greater than those of the native ligand. Such a detailed understanding may be required to improve efficacy and reduce side effects. These studies are laying the groundwork for understanding the action mechanism of new compounds that inhibit riboswitch activity. Future directions such as magnesium effects, large-scale conformational changes, expression platforms and co-transcriptional folding are also discussed. This article is part of a Special Issue entitled: Riboswitches. PMID:24953187
Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock
Soares, Pedro; Ermini, Luca; Thomson, Noel; Mormina, Maru; Rito, Teresa; Röhl, Arne; Salas, Antonio; Oppenheimer, Stephen; Macaulay, Vincent; Richards, Martin B.
2009-01-01
There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at ∼15 kya that—unlike the uncorrected clock—matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 55–70 kya, 5–20 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses. PMID:19500773
Localised distributions and criteria for correctness in complex Langevin dynamics
Aarts, Gert; Giudice, Pietro; Seiler, Erhard
2013-10-15
Complex Langevin dynamics can solve the sign problem appearing in numerical simulations of theories with a complex action. In order to justify the procedure, it is important to understand the properties of the real and positive distribution, which is effectively sampled during the stochastic process. In the context of a simple model, we study this distribution by solving the Fokker–Planck equation as well as by brute force and relate the results to the recently derived criteria for correctness. We demonstrate analytically that it is possible that the distribution has support in a strip in the complexified configuration space only, in which case correct results are expected. -- Highlights: •Characterisation of the equilibrium distribution sampled in complex Langevin dynamics. •Connection between criteria for correctness and breakdown. •Solution of the Fokker–Planck equation in the case of real noise. •Analytical determination of support in complexified space.
Erba, Alessandro; Maul, Jefferson; Civalleri, Bartolomeo
2016-01-31
An ab initio quantum-mechanical theoretical framework is presented to compute the thermal properties of molecular crystals. The present strategy combines dispersion-corrected density-functional-theory (DFT-D), harmonic phonon dispersion, quasi-harmonic approximation to the lattice dynamics for thermal expansion and thermodynamic functions, and quasi-static approximation for anisotropic thermo-elasticity. The proposed scheme is shown to reliably describe thermal properties of the urea molecular crystal by a thorough comparison with experimental data. PMID:26670006
Time-Dependent Molecular Reaction Dynamics
Oehrn, Yngve
2007-11-29
This paper is a brief review of a time-dependent, direct, nonadiabatic theory of molecular processes called Electron Nuclear Dynamics (END). This approach to the study of molecular reaction dynamics is a hierarchical theory that can be applied at various levels of approximation. The simplest level of END uses classical nuclei and represents all electrons by a single, complex, determinantal wave function. The wave function parameters such as average nuclear positions and momenta, and molecular orbital coefcients carry the time dependence and serve as dynamical variables. Examples of application are given of the simplest level of END to ion-atom and ion-molecule reactions.
Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.
2015-05-21
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.
Modeling the Hydrogen Bond within Molecular Dynamics
ERIC Educational Resources Information Center
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
ERIC Educational Resources Information Center
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.
Molecular ions, Rydberg spectroscopy and dynamics
Jungen, Ch.
2015-01-22
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.
Parallel Molecular Dynamics Program for Molecules
Energy Science and Technology Software Center (ESTSC)
1995-03-07
ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.
Sergiievskyi, Volodymyr P; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel
2014-06-01
Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently. PMID:26273876
Fermionic Molecular Dynamics for Nuclear Dynamics and Thermodynamics
NASA Astrophysics Data System (ADS)
Hasnaoui, K. H. O.; Chomaz, Ph; Gulminelli, F.
A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented.
Molecular dynamics: A stitch in time
NASA Astrophysics Data System (ADS)
Deupi, Xavier
2014-01-01
Lengthy molecular dynamics simulations of complex systems at the atomic scale usually require supercomputers. Now, by stitching together many shorter independent simulations run 'in the cloud', this requirement has been circumvented, allowing two milliseconds of the dynamics of a G-protein-coupled receptor to be simulated.
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. PMID:27325090
Molecular dynamics simulations: advances and applications
Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L
2015-01-01
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
Molecular dynamics simulations of large macromolecular complexes
Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus
2015-01-01
Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770
Dynamic shear modulus of glycerol: Corrections due to instrument compliance
NASA Astrophysics Data System (ADS)
Schröter, K.; Hutcheson, S. A.; Shi, X.; Mandanici, A.; McKenna, G. B.
2006-12-01
A recent article by Shi et al. [J. Chem. Phys.123, 174507 (2005)] reports results from mechanical measurements on three simple inorganic glass formers: glycerol, m-toluidine, and sucrose benzoate. The experiments carried out were stress relaxation, aging, and dynamic (all in shear) using a torsional rheometer, an advanced rheometric expansion system (TA Instruments). The original force rebalance transducer (2KFRT) supplied with the system was replaced with a custom-made load cell (Sensotec) that had a capacity of 20000gcm in torque and 5000g in normal force. The replacement of the load cell was done due to the belief that the main source of compliance in this instrument was from the 2KFRT. With this assumption, the authors published their results for the three materials of interest and compared their results with the techniques of Schröter and Donth [J. Chem. Phys.113, 9101 (2000)] for the measurements on glycerol and reported important differences. These differences were disputed by one of the present authors (Schröter), and the present report shows that the results from Schröter and Donth are correct. We show that the reasons have to do with the instrument compliance being greater than originally thought by Shi et al. Here we examine the effects of platen diameter/geometry on the glycerol dynamic moduli, describe a means to correct dynamic data, present a revised comparison of the corrected data with that of Schröter and Donth, and provide a discussion of future work and conclusions.
Dynamically corrected gates for an exchange-only qubit
NASA Astrophysics Data System (ADS)
Hickman, G. T.; Wang, Xin; Kestner, J. P.; Das Sarma, S.
2013-10-01
We provide analytical composite pulse sequences that perform dynamical decoupling concurrently with arbitrary rotations for a qubit coded in the spin state of a triple quantum dot. The sequences are designed to respect realistic experimental constraints such as strictly nonnegative couplings. Logical errors and leakage errors are simultaneously corrected. A short pulse sequence is presented to compensate nuclear noise and a longer sequence is presented to simultaneously compensate nuclear and charge noise. The capability developed in this work provides a clear prescription for combatting the relevant sources of noise that currently hinder exchange-only qubit experiments.
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. PMID:24073784
Annihilation of craters: Molecular dynamic simulations on a silver surface
Henriksson, K. O. E.; Nordlund, K.; Keinonen, J.
2007-12-15
The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.
Molecular Scale Dynamics of Large Ring Polymers
NASA Astrophysics Data System (ADS)
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.
Dynamic signature of molecular association in methanol
NASA Astrophysics Data System (ADS)
Bertrand, C. E.; Self, J. L.; Copley, J. R. D.; Faraone, A.
2016-07-01
Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.
Dynamic signature of molecular association in methanol.
Bertrand, C E; Self, J L; Copley, J R D; Faraone, A
2016-07-01
Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids. PMID:27394112
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
2014-10-17
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. PMID:25361284
Numerical methods for molecular dynamics
Skeel, R.D.
1991-01-01
This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.
Semiclassical guided optimal control of molecular dynamics
Kondorskiy, A.; Mil'nikov, G.; Nakamura, H.
2005-10-15
An efficient semiclassical optimal control theory applicable to multidimensional systems is formulated for controlling wave packet dynamics on a single adiabatic potential energy surface. The approach combines advantages of different formulations of optimal control theory: quantum and classical on one hand and global and local on the other. Numerical applications to the control of HCN-CNH isomerization demonstrate that this theory can provide an efficient tool to manipulate molecular dynamics of many degrees of freedom by laser pulses.
Leading concentration correction to polymer dynamic self-structure factor
NASA Astrophysics Data System (ADS)
Perico, Angelo; La Ferla, Roberto; Freed, Karl F.
1989-10-01
The discrete chain representation of multiple scattering theory of the concentration dependence of the hydrodynamics of polymer solutions is applied to the calculation of the leading concentration correction to the dynamic structure factor S(k,t) and its first and second cumulants of individual labeled Gaussian chains in theta solutions at nonzero concentrations. Contributions are separated into those from overall translational and internal chain motions as well as couplings between different internal modes and between translation and internal modes, coupling that are introduced by interchain hydrodynamic interactions. The separate contributions are analyzed as a function of k and of t in order to isolate regions where certain contributions are dominant. As expected, short times and larger k tend to favor contributions from internal chain dynamics, while longer times and smaller k make concentration dependent translational effects predominate. Computations for shorter chains are extrapolated to provide the asymptotic long chain behavior.
Susceptibility artefact correction using dynamic graph cuts: application to neurosurgery.
Daga, Pankaj; Pendse, Tejas; Modat, Marc; White, Mark; Mancini, Laura; Winston, Gavin P; McEvoy, Andrew W; Thornton, John; Yousry, Tarek; Drobnjak, Ivana; Duncan, John S; Ourselin, Sebastien
2014-10-01
Echo Planar Imaging (EPI) is routinely used in diffusion and functional MR imaging due to its rapid acquisition time. However, the long readout period makes it prone to susceptibility artefacts which results in geometric and intensity distortions of the acquired image. The use of these distorted images for neuronavigation hampers the effectiveness of image-guided surgery systems as critical white matter tracts and functionally eloquent brain areas cannot be accurately localised. In this paper, we present a novel method for correction of distortions arising from susceptibility artefacts in EPI images. The proposed method combines fieldmap and image registration based correction techniques in a unified framework. A phase unwrapping algorithm is presented that can efficiently compute the B0 magnetic field inhomogeneity map as well as the uncertainty associated with the estimated solution through the use of dynamic graph cuts. This information is fed to a subsequent image registration step to further refine the results in areas with high uncertainty. This work has been integrated into the surgical workflow at the National Hospital for Neurology and Neurosurgery and its effectiveness in correcting for geometric distortions due to susceptibility artefacts is demonstrated on EPI images acquired with an interventional MRI scanner during neurosurgery. PMID:25047865
Dynamic Distortion Correction for Endoscopy Systems with Exchangeable Optics
NASA Astrophysics Data System (ADS)
Stehle, Thomas; Hennes, Michael; Gross, Sebastian; Behrens, Alexander; Wulff, Jonas; Aach, Til
Endoscopic images are strongly affected by lens distortion caused by the use of wide angle lenses. In case of endoscopy systems with exchangeable optics, e.g. in bladder endoscopy or sinus endoscopy, the camera sensor and the optics do not form a rigid system but they can be shifted and rotated with respect to each other during an examination. This flexibility has a major impact on the location of the distortion centre as it is moved along with the optics. In this paper, we describe an algorithm for the dynamic correction of lens distortion in cystoscopy which is based on a one time calibration. For the compensation, we combine a conventional static method for distortion correction with an algorithm to detect the position and the orientation of the elliptic field of view. This enables us to estimate the position of the distortion centre according to the relative movement of camera and optics. Therewith, a distortion correction for arbitrary rotation angles and shifts becomes possible without performing static calibrations for every possible combination of shifts and angles beforehand.
Optimizing replica exchange moves for molecular dynamics.
Nadler, Walter; Hansmann, Ulrich H E
2007-11-01
We sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method. PMID:18233794
Molecular dynamics calculations of nuclear stimulated desorption
Glikman, E.; Kelson, I. ); Doan, N.V. )
1991-09-01
Molecular dynamics calculations of nuclear stimulated desorption are carried out for a palladium crystal containing radioactive palladium atoms. The total desorption probability from various sites are computed, as well as the angular distribution of the desorbing atoms. The implications of the results to different experimental scenarios are discussed.
Reaction dynamics in polyatomic molecular systems
Miller, W.H.
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 Simulations of Graphene Oxide Frameworks
Zhu, Pan; Sumpter, Bobby G; Meunier, V.; Nicolai, Adrien
2013-01-01
We use quantum mechanical calculations to develop a full set of force field parameters in order to perform molecular dynamics simulations to understand and optimize the molecular storage properties inside Graphene Oxide Frameworks (GOFs). A set of boron-related parameters for commonly used empirical force fields is determined to describe the non-bonded and bonded interactions between linear boronic acid linkers and graphene sheets of GOF materials. The transferability of the parameters is discussed and their validity is quantified by comparing quantum mechanical and molecular mechanical structural and vibrational properties. The application of the model to the dynamics of water inside the GOFs reveals significant variations in structural flexibility of GOF depending on the linker density, which is shown to be usable as a tuning parameter for desired diffusion properties.
Molecular dynamics simulations of weak detonations.
Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie
2011-12-01
Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055
Molecular dynamics of PLK1 during mitosis
Schmucker, Stephane; Sumara, Izabela
2014-01-01
Polo-like kinase 1 (PLK1) is a key regulator of eukaryotic cell division. During mitosis, dynamic regulation of PLK1 is crucial for its roles in centrosome maturation, spindle assembly, microtubule–kinetochore attachment, and cytokinesis. Similar to other members of the PLK family, the molecular architecture of PLK1 protein is characterized by 2 domains—the kinase domain and the regulatory substrate-binding domain (polo-box domain)—that cooperate and control PLK1 function during mitosis. Mitotic cells employ many layers of regulation to activate and target PLK1 to different cellular structures in a timely manner. During the last decade, numerous studies have shed light on the precise molecular mechanisms orchestrating the mitotic activity of PLK1 in time and space. This review aims to discuss available data and concepts related to regulation of the molecular dynamics of human PLK1 during mitotic progression. PMID:27308323
Parallel molecular dynamics on a multi signalprocessor system
NASA Astrophysics Data System (ADS)
Scott, W.; Gunzinger, A.; Bäumle, B.; Kohler, P.; Müller, U. A.; Mühll, H.-R. Vonder; Eichenberger, A.; Guggenbühl, W.; Ironmonger, N.; Müller-Plathe, F.; van Gunsteren, W. F.
1993-04-01
This paper gives an overview of a parallel computer architecture called MUSIC (Multi Signalprocessor System with Intelligent Communication), which has been developed at the Swiss Federal Institute of Technology. The current version achieves a peak performance of 3.8 GFlops. We discuss the system software and tools used to program the system and then present our implementation of a molecular dynamics simulation program which uses the architecture of MUSIC in an efficient way. We demonstrate the correctness of our implementation and give measurements of the performance of the system. To the best of our knowledge, MUSIC outperforms the most powerful present-day vector supercomputers.
Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M.
2014-10-15
The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.
Shadow correction in high dynamic range images for generating orthophotos
NASA Astrophysics Data System (ADS)
Suzuki, Hideo; Chikatsu, Hirofumi
2011-07-01
High dynamic range imagery is widely used in remote sensing. With the widespread use of aerial digital cameras such as the DMC, ADS40, RMK-D, and UltraCamD, high dynamic range imaging is generally expected for generating minuteness orthophotos in digital aerial photogrammetry. However, high dynamic range images (12-bit, 4,096 gray levels) are generally compressed into an 8-bit depth digital image (256 gray levels) owing to huge amount of data and interface with peripherals such as monitors and printers. This means that a great deal of image data is eliminated from the original image, and this introduces a new shadow problem. In particular, the influence of shadows in urban areas causes serious problems when generating minuteness orthophotos and performing house detection. Therefore, shadow problems can be solved by addressing the image compression problems. There is a large body of literature on image compression techniques such as logarithmic compression and tone mapping algorithms. However, logarithmic compression tends to cause loss of details in dark and/or light areas. Furthermore, the logarithmic method intends to operate on the full scene. This means that high-resolution luminance information can not be obtained. Even though tone mapping algorithms have the ability to operate over both full scene and local scene, background knowledge is required. To resolve the shadow problem in digital aerial photogrammetry, shadow areas should be recognized and corrected automatically without the loss of luminance information. To this end, a practical shadow correction method using 12-bit real data acquired by DMC is investigated in this paper.
Telescopic systems with dynamic nonlinear optical correction for distortions
Vasil'ev, Michail V; Venediktov, Vladimir Yu; Leshchev, Alexey A
2001-01-31
The review of basic achievements in the field of non-linear adaptive optics is presented. In particular, schematics and properties of adaptive optical telescopes considered in which the image distortions introduced by defects of the primary mirror and other optical elements are compensated by nonlinear optical methods. The conventional methods of laser optics, such as phase conjugation and dynamic holography, make it possible both to solve the problems of classical (imaging) optics related to the building of telescopes for imaging remote objects with high resolution, which are based on large, light-weight or sectional mirrors, and create the systems that produce laser beams with the high-quality wave front. The basic designs of such telescopes are considered and the possibilities of corrections for distortions in them are analysed and confirmed by experiments. (review)
Exciton dynamics in perturbed vibronic molecular aggregates
Brüning, C.; Wehner, J.; Hausner, J.; Wenzel, M.; Engel, V.
2015-01-01
A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840
Exciton dynamics in perturbed vibronic molecular aggregates.
Brüning, C; Wehner, J; Hausner, J; Wenzel, M; Engel, V
2016-07-01
A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840
Frequency-domain correction of sensor dynamic error for step response.
Yang, Shuang-Long; Xu, Ke-Jun
2012-11-01
To obtain accurate results in dynamic measurements it is required that the sensors should have good dynamic performance. In practice, sensors have non-ideal dynamic characteristics due to their small damp ratios and low natural frequencies. In this case some dynamic error correction methods can be adopted for dealing with the sensor responses to eliminate the effect of their dynamic characteristics. The frequency-domain correction of sensor dynamic error is a common method. Using the existing calculation method, however, the correct frequency-domain correction function (FCF) cannot be obtained according to the step response calibration experimental data. This is because of the leakage error and invalid FCF value caused by the cycle extension of the finite length step input-output intercepting data. In order to solve these problems the data splicing preprocessing and FCF interpolation are put forward, and the FCF calculation steps as well as sensor dynamic error correction procedure by the calculated FCF are presented in this paper. The proposed solution is applied to the dynamic error correction of the bar-shaped wind tunnel strain gauge balance so as to verify its effectiveness. The dynamic error correction results show that the adjust time of the balance step response is shortened to 10 ms (shorter than 1/30 before correction) after frequency-domain correction, and the overshoot is fallen within 5% (less than 1/10 before correction) as well. The dynamic measurement accuracy of the balance is improved significantly. PMID:23206091
Frequency-domain correction of sensor dynamic error for step response
NASA Astrophysics Data System (ADS)
Yang, Shuang-Long; Xu, Ke-Jun
2012-11-01
To obtain accurate results in dynamic measurements it is required that the sensors should have good dynamic performance. In practice, sensors have non-ideal dynamic characteristics due to their small damp ratios and low natural frequencies. In this case some dynamic error correction methods can be adopted for dealing with the sensor responses to eliminate the effect of their dynamic characteristics. The frequency-domain correction of sensor dynamic error is a common method. Using the existing calculation method, however, the correct frequency-domain correction function (FCF) cannot be obtained according to the step response calibration experimental data. This is because of the leakage error and invalid FCF value caused by the cycle extension of the finite length step input-output intercepting data. In order to solve these problems the data splicing preprocessing and FCF interpolation are put forward, and the FCF calculation steps as well as sensor dynamic error correction procedure by the calculated FCF are presented in this paper. The proposed solution is applied to the dynamic error correction of the bar-shaped wind tunnel strain gauge balance so as to verify its effectiveness. The dynamic error correction results show that the adjust time of the balance step response is shortened to 10 ms (shorter than 1/30 before correction) after frequency-domain correction, and the overshoot is fallen within 5% (less than 1/10 before correction) as well. The dynamic measurement accuracy of the balance is improved significantly.
Molecular dynamics at constant Cauchy stress
NASA Astrophysics Data System (ADS)
Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio
2016-05-01
The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.
Molecular dynamics at constant Cauchy stress.
Miller, Ronald E; Tadmor, Ellad B; Gibson, Joshua S; Bernstein, Noam; Pavia, Fabio
2016-05-14
The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress. PMID:27179471
Molecular dynamics study of cyclohexane interconversion
NASA Astrophysics Data System (ADS)
Wilson, Michael A.; Chandler, David
1990-12-01
Classical molecular dynamics calculations are reported for one C 6H 12 molecule in a bath of 250 CS 2 molecules at roomtemperature and liquid densities of 1.0, 1.3, 1.4 and 1.5 g/cm 3. The solvent contribution to the free energy of activation for the chair-boat isomerization has been determined to high accuracy. The transmission coefficient and reactive flux correlation functions have also been computed. The results obtained agree with earlier conclusions drawn from RISM integral equation calculations and stochastic molecular dynamics calculations. Namely, the solvent effect on the rate manifests a qualitative breakdown of transition state theory and the RRKM picture of unimolecular kinetics. Analysis of the activated trajectories indicate a significant degree of quasiperiodicity.
ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*
Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan
2014-01-01
Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670
Molecular dynamics studies of polyurethane nanocomposite hydrogels
NASA Astrophysics Data System (ADS)
Strankowska, J.; Piszczyk, Ł.; Strankowski, M.; Danowska, M.; Szutkowski, K.; Jurga, S.; Kwela, J.
2013-10-01
Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite® 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means of NMR spectroscopy, DMA and DSC analysis. The mechanical properties and thermal stability of the systems were improved by incorporation of clay and controlled by varying the clay content in polymeric matrix. Molecular dynamics of polymer chains depends on interaction of Cloisite® 30B nanoparticles with soft segments of polyurethanes. The characteristic nanosize effect is observed.
New faster CHARMM molecular dynamics engine
Hynninen, Antti-Pekka; Crowley, Michael F
2014-01-01
We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. PMID:24302199
Nanoindentation of Zr by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.
2015-12-01
Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.
Molecular dynamics modelling of solidification in metals
Boercker, D.B.; Belak, J.; Glosli, J.
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.
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. PMID:22476233
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
Optimally designed fields for controlling molecular dynamics
NASA Astrophysics Data System (ADS)
Rabitz, Herschel
1991-10-01
This research concerns the development of molecular control theory techniques for designing optical fields capable of manipulating molecular dynamic phenomena. Although is has been long recognized that lasers should be capable of manipulating dynamic events, many frustrating years of intuitively driven laboratory studies only serve to illustrate the point that the task is complex and defies intuition. The principal new component in the present research is the recognition that this problem falls into the category of control theory and its inherent complexities require the use of modern control theory tools largely developed in the engineering disciplines. Thus, the research has initiated a transfer of the control theory concepts to the molecular scale. Although much contained effort will be needed to fully develop these concepts, the research in this grant set forth the basic components of the theory and carried out illustrative studies involving the design of optical fields capable of controlling rotational, vibrational and electronic degrees of freedom. Optimal control within the quantum mechanical molecular realm represents a frontier area with many possible ultimate applications. At this stage, the theoretical tools need to be joined with merging laboratory optical pulse shaping capabilities to illustrate the power of the concepts.
Structure and dynamics of complex liquid water: Molecular dynamics simulation
NASA Astrophysics Data System (ADS)
S, Indrajith V.; Natesan, Baskaran
2015-06-01
We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.
Dynamic Maintenance and Visualization of Molecular Surfaces
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.
The 2011 Dynamics of Molecular Collisions Conference
Nesbitt, David J.
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
Polymer Fluid Dynamics: Continuum and Molecular Approaches.
Bird, R B; Giacomin, A J
2016-06-01
To solve problems in polymer fluid dynamics, one needs the equations of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (a) One can write a continuum expression for the stress tensor in terms of kinematic tensors, or (b) one can select a molecular model that represents the polymer molecule and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. We restrict the discussion primarily to the simplest stress tensor expressions or constitutive equations containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. Studying the simplest models allows us to discover which types of empiricisms or molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows, which are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems. PMID:27276553
Motion correction via nonrigid coregistration of dynamic MR mammography series
NASA Astrophysics Data System (ADS)
Krol, Andrzej; Magri, Alphonso; Unlu, Mehmet; Feiglin, David; Lipson, Edward; Mandel, James; Tillapaugh-Fay, Gwen; Lee, Wei; Coman, Ioana; Szeverenyi, Nikolaus M.
2006-03-01
The objectives of this investigation are to improve quality of subtraction MR breast images and improve accuracy of time-signal intensity curves (TSIC) related to local contrast-agent concentration in dynamic MR mammography. The patients, with up to nine fiducial skin markers (FSMs) taped to each breast, were prone with both breasts suspended into a single well that housed the receiver coil. After a preliminary scan, paramagnetic contrast agent gadopentate digmeglumine (Gd) was delivered intravenously, followed by physiological saline. The field of view was centered over the breasts. We used a gradient recalled echo (GRE) technique for pre-Gd baseline, and five more measurements at 60s intervals. Centroids were determined for corresponding FSMs visible on pre-Gd and any post-Gd images. This was followed by segmentation of breast surfaces in all dynamic-series images, and meshing of all post-Gd breast images. Tetrahedral volume and triangular surface elements were used to construct a finite element method (FEM) model. We used ANSYS TM software and an analogy between orthogonal components of the displacement field and the temperature differences in steady-state heat transfer (SSHT) in solids. The floating images were warped to a fixed image using an appropriate shape function for interpolation from mesh nodes to voxels. To reduce any residual misregistration, we performed surface matching between the previously warped floating image and the target image. Our method of motion correction via nonrigid coregistration yielded excellent differential-image series that clearly revealed lesions not visible in unregistered differential-image series. Further, it produced clinically useful maximum intensity projection (MIP) 3D images.
Local Refinements in Classical Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Fackeldey, Konstantin; Weber, Marcus
2014-03-01
Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.
Symmetry Reduced Dynamics of Charged Molecular Strands
NASA Astrophysics Data System (ADS)
Ellis, David C. P.; Gay-Balmaz, François; Holm, Darryl D.; Putkaradze, Vakhtang; Ratiu, Tudor S.
2010-09-01
The equations of motion are derived for the dynamical folding of charged molecular strands (such as DNA) modeled as flexible continuous filamentary distributions of interacting rigid charge conformations. The new feature is that these equations are nonlocal when the screened Coulomb interactions, or Lennard-Jones potentials between pairs of charges, are included. The nonlocal dynamics is derived in the convective representation of continuum motion by using modified Euler-Poincaré and Hamilton-Pontryagin variational formulations that illuminate the various approaches within the framework of symmetry reduction of Hamilton’s principle for exact geometric rods. In the absence of nonlocal interactions, the equations recover the classical Kirchhoff theory of elastic rods. The motion equations in the convective representation are shown to arise by a classical Lagrangian reduction associated to the symmetry group of the system. This approach uses the process of affine Euler-Poincaré reduction initially developed for complex fluids. On the Hamiltonian side, the Poisson bracket of the molecular strand is obtained by reduction of the canonical symplectic structure on phase space. A change of variables allows a direct passage from this classical point of view to the covariant formulation in terms of Lagrange-Poincaré equations of field theory. In another revealing perspective, the convective representation of the nonlocal equations of molecular strand motion is transformed into quaternionic form.
2015-11-01
In the article by Heuslein et al, which published online ahead of print on September 3, 2015 (DOI: 10.1161/ATVBAHA.115.305775), a correction was needed. Brett R. Blackman was added as the penultimate author of the article. The article has been corrected for publication in the November 2015 issue. PMID:26490278
Stochastic Event-Driven Molecular Dynamics
Donev, Aleksandar Garcia, Alejandro L.; Alder, Berni J.
2008-02-01
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in EDMD, rather, the momentum and energy exchange in the solvent is determined stochastically using DSMC. The coupling between the solvent and the solute is consistently represented at the particle level retaining hydrodynamic interactions and thermodynamic fluctuations. However, unlike full MD simulations of both the solvent and the solute, in SEDMD the spatial structure of the solvent is ignored. The SEDMD algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard-wall subjected to uniform shear. SEDMD closely reproduces results obtained using traditional EDMD simulations with two orders of magnitude greater efficiency. Results question the existence of periodic (cycling) motion of the polymer chain.
Electronic continuum model for molecular dynamics simulations.
Leontyev, I V; Stuchebrukhov, A A
2009-02-28
A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627
Molecular dynamics simulation of liquid water: Hybrid density functionals
Todorova, T; Seitsonen, A; Hutter, J; Kuo, W; Mundy, C
2005-09-12
The structure, dynamical and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta functional, four gradient corrected functionals, the local density and Hartree-Fock approximation. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and under-structured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller averaged numbers of hydrogen bonds and similar hydrogen bond populations as pure density functionals. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than from the corresponding pure density functionals.
Molecular dynamics studies of aromatic hydrocarbon liquids
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.
Molecular dynamics in high electric fields
NASA Astrophysics Data System (ADS)
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.
Validation of Bubble Dynamics Equation for a Nano-scale Bubble via Molecular Dynamics Simulation
NASA Astrophysics Data System (ADS)
Tsuda, S.; Hyodo, H.; Watanabe, S.
2015-12-01
For a validation of the application of conventional bubble dynamics to a nano-scale bubble behaviour, we simulated a nano-scale bubble collapsing or vibration by Molecular Dynamics (MD) method and compared the result with the solution of Rayleigh-Plesset (RP) equation and that of Confined RP (CRP) equation, whose boundary condition was corrected to be consistent with that of MD simulation. As a result, a good coincidence was obtained between MD, RP, and CRP in the case of one-component fluid. In addition, also a good correspondence was obtained particularly in the comparison between MD and CRP in the case of two-component fluid containing non-condensable gas. The present results indicate that conventional bubble dynamics equation can be applied even to a nano-scale tiny bubble.
Accelerated molecular dynamics methods: introduction and recent developments
Uberuaga, Blas Pedro; Voter, Arthur F; Perez, Danny; Shim, Y; Amar, J G
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what
Thermostability of Enzymes from Molecular Dynamics Simulations.
Zeiske, Tim; Stafford, Kate A; Palmer, Arthur G
2016-06-14
Thermodynamic stability is a central requirement for protein function, and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitro thermostability of members of the bacterial ribonuclease HI (RNase H) family of endonucleases. The temperature dependence of the generalized order parameter, S, for four RNase H homologues, from psychrotrophic, mesophilic, and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. PMID:27123810
8B structure in Fermionic Molecular Dynamics
NASA Astrophysics Data System (ADS)
Henninger, K. R.; Neff, T.; Feldmeier, H.
2015-04-01
The structure of the light exotic nucleus 8B is investigated in the Fermionic Molecular Dynamics (FMD) model. The decay of 8B is responsible for almost the entire high- energy solar-neutrino flux, making structure calculations of 8B important for determining the solar core temperature. 8B is a proton halo candidate thought to exhibit clustering. FMD uses a wave-packet basis and is well-suited for modelling clustering and halos. For a multiconfiguration treatment we construct the many-body Hilbert space from antisymmetrised angular-momentum projected 8-particle states. First results show formation of a proton halo.
Molecular dynamics simulations of dense plasmas
Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.
1993-12-31
We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.
Molecular beam studies of reaction dynamics
Lee, Y.T.
1987-03-01
Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.
Molecular dynamics simulation of ice XII
NASA Astrophysics Data System (ADS)
Borzsák, István; Cummings, Peter T.
1999-02-01
Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.
Crystallization of nickel nanoclusters by molecular dynamics
NASA Astrophysics Data System (ADS)
Chamati, H.; Gaminchev, K.
2012-12-01
We investigated the melting properties of bulk nickel and the crystallization of nickel nanocrystals via molecular dynamics using a potential in the framework of the second moment approximation of tight-binding theory. The melting behavior was simulated with the hysteresis approach by subsequently heating and cooling gradually the system over a wide range of temperatures. The crystallization of nickel nanoclusters consisting of 55, 147 and 309 atoms was achieved after repeatedly annealing and quenching the corresponding quasicrystals several times to avoid being trapped in a local energy minimum. The time over which the global minimum was reached was found to increase with the cluster size.
Charge transport network dynamics in molecular aggregates.
Jackson, Nicholas E; Chen, Lin X; Ratner, Mark A
2016-08-01
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, [Formula: see text] Simulations reveal the relevant timescale for local transfer integral decorrelation to be [Formula: see text]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. PMID:27439871
Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations
NASA Astrophysics Data System (ADS)
Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein
2015-12-01
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
Molecular dynamics simulation of liquid sulfur dioxide.
Ribeiro, Mauro C C
2006-05-01
A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k). PMID:16640437
Frank, Martin; Gutbrod, Peter; Hassayoun, Chokri; von Der Lieth, Claus-W
2003-10-01
Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions at an atomic level. The "Dynamic Molecules" approach is the first internet portal that provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The aim is to open molecular dynamics techniques to a broader range of users including undergraduate students, teachers and scientists outside the bioinformatics field. The time-limiting factors are the availability of free capacity on the computing server to run the simulations and the time required to transport the history file through the internet for the animation mode. The interactive access mode of the portal is acceptable for animations of molecules having up to about 500 atoms. PMID:12908101
2015-12-01
In the article by Narayan et al (Narayan O, Davies JE, Hughes AD, Dart AM, Parker KH, Reid C, Cameron JD. Central aortic reservoir-wave analysis improves prediction of cardiovascular events in elderly hypertensives. Hypertension. 2015;65:629–635. doi: 10.1161/HYPERTENSIONAHA.114.04824), which published online ahead of print December 22, 2014, and appeared in the March 2015 issue of the journal, some corrections were needed.On page 632, Figure, panel A, the label PRI has been corrected to read RPI. In panel B, the text by the upward arrow, "10% increase in kd,” has been corrected to read, "10% decrease in kd." The corrected figure is shown below.The authors apologize for these errors. PMID:26558821
Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Byutner, Oleksiy; Smith, Grant
2001-03-01
In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.
Exact dynamic properties of molecular motors
NASA Astrophysics Data System (ADS)
Boon, N. J.; Hoyle, R. B.
2012-08-01
Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.
Structure and Dynamics of Cellulose Molecular Solutions
NASA Astrophysics Data System (ADS)
Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert
Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.
Exact dynamic properties of molecular motors.
Boon, N J; Hoyle, R B
2012-08-28
Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)] on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods. PMID:22938213
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2015-01-28
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2015-01-01
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme
NASA Astrophysics Data System (ADS)
Okiyama, Yoshio; Fukuzawa, Kaori; Yamada, Haruka; Mochizuki, Yuji; Nakano, Tatsuya; Tanaka, Shigenori
2011-06-01
Basis set superposition error (BSSE) correction with counterpoise (CP) procedure under the environmental electrostatic potential is newly introduced to interfragment interaction energy (IFIE), which is important for interaction analysis in the fragment molecular orbital method. The CP correction for IFIE is applied to a stacked dimer of base pair and a protein-ligand complex of estrogen receptor and 17β-estradiol with scaled third-order Møller-Plesset perturbation theory. The BSSEs amount to about quarter of IFIE for hydrogen-bonding and electrostatic interactions and half or even more for dispersion interactions. Estimation of IFIE with the CP correction is therefore preferred for the quantitative discussion.
Dynamic transitions in molecular dynamics simulations of supercooled silicon
NASA Astrophysics Data System (ADS)
Mei, Xiaojun; Eapen, Jacob
2013-04-01
Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.
Zhang, Lin; Tang, Ronghong; Bai, Shu; Connors, Natalie K; Lua, Linda H L; Chuan, Yap P; Middelberg, Anton P J; Sun, Yan
2013-05-01
Virus-like particles (VLPs) are highly organized nanoparticles that have great potential in vaccinology, gene therapy, drug delivery, and materials science. However, the application of VLPs is hindered by obstacles in their design and production due to low efficiency of self-assembly. In the present study, all-atom (AA) molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method are utilized to examine the molecular interactions in the capsomere of a murine polyomavirus (MPV) VLP. It is found that both low ionic strength and the intracapsomere disulfide bonds are favorable for maintaining a stable capsomere. Simulation results examining the effects of solution conditions on the stabilization of a capsomere were verified by calorimetry experiments. Simulation results of free energy decomposition indicate that hydrophobic interaction is favorable for the formation of a capsomere, whereas electrostatic interaction is unfavorable. With increasing ionic strength, the dominant interaction for the stabilization of a capsomere changes from hydrophobic to electrostatic. By comprehensive analyses, the key amino acid residues (hot spots) in VP1 protein aiding formation of a capsomere in different solution conditions have been identified. These results provide molecular insights into the stabilization of building blocks for VLP and are expected to have implications in their partitioning between the correct and off-pathway reactions in VLP assembly. PMID:23586433
NASA Astrophysics Data System (ADS)
1995-04-01
Seismic images of the Brooks Range, Arctic Alaska, reveal crustal-scale duplexing: Correction Geology, v. 23, p. 65 68 (January 1995) The correct Figure 4A, for the loose insert, is given here. See Figure 4A below. Corrected inserts will be available to those requesting copies of the article from the senior author, Gary S. Fuis, U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025. Figure 4A. P-wave velocity model of Brooks Range region (thin gray contours) with migrated wide-angle reflections (heavy red lines) and migreated vertical-incidence reflections (short black lines) superimposed. Velocity contour interval is 0.25 km/s; 4,5, and 6 km/s contours are labeled. Estimated error in velocities is one contour interval. Symbols on faults shown at top are as in Figure 2 caption.
Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M; Benedict, L; Hau-Riege, S; Langdon, A; London, R
2008-02-14
The temperature equilibration rate in dense hydrogen (for both T{sub i} > T{sub e} and T{sub i} < T{sub e}) has been calculated with large-scale molecular dynamics simulations for temperatures between 10 and 300 eV and densities between 10{sup 20}/cc to 10{sup 24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L {approx}> 1, Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] with the sub-leading corrections and the fit of Gericke-Murillo-Schlanges [Gericke et al., PRE 65, 036418 (2003)] to the T-matrix evaluation of the collision operator, agrees with the MD data to within the error bars of the simulation. For more strongly-coupled plasmas where L {approx}< 1, our numerical results are consistent with the fit of Gericke-Murillo-Schlanges.
Atomistic molecular dynamic simulations of multiferroics.
Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L
2012-08-10
A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300
Atomistic Molecular Dynamic Simulations of Multiferroics
NASA Astrophysics Data System (ADS)
Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.
2012-08-01
A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.
Quantum Thermal Bath for Path Integral Molecular Dynamics Simulation.
Brieuc, Fabien; Dammak, Hichem; Hayoun, Marc
2016-03-01
The quantum thermal bath (QTB) method has been recently developed to account for the quantum nature of the nuclei by using standard molecular dynamics (MD) simulation. QTB-MD is an efficient but approximate method when dealing with strongly anharmonic systems, while path integral molecular dynamics (PIMD) gives exact results but in a huge amount of computation time. The QTB and PIMD methods have been combined in order to improve the PIMD convergence or correct the failures of the QTB-MD technique. Therefore, a new power spectral density of the random force within the QTB has been developed. A modified centroid-virial estimator of the kinetic energy, especially adapted to QTB-PIMD, has also been proposed. The method is applied to selected systems: a one-dimensional double-well system, a ferroelectric phase transition, and the position distribution of an hydrogen atom in a fuel cell material. The advantage of the QTB-PIMD method is its ability to give exact results with a more reasonable computation time for strongly anharmonic systems. PMID:26799437
Accelerated Molecular Dynamics studies of He Bubble Growth in Tungsten
NASA Astrophysics Data System (ADS)
Uberuaga, Blas; Sandoval, Luis; Perez, Danny; Voter, Arthur
2015-11-01
Understanding how materials respond to extreme environments is critical for predicting and improving performance. In materials such as tungsten exposed to plasmas for nuclear fusion applications, novel nanoscale fuzzes, comprised of tendrils of tungsten, form as a consequence of the implantation of He into the near surface. However, the detailed mechanisms that link He bubble formation to the ultimate development of fuzz are unclear. Molecular dynamics simulations provide insight into the He implantation process, but are necessarily performed at implantation rates that are orders of magnitudes faster than experiment. Here, using accelerated molecular dynamics methods, we examine the role of He implantation rates on the physical evolution of He bubbles in tungsten. We find that, as the He rate is reduced, new types of events involving the response of the tungsten matrix to the pressure in the bubble become competitive and change the overall evolution of the bubble as well as the subsequent morphology of the tungsten surface. We have also examined how bubble growth differs at various microstructural features. These results highlight the importance of performing simulations at experimentally relevant conditions in order to correctly capture the contributions of the various significant kinetic processes and predict the overall response of the material.
Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Pagliai, Marco; Cavazzoni, Carlo; Cardini, Gianni; Erbacci, Giovanni; Parrinello, Michele; Schettino, Vincenzo
2008-06-01
The infrared and Raman spectra of naphthalene crystal with inclusion of anharmonic effects have been calculated by adopting the generalized variational density functional perturbation theory in the framework of Car-Parrinello molecular dynamics simulations. The computational approach has been generalized for cells of arbitrary shape. The intermolecular interactions have been analyzed with and without the van der Waals corrections, showing the importance of such interactions in the naphthalene crystal to reproduce the structural, dynamical, and spectroscopic properties.
2016-02-01
Neogi T, Jansen TLTA, Dalbeth N, et al. 2015 Gout classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative. Ann Rheum Dis 2015;74:1789–98. The name of the 20th author was misspelled. The correct spelling is Janitzia Vazquez-Mellado. We regret the error. PMID:26881284
Local Dynamic Reactive Power for Correction of System Voltage Problems
Kueck, John D; Rizy, D Tom; Li, Fangxing; Xu, Yan; Li, Huijuan; Adhikari, Sarina; Irminger, Philip
2008-12-01
Distribution systems are experiencing outages due to a phenomenon known as local voltage collapse. Local voltage collapse is occurring in part because modern air conditioner compressor motors are much more susceptible to stalling during a voltage dip than older motors. These motors can stall in less than 3 cycles (.05s) when a fault, such as on the sub-transmission system, causes voltage to sag to 70 to 60%. The reasons for this susceptibility are discussed in the report. During the local voltage collapse, voltages are depressed for a period of perhaps one or two minutes. There is a concern that these local events are interacting together over larger areas and may present a challenge to system reliability. An effective method of preventing local voltage collapse is the use of voltage regulation from Distributed Energy Resources (DER) that can supply or absorb reactive power. DER, when properly controlled, can provide a rapid correction to voltage dips and prevent motor stall. This report discusses the phenomenon and causes of local voltage collapse as well as the control methodology we have developed to counter voltage sag. The problem is growing because of the use of low inertia, high efficiency air conditioner (A/C) compressor motors and because the use of electric A/C is growing in use and becoming a larger percentage of system load. A method for local dynamic voltage regulation is discussed which uses reactive power injection or absorption from local DER. This method is independent, rapid, and will not interfere with conventional utility system voltage control. The results of simulations of this method are provided. The method has also been tested at the ORNL s Distributed Energy Communications and Control (DECC) Laboratory using our research inverter and synchronous condenser. These systems at the DECC Lab are interconnected to an actual distribution system, the ORNL distribution system, which is fed from TVA s 161kV sub-transmission backbone. The test results
Osmosis : a molecular dynamics computer simulation study
NASA Astrophysics Data System (ADS)
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..
Fiber lubrication: A molecular dynamics simulation study
NASA Astrophysics Data System (ADS)
Liu, Hongyi
Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence
Development of semiclassical molecular dynamics simulation method.
Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi
2016-04-28
Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383
Molecular Dynamics Simulation of Shock Induced Detonation
NASA Astrophysics Data System (ADS)
Tomar, Vikas; Zhou, Min
2004-07-01
This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
Schwabe, Tobias
2015-08-20
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273
Nonequilibrium molecular dynamics: The first 25 years
Hoover, W.G. |
1992-08-01
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.
Molecular Dynamics Simulations of Water Evaporation
NASA Astrophysics Data System (ADS)
Wen, Chengyuan; Grest, Gary; Cheng, Shengfeng
2015-03-01
The evaporation of water from the liquid/vapor interface is studied via large-scale molecular dynamics simulations for systems of more than a million atoms at 550K and 600K. The TIP4P-2005 water model whose liquid/vapor surface tension is in excellent agreement with experiments is used. Evaporative cooling at the interface is observed from temperature profiles determined from both translational and rotational kinetic energy. During evaporation, the density of water is slightly enhanced near the liquid-vapor interface. The velocity distribution of water molecules in the vapor phase during evaporation at various distances relative to the interface fit a Maxwell-Boltzmann distribution. While our results indicate an imbalance between evaporating and condensing water molecules, local thermal equilibrium is found to hold in addition to mechanical equilibrium. Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
Cluster production within antisymmetrized molecular dynamics
NASA Astrophysics Data System (ADS)
Ono, Akira
2016-06-01
Clusters are quite important at various situations in heavy-ion collisions. Antisymmetrized molecular dynamics was improved to take into account the correlations to form light clusters, such as deuterons and α particles, and light nuclei composed of several clusters. The momentum fluctuations of emitted particles are also taken into account by a simple method. Formation of fragments and light clusters in a wide range of heavy-ion collisions was well described with a single set of model parameters. Fragmentation in a proton induced reaction was also well reproduced by introducing cluster correlations. Calculated results demonstrate strong impacts of clusters in various observables including those usually regarded as probes of the density dependence of symmetry energy.
Cell list algorithms for nonequilibrium molecular dynamics
NASA Astrophysics Data System (ADS)
Dobson, Matthew; Fox, Ian; Saracino, Alexandra
2016-06-01
We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.
Molecular-dynamics simulations of lead clusters
NASA Astrophysics Data System (ADS)
Hendy, S. C.; Hall, B. D.
2001-08-01
Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.
Dielectrophoresis of nanocolloids: a molecular dynamics study.
Salonen, E; Terama, E; Vattulainen, I; Karttunen, M
2005-10-01
Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for a polarizable nanoparticle, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature. PMID:16195818
Dynamics of dewetting at the nanoscale using molecular dynamics.
Bertrand, E; Blake, T D; Ledauphin, V; Ogonowski, G; Coninck, J De; Fornasiero, D; Ralston, J
2007-03-27
Large-scale molecular dynamics simulations are used to model the dewetting of solid surfaces by partially wetting thin liquid films. Two levels of solid-liquid interaction are considered that give rise to large equilibrium contact angles. The initial length and thickness of the films are varied over a wide range at the nanoscale. Spontaneous dewetting is initiated by removing a band of molecules either from each end of the film or from its center. As observed experimentally and in previous simulations, the films recede at an initially constant speed, creating a growing rim of liquid with a constant receding dynamic contact angle. Consistent with the current understanding of wetting dynamics, film recession is faster on the more poorly wetted surface to an extent that cannot be explained solely by the increase in the surface tension driving force. In addition, the rates of recession of the thinnest films are found to increase with decreasing film thickness. These new results imply not only that the mobility of the liquid molecules adjacent to the solid increases with decreasing solid-liquid interactions, but also that the mobility adjacent to the free surface of the film is higher than in the bulk, so that the effective viscosity of the film decreases with thickness. PMID:17328565
Molecular dynamics simulations of microscale fluid transport
Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.
1998-02-01
Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.
Molecular dynamics simulations of supramolecular polymer rheology
NASA Astrophysics Data System (ADS)
Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.
2010-11-01
Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.
2016-02-01
In the article by Guessous et al (Guessous I, Pruijm M, Ponte B, Ackermann D, Ehret G, Ansermot N, Vuistiner P, Staessen J, Gu Y, Paccaud F, Mohaupt M, Vogt B, Pechère-Bertschi A, Martin PY, Burnier M, Eap CB, Bochud M. Associations of ambulatory blood pressure with urinary caffeine and caffeine metabolite excretions. Hypertension. 2015;65:691–696. doi: 10.1161/HYPERTENSIONAHA.114.04512), which published online ahead of print December 8, 2014, and appeared in the March 2015 issue of the journal, a correction was needed.One of the author surnames was misspelled. Antoinette Pechère-Berstchi has been corrected to read Antoinette Pechère-Bertschi.The authors apologize for this error. PMID:26763012
Walters, Chris; Errington, Neil; Rowe, Arther J; Harding, Stephen E
2002-01-01
Over recent years the binding ability of the molecular chaperone cpn60 (GroEL14) and its co-chaperone cpn10 (GroES7) has been reported to occur under an assortment of specific conditions from the use of non-hydrolysable ATP analogues (namely adenosine 5'-[gamma-thio]triphosphate) to requiring hydrolysable ATP for any interaction to occur. We have investigated this further using the molecular hydrodynamic methods (hydrodynamic bead modelling, sedimentation-velocity analytical ultracentrifugation and dynamic light-scattering), allowing the process to be followed under physiologically relevant dilute solution conditions, combined with absorption spectrophotometry to determine GroES7-GroEL14 interaction through the rate inhibition of the cpn60's ATPase activity by GroES7. The results found here indicate that the presence of hydrolysable ATP is required to facilitate correct GroES7 interaction with GroEL14 in solution. PMID:12049650
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
NASA Technical Reports Server (NTRS)
Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.
1993-01-01
The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.
Molecular beam studies of reaction dynamics
Lee, Y.T.
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 beam studies of reaction dynamics
Lee, Yuan T.
1991-03-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Dynamic pressure corrections in a clearance-sealed piston prover for gas flow measurements
NASA Astrophysics Data System (ADS)
Kutin, Jože; Bobovnik, Gregor; Bajsić, Ivan
2013-02-01
The dynamic pressure effects and their corrections in a high-speed, clearance-sealed realization of a piston prover for gas flow measurements are discussed. The experimental results show the deterministic, rather than stochastic, nature of the dynamic pressure conditions and, consequently, the repeatable nature of their influence on the flow measurements. The experimental validation proves the advantage of the polytropic/adiabatic pressure correction model, which was proposed by the authors, as compared with the isothermal pressure correction model. The paper ends with an estimation of the measurement uncertainty related to the pressure corrections using either the adiabatic or isothermal model.
Molecular dynamics studies on nanoscale gas transport
NASA Astrophysics Data System (ADS)
Barisik, Murat
Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the
Molecular dynamics simulation of amorphous indomethacin.
Xiang, Tian-Xiang; Anderson, Bradley D
2013-01-01
Molecular dynamics (MD) simulations have been conducted using an assembly consisting of 105 indomethacin (IMC) molecules and 12 water molecules to investigate the underlying dynamic (e.g., rotational and translational diffusivities and conformation relaxation rates) and structural properties (e.g., conformation, hydrogen-bonding distributions, and interactions of water with IMC) of amorphous IMC. These properties may be important in predicting physical stability of this metastable material. The IMC model was constructed using X-ray diffraction data with the force-field parameters mostly assigned by analogy with similar groups in Amber-ff03 and atomic charges calculated with the B3LYP/ccpVTZ30, IEFPCM, and RESP models. The assemblies were initially equilibrated in their molten state and cooled through the glass transition temperature to form amorphous solids. Constant temperature dynamic runs were then carried out above and below the T(g) (i.e., at 600 K (10 ns), 400 K (350 ns), and 298 K (240 ns)). The density (1.312 ± 0.003 g/cm(3)) of the simulated amorphous solid at 298 K was close to the experimental value (1.32 g/cm(3)) while the estimated T(g) (384 K) was ~64 degrees higher than the experimental value (320 K) due to the faster cooling rate. Due to the hindered rotation of its amide bond, IMC can exist in different diastereomeric states. Different IMC conformations were sufficiently sampled in the IMC melt or vapor, but transitions occurred rarely in the glass. The hydrogen-bonding patterns in amorphous IMC are more complex in the amorphous state than in the crystalline polymorphs. Carboxylic dimers that are dominant in α- and γ-crystals were found to occur at a much lower probability in the simulated IMC glasses while hydrogen-bonded IMC chains were more easily identified patterns in the simulated amorphous solids. To determine molecular diffusivity, a novel analytical method is proposed to deal with the non-Einsteinian behavior, in which the temporal
GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES
MUCKERMAN,J.T.
1999-06-09
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.
Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules
Muckerman, J.T.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometic sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.
Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics
2015-01-01
Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406
Molecular-dynamics simulation of hydrogen diffusion in palladium
NASA Astrophysics Data System (ADS)
Li, Yinggang; Wahnström, Göran
1992-12-01
Molecular-dynamics simulations for hydrogen diffusion in Pd are performed for a system consisting of 256 Pd atoms and 8 H atoms at the temperature T=623 K. Under these conditions detailed quasielastic-neutron-scattering (QNS) data are available. For the interatomic interactions we use the embedded-atom method (EAM), which incorporates some essential many-body effects in metals. Based on the EAM approach, the wave-vector dependence of the width of the QNS peak is investigated in detail. It is found that a single electronically adiabatic potential-energy surface cannot reproduce the observed wave-vector dependence. After incorporating the coupling of hydrogen atoms to the low-lying electron-hole pair excitations among the conduction electrons, close agreement with the experimental data is obtained. This is a strong indication that one has to go beyond the Born-Oppenheimer approximation in order to characterize correctly the diffusive motion of hydrogen in metals. To reveal the diffusive behavior in more detail, the residence time distribution and the correlation character in diffusion direction are investigated. We found that including the nonadiabatic corrections reduces the probability for the H atoms to move over several lattice sites without getting trapped in between. As a result, the motion of the H atoms becomes more similar to that assumed in the Chudley-Elliott model, which describes well the QNS data for the wave-vector dependence of the width.
Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations.
Soares, Rosemberg O; Torres, Pedro H M; da Silva, Manuela L; Pascutti, Pedro G
2016-08-01
The active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pH-dependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25' and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding. PMID:27291071
Automated motion correction based on target tracking for dynamic nuclear medicine studies
NASA Astrophysics Data System (ADS)
Cao, Xinhua; Tetrault, Tracy; Fahey, Fred; Treves, Ted
2008-03-01
Nuclear medicine dynamic studies of kidneys, bladder and stomach are important diagnostic tools. Accurate generation of time-activity curves from regions of interest (ROIs) requires that the patient remains motionless for the duration of the study. This is not always possible since some dynamic studies may last from several minutes to one hour. Several motion correction solutions have been explored. Motion correction using external point sources is inconvenient and not accurate especially when motion results from breathing, organ motion or feeding rather than from body motion alone. Centroid-based motion correction assumes that activity distribution is only inside the single organ (without background) and uniform, but this approach is impractical in most clinical studies. In this paper, we present a novel technique of motion correction that first tracks the organ of interest in a dynamic series then aligns the organ. The implementation algorithm for target tracking-based motion correction consists of image preprocessing, target detection, target positioning, motion estimation and prediction, tracking (new search region generation) and target alignment. The targeted organ is tracked from the first frame to the last one in the dynamic series to generate a moving trajectory of the organ. Motion correction is implemented by aligning the organ ROIs in the image series to the location of the organ in the first image. The proposed method of motion correction has been applied to several dynamic nuclear medicine studies including radionuclide cystography, dynamic renal scintigraphy, diuretic renography and gastric emptying scintigraphy.
2015-05-22
The Circulation Research article by Keith and Bolli (“String Theory” of c-kitpos Cardiac Cells: A New Paradigm Regarding the Nature of These Cells That May Reconcile Apparently Discrepant Results. Circ Res. 2015:116:1216-1230. doi: 10.1161/CIRCRESAHA.116.305557) states that van Berlo et al (2014) observed that large numbers of fibroblasts and adventitial cells, some smooth muscle and endothelial cells, and rare cardiomyocytes originated from c-kit positive progenitors. However, van Berlo et al reported that only occasional fibroblasts and adventitial cells derived from c-kit positive progenitors in their studies. Accordingly, the review has been corrected to indicate that van Berlo et al (2014) observed that large numbers of endothelial cells, with some smooth muscle cells and fibroblasts, and more rarely cardiomyocytes, originated from c-kit positive progenitors in their murine model. The authors apologize for this error, and the error has been noted and corrected in the online version of the article, which is available at http://circres.ahajournals.org/content/116/7/1216.full ( PMID:25999426
NASA Astrophysics Data System (ADS)
1998-12-01
Alleged mosasaur bite marks on Late Cretaceous ammonites are limpet (patellogastropod) home scars Geology, v. 26, p. 947 950 (October 1998) This article had the following printing errors: p. 947, Abstract, line 11, “sepia” should be “septa” p. 947, 1st paragraph under Introduction, line 2, “creep” should be “deep” p. 948, column 1, 2nd paragraph, line 7, “creep” should be “deep” p. 949, column 1, 1st paragraph, line 1, “creep” should be “deep” p. 949, column 1, 1st paragraph, line 5, “19774” should be “1977)” p. 949, column 1, 4th paragraph, line 7, “in particular” should be “In particular” CORRECTION Mammalian community response to the latest Paleocene thermal maximum: An isotaphonomic study in the northern Bighorn Basin, Wyoming Geology, v. 26, p. 1011 1014 (November 1998) An error appeared in the References Cited. The correct reference appears below: Fricke, H. C., Clyde, W. C., O'Neil, J. R., and Gingerich, P. D., 1998, Evidence for rapid climate change in North America during the latest Paleocene thermal maximum: Oxygen isotope compositions of biogenic phosphate from the Bighorn Basin (Wyoming): Earth and Planetary Science Letters, v. 160, p. 193 208.
[Performance analysis and radiometric correction of novel molecular hyperspectral imaging system].
Liu, Hong-Ying; Li, Qing-Li; Gu, Bin; Wang, Yi-Ting; Xue, Yong-Qi
2012-11-01
Integrating molecular imaging technology and hyperspectral technology, a novel molecular hyperspectral imaging (MHSI) system based on AOTF was presented. The system consists of microscope, spectrometer, matrix CCD, image collection card and computer. The system's performance was synthetically evaluated referring every part's performance. The spectral range of the MHSI system is from 550 to 1 000 nm. Two hundred twenty five bands can be continuously captured at a time. The spectral resolution is less than 2 nm. The spatial resolution is about 0.061 5 microm. CCD acquisition speed achieved 2.612 5 s x B(-1) in the integration mode and about 0.11 micros x B(-1) in the non-integration mode. Due to the infection of lamp, a spectral curve extracted directly from the original hyperspectral data can not truly present biochemical character and needs to be corrected. The paper proposes the gray correction coefficient algorithm with spatial dimension and spectral dimension, and gives concrete realization of the algorithm. Taking the sample of leukemia blood, by comparing the single-band images, pseudo-color images and spectra before and after correction, the results indicate the effectiveness of correction algorithm. The corrected data is effective for subsequent analysis. PMID:23387200
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D. Kühn, Oliver
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.
Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics
NASA Astrophysics Data System (ADS)
Rakesh, L.
2009-09-01
Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the
Thermal transpiration: A molecular dynamics study
NASA Astrophysics Data System (ADS)
T, Joe Francis; Sathian, Sarith P.
2014-12-01
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Thermal transpiration: A molecular dynamics study
T, Joe Francis; Sathian, Sarith P.
2014-12-09
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Nanoscale deicing by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
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
ERIC Educational Resources Information Center
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…
Ruggiero, Michael T; Gooch, Jonathan; Zubieta, Jon; Korter, Timothy M
2016-02-18
The problem of nonlocal interactions in density functional theory calculations has in part been mitigated by the introduction of range-corrected functional methods. While promising solutions, the continued evaluation of range corrections in the structural simulations of complex molecular crystals is required to judge their efficacy in challenging chemical environments. Here, three pyridinium-based crystals, exhibiting a wide range of intramolecular and intermolecular interactions, are used as benchmark systems for gauging the accuracy of several range-corrected density functional techniques. The computational results are compared to low-temperature experimental single-crystal X-ray diffraction and terahertz spectroscopic measurements, enabling the direct assessment of range correction in the accurate simulation of the potential energy surface minima and curvatures. Ultimately, the simultaneous treatment of both short- and long-range effects by the ωB97-X functional was found to be central to its rank as the top performer in reproducing the complex array of forces that occur in the studied pyridinium solids. These results demonstrate that while long-range corrections are the most commonly implemented range-dependent improvements to density functionals, short-range corrections are vital for the accurate reproduction of forces that rapidly diminish with distance, such as quadrupole-quadrupole interactions. PMID:26814572
Emergence of spacetime dynamics in entropy corrected and braneworld models
Sheykhi, A.; Dehghani, M.H.; Hosseini, S.E. E-mail: mhd@shirazu.ac.ir
2013-04-01
A very interesting new proposal on the origin of the cosmic expansion was recently suggested by Padmanabhan [arXiv:1206.4916]. He argued that the difference between the surface degrees of freedom and the bulk degrees of freedom in a region of space drives the accelerated expansion of the universe, as well as the standard Friedmann equation through relation ΔV = Δt(N{sub sur}−N{sub bulk}). In this paper, we first present the general expression for the number of degrees of freedom on the holographic surface, N{sub sur}, using the general entropy corrected formula S = A/(4L{sub p}{sup 2})+s(A). Then, as two example, by applying the Padmanabhan's idea we extract the corresponding Friedmann equations in the presence of power-law and logarithmic correction terms in the entropy. We also extend the study to RS II and DGP braneworld models and derive successfully the correct form of the Friedmann equations in these theories. Our study further supports the viability of Padmanabhan's proposal.
Statistical coarse-graining of molecular dynamics into peridynamics.
Silling, Stewart Andrew; Lehoucq, Richard B.
2007-10-01
This paper describes an elegant statistical coarse-graining of molecular dynamics at finite temperature into peridynamics, a continuum theory. Peridynamics is an efficient alternative to molecular dynamics enabling dynamics at larger length and time scales. In direct analogy with molecular dynamics, peridynamics uses a nonlocal model of force and does not employ stress/strain relationships germane to classical continuum mechanics. In contrast with classical continuum mechanics, the peridynamic representation of a system of linear springs and masses is shown to have the same dispersion relation as the original spring-mass system.
Constant pressure and temperature discrete-time Langevin molecular dynamics.
Grønbech-Jensen, Niels; Farago, Oded
2014-11-21
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are built on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems-a one-dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three-dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb and Dünweg [J. Chem. Phys. 111, 4453 (1999)], show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation. PMID:25416875
Constant pressure and temperature discrete-time Langevin molecular dynamics
Grønbech-Jensen, Niels; Farago, Oded
2014-11-21
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are built on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems—a one-dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three-dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb and Dünweg [J. Chem. Phys. 111, 4453 (1999)], show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.
Molecular Dynamics Simulations of Coulomb Explosion
Bringa, E M
2002-05-17
A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a ''Coulomb Explosion'', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) simulations of Coulomb explosion for a cylindrical track as a function of charge density and neutralization/quenching time, {tau}. Screening by the free electrons is accounted for using a screened Coulomb potential for the interaction among charges. The yield exhibits a prompt component from the track core and a component, which dominates at higher excitation density, from the heated region produced. For the cases studied, the number of atoms ejected per incident ion, i.e. the sputtering yield Y, is quadratic with charge density along the track as suggested by simple models. Y({tau} = 0.2 Debye periods) is nearly 20% of the yield when there is no neutralization ({tau} {yields} {infinity}). The connections between ''Coulomb explosions'', thermal spikes and measurements of electronic sputtering are discussed.
A molecular dynamics study of dielectric friction
Kurnikova, M.G.; Waldeck, D.H.; Coalson, R.D.
1996-07-01
A molecular dynamics study of the friction experienced by the dye molecule resorufamine rotating in a polar solvent is performed. The validity of simple continuum theories of dielectric friction is tested. It is found that the Alavi{endash}Waldeck theory gives reasonable results for the zero frequency dielectric friction coefficient while the Nee{endash}Zwanzig theory requires an unphysically small cavity radius. A procedure for evaluating the time dependent friction kernel from torques and angular velocities, which enables the contributions to the friction from the van der Waals and Coulomb forces to be evaluated separately, is suggested. This study of a realistic system shows that electrostatic interactions can enhance friction by at least two physical mechanisms. First is a contribution to the friction which arises solely from retardation of the solvent reaction field. Second is a contribution arising from local structural changes of the solvent which are driven by the electrostatic field, i.e., a change in the local viscosity. {copyright} {ital 1996 American Institute of Physics.}
Quantum molecular dynamics simulations of dense matter
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.
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.
Integrating influenza antigenic dynamics with molecular evolution
Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew
2014-01-01
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001 PMID:24497547
Molecular chaperone-mediated nuclear protein dynamics.
Echtenkamp, Frank J; Freeman, Brian C
2014-05-01
Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus. PMID:24694369
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. PMID:27431975
NASA Astrophysics Data System (ADS)
Brennan, John K.; Lísal, Martin; Gubbins, Keith E.; Rice, Betsy M.
2004-12-01
A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2+3H2⇔2NH3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.
Dynamic stresses, coulomb failure, and remote triggering: corrected
Hill, David P.
2012-01-01
Dynamic stresses associated with crustal surface waves with 15–30 s periods and peak amplitudes <1 MPa are capable of triggering seismicity at sites remote from the generating mainshock under appropriate conditions. Coulomb failure models based on a frictional strength threshold offer one explanation for instances of rapid‐onset triggered seismicity that develop during the surface‐wave peak dynamic stressing. Evaluation of the triggering potential of surface‐wave dynamic stresses acting on critically stressed faults using a Mohr’s circle representation together with the Coulomb failure criteria indicates that Love waves should have a higher triggering potential than Rayleigh waves for most fault orientations and wave incidence angles. That (1) the onset of triggered seismicity often appears to begin during the Rayleigh wave rather than the earlier arriving Love wave, and (2) Love‐wave amplitudes typically exceed those for Rayleigh waves suggests that the explanation for rapid‐onset dynamic triggering may not reside solely with a simple static‐threshold friction mode. The results also indicate that normal faults should be more susceptible to dynamic triggering by 20‐s Rayleigh‐wave stresses than thrust faults in the shallow seismogenic crust (<10 km) while the advantage tips in favor of reverse faults greater depths. This transition depth scales with wavelength and coincides roughly with the transition from retrograde‐to‐prograde particle motion. Locally elevated pore pressures may have a role in the observed prevalence of dynamic triggering in extensional regimes and geothermal/volcanic systems. The result is consistent with the apparent elevated susceptibility of extensional or transtensional tectonic regimes to remote triggering by Rayleigh‐wave dynamic stresses than compressional or transpressional regimes.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Bossis, Fabrizio; Palese, Luigi L.
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.
Free energy calculations using dual-level Born-Oppenheimer molecular dynamics
NASA Astrophysics Data System (ADS)
Retegan, Marius; Martins-Costa, Marilia; Ruiz-López, Manuel F.
2010-08-01
We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.
Combined molecular dynamics-spin dynamics simulations of bcc iron
Perera, Meewanage Dilina N; Yin, Junqi; Landau, David P; Nicholson, Don M; Stocks, George Malcolm; Eisenbach, Markus; Brown, Greg
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.
Singh, Surya Pratap; Gupta, Dwijendra K
2016-04-01
Casein kinase-1 (CK1) isoforms actively participate in the down-regulation of canonical Wnt signaling pathway; however recent studies have shown their active roles in oncogenesis of various tissues through this pathway. Functional loss of two isoforms (CK1-α/ε) has been shown to activate the carcinogenic pathway which involves the stabilization of of cytoplasmic β-catenin. Development of anticancer therapeutics is very laborious task and depends upon the structural and conformational details of the target. This study focuses on, how the structural dynamics and conformational changes of two CK1 isoforms are synchronized in carcinogenic pathway. The conformational dynamics in kinases is the responsible for their action as has been supported by the molecular docking experiments. PMID:26788877
Molecular Dynamics Simulation of Disordered Zircon
Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin
2004-02-27
The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.
Condensation on nanorods by molecular dynamics
NASA Astrophysics Data System (ADS)
Suh, Donguk; Yasuoka, Kenji
2016-06-01
Many recent experimental studies have been conducted on constructing nanorods and nanowires to use in a wide range of applications. In this study, molecular dynamics is used to directly examine the condensation rate of nanorods and the results are compared with other basic configurations such as cubes or spheres. According to previous studies conducted by Suh and Yasuoka [J. Phys. Chem. B 115, 10631 (2011); 116, 14637 (2012)], a simple change in the configuration of the seed produces a shape effect, where the curvature of the solid seed surface directly affects the growth generating an orderly difference depending on the curvature. Nanoscale cuboids or nanorods were studied to find an aspect ratio effect when condensation occurs on the surface. Various aspect ratios were examined for different nanorod sizes over a wide range of supersaturation ratios. The results show that the growth rate of the nanorod is independent of the supersaturation ratio, which was also observed for the sphere and cube. The growth rate for the rod fell between those of the cube and the sphere, and this is due to an increase in the surface area of the nanorod compared to the cube and curvature effect in comparison with the sphere. A clear size dependence of the seed was observed, which is also similar to the cube and sphere. Furthermore, no aspect ratio influence was seen for the growth rate. This does not mean that the actual amount of condensation is the same for longer seeds, but rather from the definition of the growth rate, the amount of accumulation per unit area is the same for all seed lengths.
NASA Astrophysics Data System (ADS)
Masunov, Artëm E.; Gangopadhyay, Shruba
2015-12-01
New method to eliminate the spin-contamination in broken symmetry density functional theory (BS DFT) calculations is introduced. Unlike conventional spin-purification correction, this method is based on canonical Natural Orbitals (NO) for each high/low spin coupled electron pair. We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher spin state built on these bonding and antibonding NOs (not self-consistent Kohn-Sham orbitals of the high spin state). Compared to the other spin-contamination correction schemes, spin-correction is applied to each correlated electron pair individually. We investigate two binuclear Mn(IV) molecular magnets using this pairwise correction. While one of the molecules is described by magnetic orbitals strongly localized on the metal centers, and spin gap is accurately predicted by Noodleman and Yamaguchi schemes, for the other one the gap is predicted poorly by these schemes due to strong delocalization of the magnetic orbitals onto the ligands. We show our new correction to yield more accurate results in both cases.
Accelerating MP2C dispersion corrections for dimers and molecular crystals
NASA Astrophysics Data System (ADS)
Huang, Yuanhang; Shao, Yihan; Beran, Gregory J. O.
2013-06-01
The MP2C dispersion correction of Pitonak and Hesselmann [J. Chem. Theory Comput. 6, 168 (2010)], 10.1021/ct9005882 substantially improves the performance of second-order Møller-Plesset perturbation theory for non-covalent interactions, albeit with non-trivial computational cost. Here, the MP2C correction is computed in a monomer-centered basis instead of a dimer-centered one. When applied to a single dimer MP2 calculation, this change accelerates the MP2C dispersion correction several-fold while introducing only trivial new errors. More significantly, in the context of fragment-based molecular crystal studies, combination of the new monomer basis algorithm and the periodic symmetry of the crystal reduces the cost of computing the dispersion correction by two orders of magnitude. This speed-up reduces the MP2C dispersion correction calculation from a significant computational expense to a negligible one in crystals like aspirin or oxalyl dihydrazide, without compromising accuracy.
Beam spot shift in a dynamic astigmatism correction type (DQ-DAF) electron gun
NASA Astrophysics Data System (ADS)
Ueda, Y.; Sukeno, M.; Suzuki, H.
This paper presents the results of an investigation to avoid the convergence error in color CRT guns operating with a dynamic focus correction. The dynamic spot shift as well as the spot coma can be avoided at the same time with a proper arrangement of the quadrupole and main lenses with an oblique incidence of the side beam. The design confirmation is also presented.
NASA Astrophysics Data System (ADS)
Grest, Gary S.
2008-03-01
Twenty years ago at the APS March Meeting, Kurt Kremer and I presented the first numerical evidence from computer simulations that the reptation model of Edwards and de Gennes correctly describes the dynamics of entangled linear polymer melts. For chains longer than the entanglement length Ne, the monomers of a chain move predominantly along their own contour. The distinctive signature of reptation dynamics, which we observed, was that on intermediate time scales, the mean squared displacement of a monomer increases with time as t^ 1/4. Though these early simulations were limited to chains of a few Ne, they demonstrated the potential of computer simulations to contribute to our understanding of polymer dynamics. Here I will review the progress over the past twenty years and present an outlook for the future in modeling entangled polymer melts and networks. With present day computers coupled with efficient parallel molecular dynamics codes, it is now possible to follow the equilibrium dynamics of chains of length 10-20Ne from the early Rouse regime to the long time diffusive regime. Result of these simulations support the earlier results obtained on chains of only a few Ne. Further evidence for the tube models of polymer dynamics has been obtained by identifying the primitive path mesh that characterizes the microscopic topological state of the computer- generated conformations of the chains. In particular, the plateau moduli derived on the basis of this analysis quantitatively reproduce experimental data for a wide spectrum of entangled polymer liquids including semi-dilute theta solutions of synthetic polymers, the corresponding dense melts, and solutions of semi-flexible (bio)polymers such as f-actin or suspensions of rodlike viruses. We also find that in agreement with the reptation model, the stress, end-to-end distance and entanglement length of an entangled melt subjected to uniaxial elongation, all relax on the same time scale.
Diamond, Jonathan S; Nashed, Joseph Y; Johansson, Roland S; Wolpert, Daniel M; Flanagan, J Randall
2015-07-22
Numerous studies have shown that people are adept at learning novel object dynamics, linking applied force and motion, when performing reaching movements with hand-held objects. Here we investigated whether the control of rapid corrective arm responses, elicited in response to visual perturbations, has access to such newly acquired knowledge of object dynamics. Participants first learned to make reaching movements while grasping an object subjected to complex load forces that depended on the distance and angle of the hand from the start position. During a subsequent test phase, we examined grip and load force coordination during corrective arm movements elicited (within ∼150 ms) in response to viewed sudden lateral shifts (1.5 cm) in target or object position. We hypothesized that, if knowledge of object dynamics is incorporated in the control of the corrective responses, grip force changes would anticipate the unusual load force changes associated with the corrective arm movements so as to support grasp stability. Indeed, we found that the participants generated grip force adjustments tightly coupled, both spatially and temporally, to the load force changes associated with the arm movement corrections. We submit that recently learned novel object dynamics are effectively integrated into sensorimotor control policies that support rapid visually driven arm corrective actions during transport of hand held objects. Significance statement: Previous studies have demonstrated that the motor system can learn, and make use of, internal models of object dynamics to generate feedforward motor commands. However, it is not known whether such internal models are incorporated into rapid, automatic arm movement corrections that compensate for errors that arise during movement. Here we demonstrate, for the first time, that internal models of novel object dynamics are integrated into rapid corrective arm movements made in response to visuomotor perturbations that, importantly, do
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
NASA Astrophysics Data System (ADS)
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to
Molecular density functional theory for water with liquid-gas coexistence and correct pressure
Jeanmairet, Guillaume Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel
2015-04-21
The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.
MOLECULAR DYNAMICS STUDIES OF MODULAR POLYKETIDE SYNTHASE KETOREDUCTASE STEREOSPECIFICITY
Mugnai, Mauro L.; Shi, Yue; Keatinge-Clay, Adrian T.; Elber, Ron
2015-01-01
Ketoreductases (KRs) from modular polyketide synthases (PKSs) can perform stereospecific catalysis, selecting a polyketide with a D-α or an L-α-methyl substituent for NADPH-mediated reduction. In this report Molecular Dynamics (MD) simulations were performed to investigate the interactions that control stereospecificity. We studied the A1-type KR from the second module of the amphotericin PKS (A1), which is known to be stereospecific for a D-α-methyl-substituted diketide substrate (dkD). MD simulations of two ternary complexes comprised of the enzyme, NADPH, and either the correct substrate, dkD, or its enantiomer (dkL) were performed. The coordinates for the A1/NADPH binary complex were obtained from a crystal structure [Zheng, J. T. et al. (2010) Structure 18, 913–922], and substrates were modeled in the binding pocket in conformations appropriate for reduction. Simulations were intended to reproduce the initial weak binding of the polyketide substrate to the enzyme. Long (tens of nanoseconds) MD simulations show that the correct substrate is retained in a conformation closer to the reactive configuration. Many short (up to a nanosecond) MD runs starting from the initial structures display evidence that Q364, three residues N-terminal to the catalytic tyrosine, forms a hydrogen bond to the incorrect dkL substrate to yield an unreactive conformation that is more favorable than the reactive configuration. This interaction is not as strong for dkD, as the D-α-methyl substituent is positioned between the glutamine and the reactive site. This result correlates with experimental findings [Zheng, J. T. et al. (2010) Structure 18, 913–922] in which a Q364H mutant was observed to lose stereospecificity. PMID:25835227
NASA Astrophysics Data System (ADS)
Kritayakornupong, Chinapong; Hannongbua, Supot
2007-01-01
The structural and dynamical properties of high-spin Ru 2+ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru 2+. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru 2+ and the 6-31G ∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru 2+-O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru 2+ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.
Kronik, Leeor; Tkatchenko, Alexandre
2014-11-18
CONSPECTUS: Molecular crystals are ubiquitous in many areas of science and engineering, including biology and medicine. Until recently, our ability to understand and predict their structure and properties using density functional theory was severely limited by the lack of approximate exchange-correlation functionals able to achieve sufficient accuracy. Here we show that there are many cases where the simple, minimally empirical pairwise correction scheme of Tkatchenko and Scheffler provides a useful prediction of the structure and properties of molecular crystals. After a brief introduction of the approach, we demonstrate its strength through some examples taken from our recent work. First, we show the accuracy of the approach using benchmark data sets of molecular complexes. Then we show its efficacy for structural determination using the hemozoin crystal, a challenging system possessing a wide range of strong and weak binding scenarios. Next, we show that it is equally useful for response properties by considering the elastic constants exhibited by the supramolecular diphenylalanine peptide solid and the infrared signature of water libration movements in brushite. Throughout, we emphasize lessons learned not only for the methodology but also for the chemistry and physics of the crystals in question. We further show that in many other scenarios where the simple pairwise correction scheme is not sufficiently accurate, one can go beyond it by employing a computationally inexpensive many-body dispersive approach that results in useful, quantitative accuracy, even in the presence of significant screening and/or multibody contributions to the dispersive energy. We explain the principles of the many-body approach and demonstrate its accuracy for benchmark data sets of small and large molecular complexes and molecular solids. PMID:24901508
CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS
Swanson, Jessica
2011-08-31
This is the final progress report for Award DE-SC0004920, entitled 'Characterizing coupled charge transport with multi scale molecular dynamics'. The technical abstract will be provided in the uploaded report.
Masses, luminosities and dynamics of galactic molecular clouds
NASA Technical Reports Server (NTRS)
Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.
1987-01-01
Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.
Thermostat artifacts in replica exchange molecular dynamics simulations.
Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard
2009-01-01
We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980
Thermostat artifacts in replica exchange molecular dynamics simulations
Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard
2009-01-01
We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980
Hydration structure of salt solutions from ab initio molecular dynamics.
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L
2013-01-01
The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed. PMID:23298049
Nuclear structure and reactions in the fermionic molecular dynamics approach
NASA Astrophysics Data System (ADS)
Neff, T.; Feldmeier, H.
2008-05-01
The Fermionic Molecular Dynamics (FMD) model uses Gaussian wave packets as single-particle states. Intrinsic many-body basis states are constructed as Slater determinants which have to be projected on parity, angular momentum and total linear momentum to restore the symmetries of the Hamiltonian. The flexibility of the Gaussian basis allows to economically describe states with shell structures as well as states featuring clustering or halos. We use an effective interaction that is derived from the realistic Argonne V18 interaction by means of the Unitary Correlation Operator Method (UCOM). A phenomenological momentum-dependent two-body correction simulates contributions from missing three-body forces and three-body correlations. We discuss 12C with a special emphasis on the structure of the excited 0+ and 2+ states. We analyze the degree of α-clustering and confirm, taking inelastic electron scattering data into account, the conjecture that the Hoyle state has to be understood as a loosely bound system of alpha particles. We will also present first results on the application of FMD for the calculation of scattering phase shifts in 3He — 4He.
Stresses and elastic constants of crystalline sodium, from molecular dynamics
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.
Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Tao, Peng; Wu, Xiongwu; Brooks, Bernard R.
2012-10-01
An algorithm is presented to maintain rigid structures in Verlet based Cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any Cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency.
Hydration structure of salt solutions from ab initio molecular dynamics
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.
2013-01-07
The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
Hydration structure of salt solutions from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.
2013-01-01
The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
Johnston, Jennifer M.
2014-01-01
The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field. PMID:24158803
Molecular Dynamics Study of Potassium Azide (KN_3)
NASA Astrophysics Data System (ADS)
Ossowski, M.; Hardy, J. R.
1998-03-01
An ab initio model developed for intermolecular and intramolecular potentials in ionic molecular solids(H. M. Lu and J. R. Hardy, Phys. Rev. B, 42, 8339 (1990)) is employed to study the phase diagram of potassium azide (KN_3). We performed first-principles static structural relaxation, supercell molecular dynamics, lattice- dynamical studies and predict the existence of a high temperature rotationally disordered phase in KN_3. A selected work on other members of the alkali azide family will also be discussed.
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. PMID:26949976
Dynamical analysis of highly excited molecular spectra
Kellman, M.E.
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.
Development of the four-body corrected fragment molecular orbital (FMO4) method
NASA Astrophysics Data System (ADS)
Nakano, Tatsuya; Mochizuki, Yuji; Yamashita, Katsumi; Watanabe, Chiduru; Fukuzawa, Kaori; Segawa, Katsunori; Okiyama, Yoshio; Tsukamoto, Takayuki; Tanaka, Shigenori
2012-01-01
The four-body corrected fragment molecular orbital (FMO4) method was implemented at the second-order Møller-Plesset perturbation (MP2) level. A series of accuracy tests relative to the previous two-body and three-body treatments were performed. As expected, FMO4 provided better accuracy in total energies in comparison with the reference values by regular MO calculations. A nonconventional fragmentation by separating main and side chains in amino acid residues was examined for Ala-pentamer and Chignolin, where the four-body corrections were shown to be substantial. A large complex of HIV-1 protease (total 198 residues) with lopinavir was calculated as well. Furthermore, this new FMO scheme was successfully applied to adamantane-shaped clusters with three-dimensional bonding framework.
An Analog Gamma Correction Scheme for High Dynamic Range CMOS Logarithmic Image Sensors
Cao, Yuan; Pan, Xiaofang; Zhao, Xiaojin; Wu, Huisi
2014-01-01
In this paper, a novel analog gamma correction scheme with a logarithmic image sensor dedicated to minimize the quantization noise of the high dynamic applications is presented. The proposed implementation exploits a non-linear voltage-controlled-oscillator (VCO) based analog-to-digital converter (ADC) to perform the gamma correction during the analog-to-digital conversion. As a result, the quantization noise does not increase while the same high dynamic range of logarithmic image sensor is preserved. Moreover, by combining the gamma correction with the analog-to-digital conversion, the silicon area and overall power consumption can be greatly reduced. The proposed gamma correction scheme is validated by the reported simulation results and the experimental results measured for our designed test structure, which is fabricated with 0.35 μm standard complementary-metal-oxide-semiconductor (CMOS) process. PMID:25517692
An analog gamma correction scheme for high dynamic range CMOS logarithmic image sensors.
Cao, Yuan; Pan, Xiaofang; Zhao, Xiaojin; Wu, Huisi
2014-01-01
In this paper, a novel analog gamma correction scheme with a logarithmic image sensor dedicated to minimize the quantization noise of the high dynamic applications is presented. The proposed implementation exploits a non-linear voltage-controlled-oscillator (VCO) based analog-to-digital converter (ADC) to perform the gamma correction during the analog-to-digital conversion. As a result, the quantization noise does not increase while the same high dynamic range of logarithmic image sensor is preserved. Moreover, by combining the gamma correction with the analog-to-digital conversion, the silicon area and overall power consumption can be greatly reduced. The proposed gamma correction scheme is validated by the reported simulation results and the experimental results measured for our designed test structure, which is fabricated with 0.35 μm standard complementary-metal-oxide-semiconductor (CMOS) process. PMID:25517692
Elucidation of molecular dynamics of invasive species of rice
Technology Transfer Automated Retrieval System (TEKTRAN)
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...
Molecular dynamics simulation of interfacial adhesion
Yarovsky, I.; Chaffee, A.L.
1996-12-31
Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.
Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations
2013-01-01
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176
Tunable Interfacial Thermal Conductance by Molecular Dynamics
NASA Astrophysics Data System (ADS)
Shen, Meng
We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1
Tunable Interfacial Thermal Conductance by Molecular Dynamics
NASA Astrophysics Data System (ADS)
Shen, Meng
We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1
The Computer Simulation of Liquids by Molecular Dynamics.
ERIC Educational Resources Information Center
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)
Identifying the mechanisms of polymer friction through molecular dynamics simulation.
Dai, Ling; Minn, M; Satyanarayana, N; Sinha, Sujeet K; Tan, V B C
2011-12-20
Mechanisms governing the tribological behavior of polymer-on-polymer sliding were investigated by molecular dynamics simulations. Three main mechanisms governing frictional behavior were identified. Interfacial "brushing" of molecular chain ends over one another was observed as the key contribution to frictional forces. With an increase of the sliding speed, fluctuations in frictional forces reduced in both magnitude and periodicity, leading to dynamic frictional behavior. While "brushing" remained prevalent, two additional irreversible mechanisms, "combing" and "chain scission", of molecular chains were observed when the interfaces were significantly diffused. PMID:22044344
New correction method for dynamic error in on-line gamma ray thickness detection.
Liang, Manchun; Yi, Hongchang; Lin, Qian
2009-11-01
In this paper, we present a new method to correct dynamic error (DE) in on-line gamma ray thickness measurement, which significantly improves measurement precision over traditional method, in most cases, by one order of magnitude. Theoretical analysis of DE is presented and the correction method is proposed. In order to further prove our theory, Monte Carlo simulation is taken and the performance improvement is given. The method has been successfully applied to our thickness measurement system and brought dramatic improvement to its dynamic precision. PMID:19682915
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
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.
Reactive Molecular Dynamics Simulations at the Petascale (Invited)
NASA Astrophysics Data System (ADS)
Nakano, A.
2013-12-01
We are developing a divide-conquer-recombine algorithmic framework into a metascalable (or 'design once, scale on new architectures') parallelization scheme to perform large spatiotemporal-scale reactive molecular dynamics simulations. The scheme has achieved parallel efficiency well over 0.9 on 786,432 IBM BlueGene/Q processors for 8.5 trillion-atom molecular dynamics and 1.9 trillion electronic degrees-of-freedom quantum molecular dynamics in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic alloy nanoparticles; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; and (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets.
Interfacial Molecular Searching Using Forager Dynamics
NASA Astrophysics Data System (ADS)
Monserud, Jon H.; Schwartz, Daniel K.
2016-03-01
Many biological and technological systems employ efficient non-Brownian intermittent search strategies where localized searches alternate with long flights. Coincidentally, molecular species exhibit intermittent behavior at the solid-liquid interface, where periods of slow motion are punctuated by fast flights through the liquid phase. Single-molecule tracking was used here to observe the interfacial search process of DNA for complementary DNA. Measured search times were qualitatively consistent with an intermittent-flight model, and ˜10 times faster than equivalent Brownian searches, suggesting that molecular searches for reactive sites benefit from similar efficiencies as biological organisms.
Dynamics of molecular superrotors in an external magnetic field
NASA Astrophysics Data System (ADS)
Korobenko, Aleksey; Milner, Valery
2015-08-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.
Self-Interaction Corrected Functional Calculations of a Dipole-Bound Molecular Anion.
Zhang, Yao; Weber, Peter M; Jónsson, Hannes
2016-06-01
A self-interaction corrected density functional is used to describe the ground state of the CH3CN(-) ion that includes a dipole bound electron with large spatial extent and low binding energy. Without the correction, some commonly used density functionals based on the generalized gradient approximation as well as hybrid functionals fail to give a bound ground state of the anion. A negative HOMO orbital energy of magnitude 0.013 eV is obtained using the self-interaction corrected PBE functional in good correspondence with the experimentally estimated binding energy of 0.019 eV. The dipole bound electron polarizes the CH3CN molecule and increases its dipole moment by 7% to 4.2 D. Because the computational effort increases slowly with system size, as the number of electrons cubed, the results presented here point to a viable approach to theoretical studies of dipole bound electrons in large and complex systems such as molecular clusters, biological systems, and solvated electrons. PMID:27166989
Stanke, Monika; Adamowicz, Ludwik
2013-10-01
In this work, we describe how the energies obtained in molecular calculations performed without assuming the Born-Oppenheimer (BO) approximation can be augmented with corrections accounting for the leading relativistic effects. Unlike the conventional BO approach, where these effects only concern the relativistic interactions between the electrons, the non-BO approach also accounts for the relativistic effects due to the nuclei and due to the coupling of the coupled electron-nucleus motion. In the numerical sections, the results obtained with the two approaches are compared. The first comparison concerns the dissociation energies of the two-electron isotopologues of the H2 molecule, H2, HD, D2, T2, and the HeH(+) ion. The comparison shows that, as expected, the differences in the relativistic contributions obtained with the two approaches increase as the nuclei become lighter. The second comparison concerns the relativistic corrections to all 23 pure vibrational states of the HD(+) ion. An interesting charge asymmetry caused by the nonadiabatic electron-nucleus interaction appears in this system, and this effect significantly increases with the vibration excitation. The comparison of the non-BO results with the results obtained with the conventional BO approach, which in the lowest order does not describe the charge-asymmetry effect, reveals how this effect affects the values of the relativistic corrections. PMID:23679131
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.
Valentini, Paolo Schwartzentruber, Thomas E.
2009-12-10
A novel combined Event-Driven/Time-Driven (ED/TD) algorithm to speed-up the Molecular Dynamics simulation of rarefied gases using realistic spherically symmetric soft potentials is presented. Due to the low density regime, the proposed method correctly identifies the time that must elapse before the next interaction occurs, similarly to Event-Driven Molecular Dynamics. However, each interaction is treated using Time-Driven Molecular Dynamics, thereby integrating Newton's Second Law using the sufficiently small time step needed to correctly resolve the atomic motion. Although infrequent, many-body interactions are also accounted for with a small approximation. The combined ED/TD method is shown to correctly reproduce translational relaxation in argon, described using the Lennard-Jones potential. For densities between {rho}=10{sup -4}kg/m{sup 3} and {rho}=10{sup -1}kg/m{sup 3}, comparisons with kinetic theory, Direct Simulation Monte Carlo, and pure Time-Driven Molecular Dynamics demonstrate that the ED/TD algorithm correctly reproduces the proper collision rates and the evolution toward thermal equilibrium. Finally, the combined ED/TD algorithm is applied to the simulation of a Mach 9 shock wave in rarefied argon. Density and temperature profiles as well as molecular velocity distributions accurately match DSMC results, and the shock thickness is within the experimental uncertainty. For the problems considered, the ED/TD algorithm ranged from several hundred to several thousand times faster than conventional Time-Driven MD. Moreover, the force calculation to integrate the molecular trajectories is found to contribute a negligible amount to the overall ED/TD simulation time. Therefore, this method could pave the way for the application of much more refined and expensive interatomic potentials, either classical or first-principles, to Molecular Dynamics simulations of shock waves in rarefied gases, involving vibrational nonequilibrium and chemical reactivity.
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber
Luchko, Tyler; Gusarov, Sergey; Roe, Daniel R.; Simmerling, Carlos; Case, David A.; Tuszynski, Jack; Kovalenko, Andriy
2010-01-01
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G. PMID:20440377
VUV studies of molecular photofragmentation dynamics
White, M.G.
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.
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. PMID:26522428
2016-01-01
Objective To evaluate characteristics of static and dynamic parameters in patients with degenerative flat back (DFB) and to compare degree of their improvement between successful and unsuccessful surgical outcome groups Methods Forty-seven patients with DFB were included who took whole spine X-ray and three-dimensional motion analysis before and 6 months after corrective surgery. Forty-four subjects were selected as a control group. As static parameters, thoracic kyphosis (TK), thoracolumbar junction (TLJ), lumbar lordosis (LL), pelvic incidence (PI), sacral slope (SS), and pelvic tilt (PT) were measured. As dynamic parameters, maximal and minimal angle of pelvic tilt, lower limb joints, and thoracic and lumbar vertebrae column (dynamic TK and LL) in sagittal plane were obtained. Results The DFB group showed smaller TK and larger LL, pelvic posterior tilt, hip flexion, knee flexion, and ankle dorsiflexion than the control group. Most of these parameters were significantly corrected by fusion surgery. Dynamic spinal parameters correlated with static spinal parameters. The successful group obtained significant improvement in maximal and minimal dynamic LL than the unsuccessful group. Conclusion The DFB group showed characteristic lower limb and spinal angles in dynamic and static parameters. Correlation between static and dynamic parameters was found in spinal segment. Dynamic LL was good predictor of successful surgical outcomes. PMID:27606275
Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics
NASA Astrophysics Data System (ADS)
Ehrlicher, Allen
2012-02-01
Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.
Theoretical analysis of dynamic processes for interacting molecular motors
NASA Astrophysics Data System (ADS)
Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem
2015-02-01
Biological transport is supported by the 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 carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the 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 motor 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. PMID:26489820
Hydrolysis of Al3+ from constrained molecular dynamics.
Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi
2006-02-21
We investigated the hydrolysis reactions of Al(3+) in AlCl(3) aqueous solution using the constrained molecular dynamics based on the Car-Parrinello molecular-dynamics method. By employing the proton-aluminum coordination number as a reaction coordinate in the constrained molecular dynamics the deprotonation as well as dehydration processes are successfully realized. From our free-energy difference of DeltaG(0) approximately 8.0 kcal mol(-1) the hydrolysis constant pK(a1) is roughly estimated as 5.8, comparable to the literature value of 5.07. We show that the free-energy difference for the hydrolysis of Al(3+) in acidic conditions is at least 4 kcal mol(-1) higher than that in neutral condition, indicating that the hydrolysis reaction is inhibited by the presence of excess protons located around the hydrated ion, in agreement with the change of the predominant species by pH. PMID:16497053
NASA Astrophysics Data System (ADS)
Ahn, J.; Lee, J.; Shim, K.; Kim, Y.
2013-12-01
In spite of dense meteorological observation conducting over South Korea (The average distance between stations: ~ 12.7km), the detailed topographical effect is not reflected properly due to its mountainous terrains and observation sites mostly situated on low altitudes. A model represents such a topographical effect well, but due to systematic biases in the model, the general temperature distribution is sometimes far different from actual observation. This study attempts to produce a detailed mean temperature distribution for South Korea through a method combining dynamical downscaling and statistical correction. For the dynamical downscaling, a multi-nesting technique is applied to obtain 3-km resolution data with a focus on the domain for the period of 10 years (1999-2008). For the correction of systematic biases, a perturbation method divided into the mean and the perturbation part was used with a different correction method being applied to each part. The mean was corrected by a weighting function while the perturbation was corrected by the self-organizing maps method. The results with correction agree well with the observed pattern compared to those without correction, improving the spatial and temporal correlations as well as the RMSE. In addition, they represented detailed spatial features of temperature including topographic signals, which cannot be expressed properly by gridded observation. Through comparison with in-situ observation with gridded values after objective analysis, it was found that the detailed structure correctly reflected topographically diverse signals that could not be derived from limited observation data. We expect that the correction method developed in this study can be effectively used for the analyses and projections of climate downscaled by using region climate models. Acknowledgements This work was carried out with the support of Korea Meteorological Administration Research and Development Program under Grant CATER 2012-3083 and
Automated Movement Correction for Dynamic PET/CT Images: Evaluation with Phantom and Patient Data
Ye, Hu; Wong, Koon-Pong; Wardak, Mirwais; Dahlbom, Magnus; Kepe, Vladimir; Barrio, Jorge R.; Nelson, Linda D.; Small, Gary W.; Huang, Sung-Cheng
2014-01-01
Head movement during a dynamic brain PET/CT imaging results in mismatch between CT and dynamic PET images. It can cause artifacts in CT-based attenuation corrected PET images, thus affecting both the qualitative and quantitative aspects of the dynamic PET images and the derived parametric images. In this study, we developed an automated retrospective image-based movement correction (MC) procedure. The MC method first registered the CT image to each dynamic PET frames, then re-reconstructed the PET frames with CT-based attenuation correction, and finally re-aligned all the PET frames to the same position. We evaluated the MC method's performance on the Hoffman phantom and dynamic FDDNP and FDG PET/CT images of patients with neurodegenerative disease or with poor compliance. Dynamic FDDNP PET/CT images (65 min) were obtained from 12 patients and dynamic FDG PET/CT images (60 min) were obtained from 6 patients. Logan analysis with cerebellum as the reference region was used to generate regional distribution volume ratio (DVR) for FDDNP scan before and after MC. For FDG studies, the image derived input function was used to generate parametric image of FDG uptake constant (Ki) before and after MC. Phantom study showed high accuracy of registration between PET and CT and improved PET images after MC. In patient study, head movement was observed in all subjects, especially in late PET frames with an average displacement of 6.92 mm. The z-direction translation (average maximum = 5.32 mm) and x-axis rotation (average maximum = 5.19 degrees) occurred most frequently. Image artifacts were significantly diminished after MC. There were significant differences (P<0.05) in the FDDNP DVR and FDG Ki values in the parietal and temporal regions after MC. In conclusion, MC applied to dynamic brain FDDNP and FDG PET/CT scans could improve the qualitative and quantitative aspects of images of both tracers. PMID:25111700
Studying Interactions by Molecular Dynamics Simulations at High Concentration
Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro
2012-01-01
Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085
Effect of correction of aberration dynamics on chaos in human ocular accommodation.
Hampson, Karen M; Cufflin, Matthew P; Mallen, Edward A H
2013-11-15
We used adaptive optics to determine the effect of monochromatic aberration dynamics on the level of chaos in the accommodation control system. Four participants viewed a stationary target while the dynamics of their aberrations were either left uncorrected, defocus was corrected, or all aberrations except defocus were corrected. Chaos theory analysis was used to discern changes in the accommodative microfluctuations. We found a statistically significant reduction in the chaotic nature of the accommodation microfluctuations during correction of defocus, but not when all aberrations except defocus were corrected. The Lyapunov exponent decreased from 0.71 ± 0.07 D/s (baseline) to 0.55 ± 0.03 D/s (correction of defocus fluctuations). As the reduction of chaos in physiological signals is indicative of stress to the system, the results indicate that for the participants included in this study, fluctuations in defocus have a more profound effect than those of the other aberrations. There were no changes in the power spectrum between experimental conditions. Hence chaos theory analysis is a more subtle marker of changes in the accommodation control system and will be of value in the study of myopia onset and progression. PMID:24322122
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.
Cawkwell, M J; Niklasson, Anders M N
2012-10-01
Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces. PMID:23039583
Mitochondrial dynamics: molecular mechanisms and the role in the heart.
Jazbutyte, V
2010-04-01
Mitochondria are dynamic organelles which actively move along the cytoskeleton within the cell, change their shape and undergo fusion and fission. The heart is a metabolically active organ with high energy demands and rich in mitochondria. Mitochondria not only supply the heart with the high energy compound, adenosine triphosphate (ATP), but also actively participate in cell signaling and apoptotic events and communicate with the cytosol. Recent advantages in molecular biology and imaging techniques helped to study mitochondrial dynamics directly in the cell and under real time conditions. In this review, I will briefly summarize current knowledge about molecular machinery mediating mitochondrial fusion/ fission, its link to apoptosis and cardiovascular disease. PMID:20440252
Replica exchange molecular dynamics simulations of amyloid peptide aggregation
NASA Astrophysics Data System (ADS)
Cecchini, M.; Rao, F.; Seeber, M.; Caflisch, A.
2004-12-01
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the β-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides.
Trillion-atom molecular dynamics becomes a reality
Kadau, Kai; Germann, Timothy C
2008-01-01
By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD{_}render.
State-to-state dynamics of molecular energy transfer
Gentry, W.R.; Giese, C.F.
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.
How Dynamic Visualization Technology can Support Molecular Reasoning
NASA Astrophysics Data System (ADS)
Levy, Dalit
2012-11-01
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 gas. They interact with the visualizations and carry out inquiry activities to make and refine connections between observable phenomena and atomic level processes related to phase change. The explanations proposed by 300 pairs of students in response to pre/post-assessment items have been analyzed using a scale for measuring the level of molecular reasoning. Results indicate that from pretest to posttest, students make progress in their level of molecular reasoning and are better able to connect intermolecular forces and phase change in their explanations. The paper presents the results through the lens of improvement patterns and the metaphor of the "ladder of molecular reasoning," and discusses how this adds to our understanding of the benefits of interacting with dynamic molecular visualizations.
Cheng, Wayne K.; Palmer, Daniel Kyle; Jadhav, Vikram
2011-01-01
Background The increase in total disc replacement procedures performed over the last 5 years has increased the occurrence of patients presenting with postoperative iatrogenic deformity requiring revision surgery. Proposed salvage treatments include device retrieval followed by anterior lumbar interbody fusion or posterior fusion. We propose a novel approach for the correction of disc tilt after total disc replacement using a posterior dynamic stabilization system. Methods Pedicle screws can be inserted either in an open manner or percutaneously by standard techniques under fluoroscopy. The collapsed side is expanded, and the convex side is compressed. Universal spacers are placed bilaterally, with the spacer on the collapsed side being taller by 6 mm. Cords are threaded through the spacers and pulled into place with the tensioning instrument. Extra tension is applied to the convex side, and the wound is closed by standard techniques. Results Three patients presenting with tilted total disc replacement devices underwent corrective surgery with posterior dynamic stabilization. Radiographs confirmed correction of deformity in all cases. Conclusions/Level of Evidence This technical note presents a novel indication for posterior dynamic stabilization and describes its surgical application to the correction of disc tilt after total disc replacement. This is level V evidence. PMID:25802667
Levy, Ronald M.; Perahia, David; Karplus, Martin
1982-01-01
The mean square amplitudes of atomic fluctuations for a polypeptide (decaglycine) α-helix evaluated from molecular dynamics simulations at seven temperatures between 5 and 300 K are compared with analytic harmonic results and with experimental values. Above 100 K the harmonic approximation significantly underestimates the amplitudes of the displacements. Analysis of the time dependence of the fluctuations shows that low-frequency modes (<75 cm-1) dominate the atomic fluctuations and that there is a contribution with a very long relaxation time (>10 ps). Quantum corrections to the amplitude of the fluctuations are found to be small above 50 K. The mean square amplitudes obtained from the molecular dynamics simulations are compared with the values derived from x-ray temperature (Debye-Waller) factors for metmyoglobin (80, 250, and 300 K) and ferrocytochrome c (300 K). PMID:16593164
NASA Astrophysics Data System (ADS)
Levy, Ronald M.; Perahia, David; Karplus, Martin
1982-02-01
The mean square amplitudes of atomic fluctuations for a polypeptide (decaglycine) α -helix evaluated from molecular dynamics simulations at seven temperatures between 5 and 300 K are compared with analytic harmonic results and with experimental values. Above 100 K the harmonic approximation significantly underestimates the amplitudes of the displacements. Analysis of the time dependence of the fluctuations shows that low-frequency modes (<75 cm-1) dominate the atomic fluctuations and that there is a contribution with a very long relaxation time (>10ps). Quantum corrections to the amplitude of the fluctuations are found to be small above 50 K. The mean square amplitudes obtained from the molecular dynamics simulations are compared with the values derived from x-ray temperature (Debye-Waller) factors for metmyoglobin (80, 250, and 300 K) and ferrocytochrome c (300 K).
Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems
Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus
2014-01-01
Background 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. Scope of review 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. Major Conclusions 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. General Significance 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. PMID:25450171
Multiple time step integrators in ab initio molecular dynamics
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-02-28
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.
Chain networking revealed by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing
Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)
Electron-phonon interaction within classical molecular dynamics
NASA Astrophysics Data System (ADS)
Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.
2016-07-01
We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e -ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.
Electron-phonon interaction within classical molecular dynamics
Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.
2016-07-14
Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less
Numerical methods for molecular dynamics. Progress report
Skeel, R.D.
1991-12-31
This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.
Shapiro like steps reveals molecular nanomagnets' spin dynamics
NASA Astrophysics Data System (ADS)
Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid
2015-09-01
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet's spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.
Social Relationships and Group Dynamics Inside a Community Correction Facility for Women.
Cantora, Andrea; Mellow, Jeff; Schlager, Melinda D
2016-07-01
This article presents research on women's perceptions and experiences residing in a female community correction facility. Qualitative interview data and field observations are used to examine resident relationships, perceptions of on-site group treatment, and benefits of receiving off-site treatment. Findings from this study indicate an overwhelming feeling of tension and lack of trust among residents, resulting in most women withdrawing from social interactions. Relationship dynamics also played a role in women's participation during on-site group treatment and desiring off-site treatment. This study supports the need to create, and sustain, therapeutic environments within community correction settings for women. PMID:26138351
Plastic dislocation motion via nonequilibrium molecular and continuum dynamics
Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.
1980-09-29
The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition.
Imaging the molecular dynamics of dissociative electron attachment to water
Adaniya, Hidihito; Rudek, B.; Osipov, Timur; Haxton, Dan; Weber, Thorsten; Rescigno, Thomas N.; McCurdy, C.W.; Belkacem, Ali
2009-10-19
Momentum imaging experiments on dissociative electron attachment to the water molecule are combined with ab initio theoretical calculations of the angular dependence of the quantum mechanical amplitude for electron attachment to provide a detailed picture of the molecular dynamics of dissociation attachment via the two lowest energy Feshbach resonances. The combination of momentum imaging experiments and theory can reveal dissociation dynamics for which the axial recoil approximation breaks down and thus provides a powerful reaction microscope for DEA to polyatomics.
Coarse-Grained Molecular Dynamics: Dissipation Due to Internal Modes
Rudd, R E
2001-12-21
We describe progress on the issue of pathological elastic wave reflection in atomistic and multiscale simulation. First we briefly review Coarse-Grained Molecular Dynamics (CGMD). Originally CGMD was formulated as a Hamiltonian system in which energy is conserved. This formulation is useful for many applications, but recently CGMD has been extended to include generalized Langevin forces. Here we describe how Langevin dynamics arise naturally in CGMD, and we examine the implication for elastic wave scattering.
Input File Creation for the Molecular Dynamics Program LAMMPS.
Energy Science and Technology Software Center (ESTSC)
2001-05-30
The program creates an input data file for the molecular dynamics program LAMMPS. The input file created is a liquid mixture between two walls explicitly composed of particles. The liquid molecules are modeled as a bead-spring molecule. The input data file specifies the position and topology of the starting state. The data structure of input allows for dynamic bond creation (cross-linking) within the LAMMPS code.
Electron trapping in amorphous silicon: A quantum molecular dynamics study
Yang, Lin H.; Kalia, R.K.; Vashishta, P.
1990-12-01
Quantum molecular dynamics (QMD) simulations provide the real-time dynamics of electrons and ions through numerical solutions of the time-dependent Schrodinger and Newton equations, respectively. Using the QMD approach we have investigated the localization behavior of an excess electron in amorphous silicon at finite temperatures. For time scales on the order of a few picoseconds, we find the excess electron is localized inside a void of radius {approximately}3 {Angstrom} at finite temperatures. 12 refs.
A fast recursive algorithm for molecular dynamics simulation
NASA Technical Reports Server (NTRS)
Jain, A.; Vaidehi, N.; Rodriguez, G.
1993-01-01
The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.
NASA Astrophysics Data System (ADS)
Shimizu, Futoshi; Kimizuka, Hajime; Kaburaki, Hideo
2002-08-01
A new parallel computing environment, called as ``Parallel Molecular Dynamics Stencil'', has been developed to carry out a large-scale short-range molecular dynamics simulation of solids. The stencil is written in C language using MPI for parallelization and designed successfully to separate and conceal parts of the programs describing cutoff schemes and parallel algorithms for data communication. This has been made possible by introducing the concept of image atoms. Therefore, only a sequential programming of the force calculation routine is required for executing the stencil in parallel environment. Typical molecular dynamics routines, such as various ensembles, time integration methods, and empirical potentials, have been implemented in the stencil. In the presentation, the performance of the stencil on parallel computers of Hitachi, IBM, SGI, and PC-cluster using the models of Lennard-Jones and the EAM type potentials for fracture problem will be reported.
Narth, Christophe; Lagardère, Louis; Polack, Étienne; Gresh, Nohad; Wang, Qiantao; Bell, David R; Rackers, Joshua A; Ponder, Jay W; Ren, Pengyu Y; Piquemal, Jean-Philip
2016-02-15
We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. PMID:26814845
NASA Astrophysics Data System (ADS)
Bartók, Albert P.; Gillan, Michael J.; Manby, Frederick R.; Csányi, Gábor
2013-08-01
We show how machine learning techniques based on Bayesian inference can be used to enhance the computer simulation of molecular materials, focusing here on water. We train our machine-learning algorithm using accurate, correlated quantum chemistry, and predict energies and forces in molecular aggregates ranging from clusters to solid and liquid phases. The widely used electronic-structure methods based on density functional theory (DFT) by themselves give poor accuracy for molecular materials like water, and we show how our techniques can be used to generate systematically improvable one- and two-body corrections to DFT with modest extra resources. The resulting corrected DFT scheme is considerably more accurate than uncorrected DFT for the relative energies of small water clusters and different ice structures and significantly improves the description of the structure and dynamics of liquid water. However, our results for ice structures and the liquid indicate that beyond-two-body DFT errors cannot be ignored, and we suggest how our machine-learning methods can be further developed to correct these errors.
Superspreading: molecular dynamics simulations and experimental results
NASA Astrophysics Data System (ADS)
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/).
Molecular circuits for dynamic noise filtering.
Zechner, Christoph; Seelig, Georg; Rullan, Marc; Khammash, Mustafa
2016-04-26
The invention of the Kalman filter is a crowning achievement of filtering theory-one that has revolutionized technology in countless ways. By dealing effectively with noise, the Kalman filter has enabled various applications in positioning, navigation, control, and telecommunications. In the emerging field of synthetic biology, noise and context dependency are among the key challenges facing the successful implementation of reliable, complex, and scalable synthetic circuits. Although substantial further advancement in the field may very well rely on effectively addressing these issues, a principled protocol to deal with noise-as provided by the Kalman filter-remains completely missing. Here we develop an optimal filtering theory that is suitable for noisy biochemical networks. We show how the resulting filters can be implemented at the molecular level and provide various simulations related to estimation, system identification, and noise cancellation problems. We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using flow cytometry measurements of a light-inducible circuit in Escherichia coli. PMID:27078094
Probing Molecular Dynamics by Laser-Induced Backscattering Holography.
Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B
2016-04-01
We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H_{2} and D_{2} molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H_{2} and D_{2} with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules. PMID:27081975
Probing Molecular Dynamics by Laser-Induced Backscattering Holography
NASA Astrophysics Data System (ADS)
Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B.
2016-04-01
We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H2 and D2 molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H2 and D2 with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules.
Ultrafast dynamics in isolated molecules and molecular clusters
NASA Astrophysics Data System (ADS)
Hertel, I. V.; Radloff, W.
2006-06-01
During the past decade the understanding of photo-induced ultrafast dynamics in molecular systems has improved at an unforeseen speed and a wealth of detailed insight into the fundamental processes has been obtained. This review summarizes our present knowledge on ultrafast dynamics in isolated molecules and molecular clusters evolving after excitation with femtosecond pulses as studied by pump-probe analysis in real time. Experimental tools and methods as well as theoretical models are described which have been developed to glean information on primary, ultrafast processes in photophysics, photochemistry and photobiology. The relevant processes are explained by way of example—from wave packet dynamics in systems with a few atoms all the way to internal conversion via conical intersections in bio-chromophores. A systematic overview on characteristic systems follows, starting with diatomic and including larger organic molecules as well as various types of molecular clusters, such as micro-solvated chromophore molecules. For conciseness the focus is on molecular systems which remain unperturbed by the laser pulses—apart from the excitation and detection processes as such. Thus, only some aspects of controlling and manipulating molecular reactions by shaped and/or very intense laser pulses are discussed briefly for particularly instructive examples, illustrating the perspectives of this prospering field. The material presented in this review comprises some prototypical examples from earlier pioneering work but emphasizes studies from recent years and covers the most important and latest developments until January 2006.
Relating Soil Organic Matter Dynamics to its Molecular Structure
Technology Transfer Automated Retrieval System (TEKTRAN)
Our understanding of the dynamics of soil organic matter (SOM) must be integrated with a sound knowledge of it biochemical complexity. The molecular structure of SOM was determined in 98% sand soils to eliminate the known protective effects of clay on the amount and turnover rate of the SOM constitu...
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. PMID:25873944
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. PMID:25873944
Molecular vibrational dynamics in PMMA studied by femtosecond CARS
NASA Astrophysics Data System (ADS)
Zhao, Yang; Zhang, Sheng; Zhou, Boyang; Fan, Rongwei; Chen, Deying; Zhang, Zhonghua; Xia, Yuanqin
2014-11-01
The ultrafast molecular vibrational dynamics in PMMA sheets is studied by femtosecond time-resolved coherent anti-Stokes Raman spectroscopy at room temperature. The C-H stretch modes at 2870 cm-1 and 3008 cm-1 in PMMA sheets are excited and detected. The coherence relaxation times and beat wavenumbers of the Raman modes are obtained.
Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
NASA Technical Reports Server (NTRS)
Menon, Madhu
1998-01-01
In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-05-14
The 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 our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also 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 LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) 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. (C) 2015 Elsevier B.V. All rights reserved.
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-05-14
The 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 our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also 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 resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) 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. (C) 2015 Elsevier B.V. All rights reserved.« less
Optimizing legacy molecular dynamics software with directive-based offload
NASA Astrophysics Data System (ADS)
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.
Reasoning with Atomic-Scale Molecular Dynamic Models
ERIC Educational Resources Information Center
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…
Open boundary molecular dynamics of sheared star-polymer melts.
Sablić, Jurij; Praprotnik, Matej; Delgado-Buscalioni, Rafael
2016-02-28
Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution. PMID:26820315
Nanoscale probing of dynamics in local molecular environments.
Atkin, Joanna M; Sass, Paul M; Teichen, Paul E; Eaves, Joel D; Raschke, Markus B
2015-11-19
Vibrational spectroscopy can provide information about structure, coupling, and dynamics underlying the properties of complex molecular systems. While measurements of spectral line broadening can probe local chemical environments, the spatial averaging in conventional spectroscopies limits insight into underlying heterogeneity, in particular in disordered molecular solids. Here, using femtosecond infrared scattering scanning near-field optical microscopy (IR s-SNOM), we resolve in vibrational free-induction decay (FID) measurements a high degree of spatial heterogeneity in polytetrafluoroethylene (PTFE) as a dense molecular model system. In nanoscopic probe volumes as small as 10(3) vibrational oscillators, we approach the homogeneous response limit, with extended vibrational dephasing times of several picoseconds, that is, up to 10 times the inhomogeneous lifetime, and spatial average converging to the bulk ensemble response. We simulate the dynamics of relaxation with a finite set of local vibrational transitions subject to random modulations in frequency. The combined results suggest that the observed heterogeneity arises due to static and dynamic variations in the local molecular environment. This approach thus provides real-space and real-time visualization of the subensemble dynamics that define the properties of many functional materials. PMID:26528865
Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks
NASA Astrophysics Data System (ADS)
Fahrenthold, Eric; Bass, Joseph
2015-06-01
Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general these potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new noholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.
Collisional dynamics in a gas of molecular super-rotors.
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh
2015-01-01
Recently, femtosecond laser techniques have been developed that are capable of bringing gas molecules to extremely fast rotation in a very short time, while keeping their translational motion relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a metastable 'gyroscopic stage' in the course of which the molecules maintain their fast rotation and orientation of the angular momentum through many collisions. The inhibited rotational-translational relaxation is characterized by a persistent anisotropy in the molecular angular distribution, and is manifested in the optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the 'gyroscopic stage' is abruptly terminated by an explosive rotational-translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules. PMID:26160223
Diversity dynamics: molecular phylogenies need the fossil record.
Quental, Tiago B; Marshall, Charles R
2010-08-01
Over the last two decades, new tools in the analysis of molecular phylogenies have enabled study of the diversification dynamics of living clades in the absence of information about extinct lineages. However, computer simulations and the fossil record show that the inability to access extinct lineages severely limits the inferences that can be drawn from molecular phylogenies. It appears that molecular phylogenies can tell us only when there have been changes in diversification rates, but are blind to the true diversity trajectories and rates of origination and extinction that have led to the species that are alive today. We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota. PMID:20646780
A dynamic data structure for flexible molecular maintenance and informatics
Bajaj, Chandrajit; Chowdhury, Rezaul Alam; Rasheed, Muhibur
2011-01-01
Motivation: We present the ‘Dynamic Packing Grid’ (DPG), a neighborhood data structure for maintaining and manipulating flexible molecules and assemblies, for efficient computation of binding affinities in drug design or in molecular dynamics calculations. Results: DPG can efficiently maintain the molecular surface using only linear space and supports quasi-constant time insertion, deletion and movement (i.e. updates) of atoms or groups of atoms. DPG also supports constant time neighborhood queries from arbitrary points. Our results for maintenance of molecular surface and polarization energy computations using DPG exhibit marked improvement in time and space requirements. Availability: http://www.cs.utexas.edu/~bajaj/cvc/software/DPG.shtml Contact: bajaj@cs.utexas.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21115440
Collisional dynamics in a gas of molecular super-rotors
NASA Astrophysics Data System (ADS)
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh.
2015-07-01
Recently, femtosecond laser techniques have been developed that are capable of bringing gas molecules to extremely fast rotation in a very short time, while keeping their translational motion relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a metastable `gyroscopic stage' in the course of which the molecules maintain their fast rotation and orientation of the angular momentum through many collisions. The inhibited rotational-translational relaxation is characterized by a persistent anisotropy in the molecular angular distribution, and is manifested in the optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the `gyroscopic stage' is abruptly terminated by an explosive rotational-translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules.
Rational Prediction with Molecular Dynamics for Hit Identification
Nichols, Sara E; Swift, Robert V; Amaro, Rommie E
2012-01-01
Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline. PMID:23110535
Mökkönen, Harri; Ala-Nissila, Tapio; Jónsson, Hannes
2016-09-01
The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort. PMID:27609008
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
Jankowska, Joanna; Sadlej, Joanna; Sobolewski, Andrzej L
2015-06-14
In this letter, we propose a novel, ultrafast, efficient molecular switch whose switching mechanism involves the electric field-driven intramolecular proton transfer. By means of ab initio quantum chemical calculations and on-the-fly dynamics simulations, we examine the switching performance of an isolated salicylidene aniline molecule and analyze the perspectives of its possible use as an electric field-controlled molecular electronics unit. PMID:25986469
Multiscale equation-free algorithms for molecular dynamics
NASA Astrophysics Data System (ADS)
Abi Mansour, Andrew
Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.
Correction for dynamic bias error in transmission measurements of void fraction.
Andersson, P; Sundén, E Andersson; Svärd, S Jacobsson; Sjöstrand, H
2012-12-01
Dynamic bias errors occur in transmission measurements, such as X-ray, gamma, or neutron radiography or tomography. This is observed when the properties of the object are not stationary in time and its average properties are assessed. The nonlinear measurement response to changes in transmission within the time scale of the measurement implies a bias, which can be difficult to correct for. A typical example is the tomographic or radiographic mapping of void content in dynamic two-phase flow systems. In this work, the dynamic bias error is described and a method to make a first-order correction is derived. A prerequisite for this method is variance estimates of the system dynamics, which can be obtained using high-speed, time-resolved data acquisition. However, in the absence of such acquisition, a priori knowledge might be used to substitute the time resolved data. Using synthetic data, a void fraction measurement case study has been simulated to demonstrate the performance of the suggested method. The transmission length of the radiation in the object under study and the type of fluctuation of the void fraction have been varied. Significant decreases in the dynamic bias error were achieved to the expense of marginal decreases in precision. PMID:23278029
Correction for dynamic bias error in transmission measurements of void fraction
NASA Astrophysics Data System (ADS)
Andersson, P.; Sundén, E. Andersson; Svärd, S. Jacobsson; Sjöstrand, H.
2012-12-01
Dynamic bias errors occur in transmission measurements, such as X-ray, gamma, or neutron radiography or tomography. This is observed when the properties of the object are not stationary in time and its average properties are assessed. The nonlinear measurement response to changes in transmission within the time scale of the measurement implies a bias, which can be difficult to correct for. A typical example is the tomographic or radiographic mapping of void content in dynamic two-phase flow systems. In this work, the dynamic bias error is described and a method to make a first-order correction is derived. A prerequisite for this method is variance estimates of the system dynamics, which can be obtained using high-speed, time-resolved data acquisition. However, in the absence of such acquisition, a priori knowledge might be used to substitute the time resolved data. Using synthetic data, a void fraction measurement case study has been simulated to demonstrate the performance of the suggested method. The transmission length of the radiation in the object under study and the type of fluctuation of the void fraction have been varied. Significant decreases in the dynamic bias error were achieved to the expense of marginal decreases in precision.
Molecular dynamics study of liquid methanol with a flexible three-site model
Palinkas, G.; Hawlicka, E.; Heinzinger, K.
1987-07-30
A new potential is presented which describes the methanol-methanol interactions on the basis of a flexible three-site model. The intramolecular part of the potential has been derived from spectroscopic data. A molecular dynamics study has been performed with this potential at 286 K. The structural properties of liquid methanol calculated from the simulations are in good agreement with X-ray measurements. The average geometrical arrangement of nearest neighbors and their hydrogen bonding are discussed. The potential describes correctly the gas-liquid frequency shifts of the intramolecular vibrations. Several thermodynamic properties calculated from the simulation compare favorably with experimental results.
Molecular dynamics simulations of an apoliprotein A I derived peptide in explicit water
NASA Astrophysics Data System (ADS)
Stavrakoudis, Athanassios
2008-08-01
Molecular dynamics simulations have been performed for the 104-117 α-helical fragment of apoliprotein A-I using the CHARMM22 force field and the N AMD simulation engine. Simulation (50 ns in explicit water) resulted in significant appearance of π-helix conformation, which was totally diminished when the CMAP correction of the CHARMM force field was applied. This is consistent with other similar studies which suggest that the observation of π-helix in peptide conformation was force field biased rather actually existed. This study suggests that the 104-117 fragment of apoliprotein A-I has a stable α-helical conformation in water.
Free energy landscapes of short peptide chains using adaptively biased molecular dynamics
NASA Astrophysics Data System (ADS)
Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste
2009-03-01
We present the results of a computational study of the free energy landscapes of short polypeptide chains, as a function of several reaction coordinates meant to distinguish between several known types of helices. The free energy landscapes were calculated using the recently developed adaptively biased molecular dynamics method followed up with equilibrium ``umbrella correction'' runs. Specific polypeptides investigated include small chains of pure and mixed alanine, glutamate, leucine, lysine and methionine (all amino acids with strong helix-forming propensities), as well as glycine, proline(having a low helix forming propensities), tyrosine, serine and arginine. Our results are consistent with the existing experimental and other theoretical evidence.
Ab initio molecular dynamics: concepts, recent developments, and future trends.
Iftimie, Radu; Minary, Peter; Tuckerman, Mark E
2005-05-10
The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204
Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms
NASA Astrophysics Data System (ADS)
Lühmann, Dirk-Sören; Weitenberg, Christof; Sengstock, Klaus
2015-07-01
In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.
Drugs That Target Dynamic Microtubules: A New Molecular Perspective
Stanton, Richard A.; Gernert, Kim M.; Nettles, James H.; Aneja, Ritu
2011-01-01
Microtubules have long been considered an ideal target for anticancer drugs because of the essential role they play in mitosis, forming the dynamic spindle apparatus. As such, there is a wide variety of compounds currently in clinical use and in development that act as antimitotic agents by altering microtubule dynamics. Although these diverse molecules are known to affect microtubule dynamics upon binding to one of the three established drug domains (taxane, vinca alkaloid, or colchicine site), the exact mechanism by which each drug works is still an area of intense speculation and research. In this study, we review the effects of microtubule-binding chemotherapeutic agents from a new perspective, considering how their mode of binding induces conformational changes and alters biological function relative to the molecular vectors of microtubule assembly or disassembly. These “biological vectors” can thus be used as a spatiotemporal context to describe molecular mechanisms by which microtubule-targeting drugs work. PMID:21381049
Multi-petaflop/s quantum and reactive molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Nakano, Aiichiro
We have developed a divide-conquer-recombine algorithmic framework for large quantum molecular dynamics (QMD) and reactive molecular dynamics (RMD) simulations. The algorithms have achieved parallel efficiency over 0.98 on 786,432 IBM Blue Gene/Q processors for 39.8 trillion electronic degrees-of-freedom QMD in the framework of density functional theory and 67.6 billion-atom RMD. We will discuss several applications including (1) 16,616-atom QMD simulation of rapid hydrogen production from water using metallic alloy nanoparticles, (2) 6,400-atom nonadiabatic QMD simulation of exciton dynamics for efficient solar cells, and (3) 112 million-atom RMD simulation of nanocarbon synthesis by high temperature oxidation of SiC nanoparticles.
Correction on the distortion of Scheimpflug imaging for dynamic central corneal thickness.
Li, Tianjie; Tian, Lei; Wang, Like; Hon, Ying; Lam, Andrew K C; Huang, Yifei; Wang, Yuanyuan; Zheng, Yongping
2015-05-01
The measurement of central corneal thickness (CCT) is important in ophthalmology. Most studies concerned the value at normal status, while rare ones focused on its dynamic changing. The commercial Corvis ST is the only commercial device currently available to visualize the two-dimensional image of dynamic corneal profiles during an air puff indentation. However, the directly observed CCT involves the Scheimpflug distortion, thus misleading the clinical diagnosis. This study aimed to correct the distortion for better measuring the dynamic CCTs. The optical path was first derived to consider the influence of factors on the use of Covis ST. A correction method was then proposed to estimate the CCT at any time during air puff indentation. Simulation results demonstrated the feasibility of the intuitive-feasible calibration for measuring the stationary CCT and indicated the necessity of correction when air puffed. Experiments on three contact lenses and four human corneas verified the prediction that the CCT would be underestimated when the improper calibration was conducted for air and overestimated when it was conducted on contact lenses made of polymethylmethacrylate. Using the proposed method, the CCT was finally observed to increase by 66 ± 34 μm at highest concavity in 48 normal human corneas. PMID:25992846
NASA Astrophysics Data System (ADS)
Raveendran, Tara; Sarkar, Saikat; Roy, D.; Vasu, R. M.
2013-06-01
Using a Girsanov change of measures, we propose novel variations within a particle-filtering algorithm, as applied to the inverse problem of state and parameter estimations of nonlinear dynamical systems of engineering interest, toward weakly correcting for the linearization or integration errors that almost invariably occur whilst numerically propagating the process dynamics, typically governed by nonlinear stochastic differential equations (SDEs). Specifically, the correction for linearization, provided by the likelihood or the Radon-Nikodym derivative, is incorporated within the evolving flow in two steps. Once the likelihood, an exponential martingale, is split into a product of two factors, correction owing to the first factor is implemented via rejection sampling in the first step. The second factor, which is directly computable, is accounted for via two different schemes, one employing resampling and the other using a gain-weighted innovation term added to the drift field of the process dynamics thereby overcoming the problem of sample dispersion posed by resampling. The proposed strategies, employed as add-ons to existing particle filters, the bootstrap and auxiliary SIR filters in this work, are found to non-trivially improve the convergence and accuracy of the estimates and also yield reduced mean square errors of such estimates vis-à-vis those obtained through the parent-filtering schemes.
Correction on the distortion of Scheimpflug imaging for dynamic central corneal thickness
NASA Astrophysics Data System (ADS)
Li, Tianjie; Tian, Lei; Wang, Like; Hon, Ying; Lam, Andrew K. C.; Huang, Yifei; Wang, Yuanyuan; Zheng, Yongping
2015-05-01
The measurement of central corneal thickness (CCT) is important in ophthalmology. Most studies concerned the value at normal status, while rare ones focused on its dynamic changing. The commercial Corvis ST is the only commercial device currently available to visualize the two-dimensional image of dynamic corneal profiles during an air puff indentation. However, the directly observed CCT involves the Scheimpflug distortion, thus misleading the clinical diagnosis. This study aimed to correct the distortion for better measuring the dynamic CCTs. The optical path was first derived to consider the influence of factors on the use of Covis ST. A correction method was then proposed to estimate the CCT at any time during air puff indentation. Simulation results demonstrated the feasibility of the intuitive-feasible calibration for measuring the stationary CCT and indicated the necessity of correction when air puffed. Experiments on three contact lenses and four human corneas verified the prediction that the CCT would be underestimated when the improper calibration was conducted for air and overestimated when it was conducted on contact lenses made of polymethylmethacrylate. Using the proposed method, the CCT was finally observed to increase by 66±34 μm at highest concavity in 48 normal human corneas.
Laser-enhanced dynamics in molecular rate processes
NASA Technical Reports Server (NTRS)
George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.
1978-01-01
The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.
Molecular dynamics computer simulation of permeation in solids
Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M.
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 random rotor molecule: Vibrational analysis and molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.
2012-12-01
Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4″″-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2″-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.
NASA Astrophysics Data System (ADS)
Danel, J.-F.; Kazandjian, L.; Piron, R.
2016-04-01
Of the two approaches of density-functional theory molecular dynamics, quantum molecular dynamics is limited at high temperature by computational cost whereas orbital-free molecular dynamics, based on an approximation of the kinetic electronic free energy, can be implemented in this domain. In the case of deuterium, it is shown how orbital-free molecular dynamics can be regarded as the limit of quantum molecular dynamics at high temperature for the calculation of the equation of state. To this end, accurate quantum molecular dynamics calculations are performed up to 20 eV at mass densities as low as 0.5 g /cm3 and up to 10 eV at mass densities as low as 0.2 g /cm3 . As a result, the limitation in temperature so far attributed to quantum molecular dynamics is overcome and an approach combining quantum and orbital-free molecular dynamics is used to construct an equation of state of deuterium. The thermodynamic domain addressed is that of the fluid phase above 1 eV and 0.2 g /cm3 . Both pressure and internal energy are calculated as functions of temperature and mass density, and various exchange-correlation contributions are compared. The generalized gradient approximation of the exchange-correlation functional, corrected to approximately include the influence of temperature, is retained and the results obtained are compared to other approaches and to experimental shock data; in parts of the thermodynamic domain addressed, these results significantly differ from those obtained in other first-principles investigations which themselves disagree. The equations of state of hydrogen and tritium above 1 eV and above, respectively, 0.1 g /cm3 and 0.3 g /cm3 , can be simply obtained by mass density scaling from the results found for deuterium. This ab initio approach allows one to consistently cover a very large domain of temperature on the domain of mass density outlined above.
GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.
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.
Special issue on ultrafast electron and molecular dynamics
NASA Astrophysics Data System (ADS)
Martin, Fernando; Hishikawa, Akiyoshi; Vrakking, Marc
2014-06-01
In the last few years, the advent of novel experimental and theoretical approaches has made possible the investigation of (time-resolved) molecular dynamics in ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation (HHG) and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain, thus opening completely new avenues for imaging electronic and nuclear dynamics in molecules. Along the way, particular types of molecular dynamics, e.g., dynamics around conical intersections, have gained an increased prominence, sparked by the realization of the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. In the short term, this will allow one to uncover and control the dynamics of elementary chemical processes such as, e.g., ultrafast charge migration, proton transfer, isomerization or multiple ionization, and to address new key questions about the role of attosecond coherent electron dynamics in chemical reactivity. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules, including biomolecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of the current
NASA Astrophysics Data System (ADS)
Wang, Tingting; Dai, Weidi; Jiao, Pengfei; Wang, Wenjun
2016-05-01
Many real-world data can be represented as dynamic networks which are the evolutionary networks with timestamps. Analyzing dynamic attributes is important to understanding the structures and functions of these complex networks. Especially, studying the influential nodes is significant to exploring and analyzing networks. In this paper, we propose a method to identify influential nodes in dynamic social networks based on identifying such nodes in the temporal communities which make up the dynamic networks. Firstly, we detect the community structures of all the snapshot networks based on the degree-corrected stochastic block model (DCBM). After getting the community structures, we capture the evolution of every community in the dynamic network by the extended Jaccard’s coefficient which is defined to map communities among all the snapshot networks. Then we obtain the initial influential nodes of the dynamic network and aggregate them based on three widely used centrality metrics. Experiments on real-world and synthetic datasets demonstrate that our method can identify influential nodes in dynamic networks accurately, at the same time, we also find some interesting phenomena and conclusions for those that have been validated in complex network or social science.
A reduced basis method for molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Vincent-Finley, Rachel Elisabeth
In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.
Modal Correction Method For Dynamically Induced Errors In Wind-Tunnel Model Attitude Measurements
NASA Technical Reports Server (NTRS)
Buehrle, R. D.; Young, C. P., Jr.
1995-01-01
This paper describes a method for correcting the dynamically induced bias errors in wind tunnel model attitude measurements using measured modal properties of the model system. At NASA Langley Research Center, the predominant instrumentation used to measure model attitude is a servo-accelerometer device that senses the model attitude with respect to the local vertical. Under smooth wind tunnel operating conditions, this inertial device can measure the model attitude with an accuracy of 0.01 degree. During wind tunnel tests when the model is responding at high dynamic amplitudes, the inertial device also senses the centrifugal acceleration associated with model vibration. This centrifugal acceleration results in a bias error in the model attitude measurement. A study of the response of a cantilevered model system to a simulated dynamic environment shows significant bias error in the model attitude measurement can occur and is vibration mode and amplitude dependent. For each vibration mode contributing to the bias error, the error is estimated from the measured modal properties and tangential accelerations at the model attitude device. Linear superposition is used to combine the bias estimates for individual modes to determine the overall bias error as a function of time. The modal correction model predicts the bias error to a high degree of accuracy for the vibration modes characterized in the simulated dynamic environment.
A molecular dynamics study of polymer/graphene interfacial systems
Rissanou, Anastassia N.; Harmandaris, Vagelis
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.
Self-interaction corrected density functional calculations of molecular Rydberg states
Gudmundsdóttir, Hildur; Zhang, Yao; Weber, Peter M.; Jónsson, Hannes
2013-11-21
A method is presented for calculating the wave function and energy of Rydberg excited states of molecules. A good estimate of the Rydberg state orbital is obtained using ground state density functional theory including Perdew-Zunger self-interaction correction and an optimized effective potential. The total energy of the excited molecule is obtained using the Delta Self-Consistent Field method where an electron is removed from the highest occupied orbital and placed in the Rydberg orbital. Results are presented for the first few Rydberg states of NH{sub 3}, H{sub 2}O, H{sub 2}CO, C{sub 2}H{sub 4}, and N(CH{sub 3}){sub 3}. The mean absolute error in the energy of the 33 molecular Rydberg states presented here is 0.18 eV. The orbitals are represented on a real space grid, avoiding the dependence on diffuse atomic basis sets. As in standard density functional theory calculations, the computational effort scales as NM{sup 2} where N is the number of orbitals and M is the number of grid points included in the calculation. Due to the slow scaling of the computational effort with system size and the high level of parallelism in the real space grid approach, the method presented here makes it possible to estimate Rydberg electron binding energy in large molecules.
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
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.
ERIC Educational Resources Information Center
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,…
Characterizing and correcting for the effect of sensor noise in the dynamic mode decomposition
NASA Astrophysics Data System (ADS)
Dawson, Scott; Hemati, Maziar; Williams, Matthew; Rowley, Clarence
2014-11-01
Dynamic mode decomposition (DMD) provides a powerful means of extracting insightful dynamical information from fluids datasets. Like any data processing technique, DMD's usefulness relies on its ability to extract real and accurate dynamical features from noise-corrupted data. Here we show analytically that sensor noise can bias the results (eigenvalues and modes) of the DMD algorithm. This bias can be accurately predicted, to the point that we may derive an analytic correction factor that facilitates its removal. We propose a number of additional modifications to the DMD algorithm that reduce or eliminate this bias, even when the noise characteristics are unknown. We demonstrate the performance of these modifications on a range of synthetic, numerical, and experimental datasets, and also compare and integrate our modified algorithms with other DMD variants proposed in recent literature. This work was supported by the Air Force Office of Scientific Research, under Award No. FA9550-12-1-0075.
Characterizing and correcting for the effect of sensor noise in the dynamic mode decomposition
NASA Astrophysics Data System (ADS)
Dawson, Scott T. M.; Hemati, Maziar S.; Williams, Matthew O.; Rowley, Clarence W.
2016-03-01
Dynamic mode decomposition (DMD) provides a practical means of extracting insightful dynamical information from fluids datasets. Like any data processing technique, DMD's usefulness is limited by its ability to extract real and accurate dynamical features from noise-corrupted data. Here, we show analytically that DMD is biased to sensor noise, and quantify how this bias depends on the size and noise level of the data. We present three modifications to DMD that can be used to remove this bias: (1) a direct correction of the identified bias using known noise properties, (2) combining the results of performing DMD forwards and backwards in time, and (3) a total least-squares-inspired algorithm. We discuss the relative merits of each algorithm and demonstrate the performance of these modifications on a range of synthetic, numerical, and experimental datasets. We further compare our modified DMD algorithms with other variants proposed in the recent literature.
Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain
Freddolino, Peter L.; Liu, Feng; Gruebele, Martin; Schulten, Klaus
2008-01-01
All-atom molecular dynamics (MD) simulations of protein folding allow analysis of the folding process at an unprecedented level of detail. Unfortunately, such simulations have not yet reached their full potential both due to difficulties in sufficiently sampling the microsecond timescales needed for folding, and because the force field used may yield neither the correct dynamical sequence of events nor the folded structure. The ongoing study of protein folding through computational methods thus requires both improvements in the performance of molecular dynamics programs to make longer timescales accessible, and testing of force fields in the context of folding simulations. We report a ten-microsecond simulation of an incipient downhill-folding WW domain mutant along with measurement of a molecular time and activated folding time of 1.5 microseconds and 13.3 microseconds, respectively. The protein simulated in explicit solvent exhibits several metastable states with incorrect topology and does not assume the native state during the present simulations. PMID:18339748
Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S
2014-10-16
The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.
Accelerating ring-polymer molecular dynamics with parallel-replica dynamics.
Lu, Chun-Yaung; Perez, Danny; Voter, Arthur F
2016-06-28
Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe-Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach. PMID:27369499
Accelerating ring-polymer molecular dynamics with parallel-replica dynamics
NASA Astrophysics Data System (ADS)
Lu, Chun-Yaung; Perez, Danny; Voter, Arthur F.
2016-06-01
Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe-Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach.
The effect of molecular dynamics sampling on the calculated observable gas-phase structures.
Tikhonov, Denis S; Otlyotov, Arseniy A; Rybkin, Vladimir V
2016-07-21
In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory. PMID:27331660
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. PMID:23879450
Finite-temperature electron correlations in the framework of a dynamic local-field correction
Schweng, H.K.; Boehm, H.M. )
1993-07-15
The quantum-mechanical version of the Singwi-Tosi-Land-Sjoelander (STLS) approximation is applied to finite temperatures. This approximation has two main advantages. First, it includes a dynamic local-field correction and second, it gives positive values for the pair-distribution function in the short-range region at zero temperature. This is even valid for rather low densities. After a description of the numerical difficulties arising with the use of a dynamic approximation, the results for the static-structure factor and the pair-distribution function are discussed thoroughly. Detailed work is performed on the static part of the local-field correction, with special emphasis put on the investigation of its structure. A peak is found at a wave vector [ital q][approx]2.8 (in units of the Fermi wave vector) for small temperatures, which tends towards higher values of [ital q] with increasing temperature. This peak causes an attractive particle-hole interaction in a certain [ital q] region and thus gives rise to the appearance of a charge-density wave. A parametric description is given for the static local-field correction in order to simplify further applications. Furthermore, the exchange-and-correlation free energy is considered. The results are compared with the STLS results and with the modified convolution approach.
Determination of sea surface height from moving ships with dynamic corrections
NASA Astrophysics Data System (ADS)
Reinking, J.; Härting, A.; Bastos, L.
2012-11-01
With the growing global efforts to estimate the influence of civilization on the climate change it would be desirable to survey sea surface heights (SSH) not only by remote sensing techniques like satellite altimetry or (GNSS) Global Navigation Satellite System reflectometry but also by direct and in-situ measurements in the open ocean. In recent years different groups attempted to determine SSH by ship-based GNSS observations. Due to recent advances in kinematic GNSS (PPP) Precise Point Positioning analysis it is already possible to derive GNSS antenna heights with a quality of a few centimeters. Therefore it is foreseeable that this technique will be used more intensively in the future, with obvious advantages in sea positioning. For the determination of actual SSH from GNSS-derived antenna heights aboard seagoing vessels some essential hydrostatic and hydrodynamic corrections must be considered in addition to ocean dynamics and related corrections. Systematic influences of ship dynamics were intensively analyzed and sophisticated techniques were developed at the Jade University during the last decades to precisely estimate mandatory corrections. In this paper we will describe the required analyses and demonstrate their application by presenting a case study from an experiment on a cruise vessel carried out in March 2011 in the Atlantic Ocean.
Deformation corrected compressed sensing (DC-CS): a novel framework for accelerated dynamic MRI
Lingala, Sajan Goud; DiBella, Edward; Jacob, Mathews
2015-01-01
We propose a novel deformation corrected compressed sensing (DC-CS) framework to recover contrast enhanced dynamic magnetic resonance images from undersampled measurements. We introduce a formulation that is capable of handling a wide class of sparsity/compactness priors on the deformation corrected dynamic signal. In this work, we consider example compactness priors such as sparsity in temporal Fourier domain, sparsity in temporal finite difference domain, and nuclear norm penalty to exploit low rank structure. Using variable splitting, we decouple the complex optimization problem to simpler and well understood sub problems; the resulting algorithm alternates between simple steps of shrinkage based denoising, deformable registration, and a quadratic optimization step. Additionally, we employ efficient continuation strategies to reduce the risk of convergence to local minima. The decoupling enabled by the proposed scheme enables us to apply this scheme to contrast enhanced MRI applications. Through experiments on numerical phantom and in vivo myocardial perfusion MRI datasets, we observe superior image quality of the proposed DC-CS scheme in comparison to the classical k-t FOCUSS with motion estimation/correction scheme, and demonstrate reduced motion artifacts over classical compressed sensing schemes that utilize the compact priors on the original deformation uncorrected signal. PMID:25095251
Pseudo generators for under-resolved molecular dynamics
NASA Astrophysics Data System (ADS)
Bittracher, A.; Hartmann, C.; Junge, O.; Koltai, P.
2015-09-01
Many features of a molecule which are of physical interest (e.g. molecular conformations, reaction rates) are described in terms of its dynamics in configuration space. This article deals with the projection of molecular dynamics in phase space onto configuration space. Specifically, we study the situation that the phase space dynamics is governed by a stochastic Langevin equation and study its relation with the configurational Smoluchowski equation in the three different scaling regimes: Firstly, the Smoluchowski equations in non-Cartesian geometries are derived from the overdamped limit of the Langevin equation. Secondly, transfer operator methods are used to describe the metastable behaviour of the system at hand, and an explicit small-time asymptotics is derived on which the Smoluchowski equation turns out to govern the dynamics of the position coordinate (without any assumptions on the damping). By using an adequate reduction technique, these considerations are then extended to one-dimensional reaction coordinates. Thirdly, we sketch three different approaches to approximate the metastable dynamics based on time-local information only.
Analysis of motion features for molecular dynamics simulation of proteins
NASA Astrophysics Data System (ADS)
Kamada, Mayumi; Toda, Mikito; Sekijima, Masakazu; Takata, Masami; Joe, Kazuki
2011-01-01
Recently, a new method for time series analysis using the wavelet transformation has been proposed by Sakurai et al. We apply it to molecular dynamics simulation of Thermomyces lanuginosa lipase (TLL). Introducing indexes to characterize collective motion of the protein, we have obtained the following two results. First, time evolution of the collective motion involves not only the dynamics within a single potential well but also takes place wandering around multiple conformations. Second, correlation of the collective motion between secondary structures shows that collective motion exists involving multiple secondary structures. We discuss future prospects of our study involving 'disordered proteins'.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
NASA Technical Reports Server (NTRS)
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.
Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms
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.
Application of two dimensional periodic molecular dynamics to interfaces.
NASA Astrophysics Data System (ADS)
Gay, David H.; Slater, Ben; Catlow, C. Richard A.
1997-08-01
We have applied two-dimensional molecular dynamics to the surface of a crystalline aspartame and the interface between the crystal face and a solvent (water). This has allowed us to look at the dynamic processes at the surface. Understanding the surface structure and properties are important to controlling the crystal morphology. The thermodynamic ensemble was constant Number, surface Area and Temperature (NAT). The calculations have been carried out using a 2D Ewald summation and 2D periodic boundary conditions for the short range potentials. The equations of motion integration has been carried out using the standard velocity Verlet algorithm.
Molecular dynamical simulations of melting behaviors of metal clusters
Hamid, Ilyar; Fang, Meng; Duan, Haiming
2015-04-15
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 and the phase transition in solid C60
NASA Astrophysics Data System (ADS)
Tycko, R.; Dabbagh, G.; Fleming, R. M.; Haddon, R. C.; Makhija, A. V.; Zahurak, S. M.
1991-09-01
The molecular reorientational dynamics in two phases of solid C60 with C-13 NMR measurements are characterized. A change in the nature of the dynamics, indicated by a change in kinetic parameters extracted from spin-lattice relaxation data, occurs at the phase transition at 260 K. Above the transition, the molecules appear to execute continuous rotational diffusion; below the transition, they appear to jump between symmetry-equivalent orientations. This interpretation is consistent with the X-ray-diffraction results of Heiney et al. (1991) as well as the NMR relaxation and spectral data.
Molecular Dynamics and Electron Density Studies of Siderophores and Peptides.
NASA Astrophysics Data System (ADS)
Fidelis, Krzysztof Andrzej
1990-08-01
The dissertation comprises three separate studies of siderophores and peptides. In the first of these studies the relative potential energies for a series of diastereomers of a siderophore neocoprogen I are evaluated with molecular mechanics force field methods. Charges on the hydroxamate moiety are determined with a synthetic model siderophore compound using valence population refinements, and alternatively, with the theoretical ab initio/ESP calculations. The single diastereomer found in the crystal structure is among four characterized by the low potential energy, while prevalence of Delta vs. Lambda configuration about the iron is found to be a property of the entire series. In the second study the crystal structure of a ferrichrome siderophore ferrirhodin is reported. The crystal structure conformation of the molecular backbone as well as the iron coordination geometry compare well with other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using the methods of molecular mechanics. The third study a 300 ps, 300 K, in vacuo molecular dynamics simulation of didemnin A and B yields distinct molecular conformers, which are different from the one found in the crystal structure or modeled in solution, using the Nuclear Overhauser Effect data. Evaluations of the relative potential energy are performed with short 10 ps simulations in solution. Didemnins are natural depsipeptides isolated from a Caribbean tunicate and characterized by particularly potent antiproliferative and immunomodulatory activity. Conformationally rigid and flexible regions of the molecule are described. A short review of the molecular mechanics methodology is given in the introduction.
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. PMID:17968118
Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.
Omelyan, I P
2006-09-01
A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations. PMID:17025782
Human Lactate Dehydrogenase A Inhibitors: A Molecular Dynamics Investigation
Shi, Yun; Pinto, B. Mario
2014-01-01
Lactate dehydrogenase A (LDHA) is an important enzyme in fermentative glycolysis, generating most energy for cancer cells that rely on anaerobic respiration even under normal oxygen concentrations. This renders LDHA a promising molecular target for the treatment of various cancers. Several efforts have been made recently to develop LDHA inhibitors with nanomolar inhibition and cellular activity, some of which have been studied in complex with the enzyme by X-ray crystallography. In this work, we present a molecular dynamics (MD) study of the binding interactions of selected ligands with human LDHA. Conventional MD simulations demonstrate different binding dynamics of inhibitors with similar binding affinities, whereas steered MD simulations yield discrimination of selected LDHA inhibitors with qualitative correlation between the in silico unbinding difficulty and the experimental binding strength. Further, our results have been used to clarify ambiguities in the binding modes of two well-known LDHA inhibitors. PMID:24466056
Tensor-optimized antisymmetrized molecular dynamics in nuclear physics
NASA Astrophysics Data System (ADS)
Myo, Takayuki; Toki, Hiroshi; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro
2015-07-01
We develop a new formalism to treat nuclear many-body systems using the bare nucleon-nucleon interaction. It has become evident that the tensor interaction plays an important role in nuclear many-body systems due to the role of the pion in strongly interacting systems. 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. 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".
Shock induced phase transition of water: Molecular dynamics investigation
NASA Astrophysics Data System (ADS)
Neogi, Anupam; Mitra, Nilanjan
2016-02-01
Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns.
An implicit divalent counterion force field for RNA molecular dynamics
NASA Astrophysics Data System (ADS)
Henke, Paul S.; Mak, Chi H.
2016-03-01
How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg2+ screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.
Molecular dynamic simulation of non-melt laser annealing process
NASA Astrophysics Data System (ADS)
Liren, Yan; Dai, Li; Wei, Zhang; Zhihong, Liu; Wei, Zhou; Quan, Wang
2016-03-01
Molecular dynamic simulation is performed to study the process of material annealing caused by a 266 nm pulsed laser. A micro-mechanism describing behaviors of silicon and impurity atoms during the laser annealing at a non-melt regime is proposed. After ion implantation, the surface of the Si wafer is acted by a high energy laser pulse, which loosens the material and partially frees both Si and impurity atoms. While the residual laser energy is absorbed by valence electrons, these atoms are recoiled and relocated to finally form a crystal. Energy-related movement behavior is observed by using the molecular dynamic method. The non-melt laser anneal appears to be quite sensitive to the energy density of the laser, as a small excess energy may causes a significant impurity diffusion. Such a result is also supported by our laser anneal experiment.
Time series analysis of molecular dynamics simulation using wavelet
NASA Astrophysics Data System (ADS)
Toda, Mikito
2012-08-01
A new method is presented to extract nonstationary features of slow collective motion toward time series data of molecular dynamics simulation for proteins. The method consists of the following two steps: (1) the wavelet transformation and (2) the singular value decomposition (SVD). The wavelet transformation enables us to characterize time varying features of oscillatory motions and SVD enables us to reduce the degrees of freedom of the movement. We apply the method to molecular dynamics simulation of various proteins such as Adenylate Kinase from Escherichia coli (AKE) and Thermomyces lanuginosa lipase (TLL). Moreover, we introduce indexes to characterize collective motion of proteins. These indexes provide us with information of nonstationary deformation of protein structures. We discuss future prospects of our study involving "intrinsically disordered proteins".
Molecular dynamics studies of U1A-RNA complexes.
Reyes, C M; Kollman, P A
1999-01-01
The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A-internal loop complex that is not observed in the U1A-hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity. PMID:10024175
Coherent Amplification of Ultrafast Molecular Dynamics in an Optical Oscillator
NASA Astrophysics Data System (ADS)
Aharonovich, Igal; Pe'er, Avi
2016-02-01
Optical oscillators present a powerful optimization mechanism. The inherent competition for the gain resources between possible modes of oscillation entails the prevalence of the most efficient single mode. We harness this "ultrafast" coherent feedback to optimize an optical field in time, and show that, when an optical oscillator based on a molecular gain medium is synchronously pumped by ultrashort pulses, a temporally coherent multimode field can develop that optimally dumps a general, dynamically evolving vibrational wave packet, into a single vibrational target state. Measuring the emitted field opens a new window to visualization and control of fast molecular dynamics. The realization of such a coherent oscillator with hot alkali dimers appears within experimental reach.
Description of ferrocenylalkylthiol SAMs on gold by molecular dynamics simulations.
Goujon, F; Bonal, C; Limoges, B; Malfreyt, P
2009-08-18
Molecular dynamics simulations of mixed monolayers consisting of Fc(CH2)12S-/C10S-Au SAMs are carried out to calculate structural (density profiles, angular distributions, positions of atoms) and energetic properties. The purpose of this paper is to explore the possible inhomogeneity of the neutral ferrocene moieties within the monolayer. Five systems have been studied using different grafting densities for the ferrocenylalkylthiolates. The angular distributions are described in terms of the relative contributions from isolated and clustered ferrocene moieties in the binary SAMs. It is shown that the energetic contributions strongly depend on the state of the ferrocene. The ability of molecular dynamics simulations to enable better understanding the SAM structure is illustrated in this work. PMID:19449821
Multiscale Reactive Molecular Dynamics for Absolute pK a Predictions and Amino Acid Deprotonation.
Nelson, J Gard; Peng, Yuxing; Silverstein, Daniel W; Swanson, Jessica M J
2014-07-01
Accurately calculating a weak acid's pK a from simulations remains a challenging task. We report a multiscale theoretical approach to calculate the free energy profile for acid ionization, resulting in accurate absolute pK a values in addition to insights into the underlying mechanism. Importantly, our approach minimizes empiricism by mapping electronic structure data (QM/MM forces) into a reactive molecular dynamics model capable of extensive sampling. Consequently, the bulk property of interest (the absolute pK a) is the natural consequence of the model, not a parameter used to fit it. This approach is applied to create reactive models of aspartic and glutamic acids. We show that these models predict the correct pK a values and provide ample statistics to probe the molecular mechanism of dissociation. This analysis shows changes in the solvation structure and Zundel-dominated transitions between the protonated acid, contact ion pair, and bulk solvated excess proton. PMID:25061442
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. PMID:19518394
Complete Characterization of Molecular Dynamics in Ultrashort Laser Fields
Feuerstein, B.; Ergler, Th.; Rudenko, A.; Zrost, K.; Schroeter, C. D.; Moshammer, R.; Ullrich, J.; Niederhausen, T.; Thumm, U.
2007-10-12
Reaction Microscope-based, complete, and time-resolved Coulomb explosion imaging of vibrating and dissociating D{sub 2}{sup +} molecules with femtosecond time-resolution allowed us to perform an internuclear distance (R-)dependent Fourier analysis of the corresponding wave packets. Calculations demonstrate that the obtained two-dimensional R-dependent frequency spectra enable the complete characterization of the wave packet dynamics and directly visualize the field-modified molecular potential curves in intense, ultrashort laser pulses.
Probing Molecular Dynamics at Attosecond Resolution with Femtosecond Laser Pulses
NASA Astrophysics Data System (ADS)
Tong, X. M.; Zhao, Z. X.; Lin, C. D.
2003-12-01
The kinetic energy distribution of D+ ions resulting from the interaction of a femtosecond laser pulse with D2 molecules is calculated based on the rescattering model. From analyzing the molecular dynamics, it is shown that the recollision time between the ionized electron and the D+2 ion can be read from the D+ kinetic energy peaks to attosecond accuracy. We further suggest that a more precise reading of the clock can be achieved by using shorter fs laser pulses (about 15fs).
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
NASA Astrophysics Data System (ADS)
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
2016-03-21
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. PMID:27004863
Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics
Hoover, W. G.; Hoover, C. G.
1993-08-01
Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.
Molecular dynamics modeling of a nanomaterials-water surface interaction
NASA Astrophysics Data System (ADS)
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.
Improving the performance of molecular dynamics simulations on parallel clusters.
Borstnik, Urban; Hodoscek, Milan; Janezic, Dusanka
2004-01-01
In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds. PMID:15032512
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. PMID:26358333
Stanzione, Francesca; Jayaraman, Arthi
2016-05-01
In-silico design of polymeric biomaterials requires molecular dynamics (MD) simulations that retain essential atomistic/molecular details (e.g., explicit water around the biofunctional macromolecule) while simultaneously achieving large length and time scales pertinent to macroscale function. Such large-scale atomistically detailed macromolecular MD simulations with explicit solvent representation are computationally expensive. One way to overcome this limitation is to use an adaptive resolution scheme (AdResS) in which the explicit solvent molecules dynamically adopt either atomistic or coarse-grained resolution depending on their location (e.g., near or far from the macromolecule) in the system. In this study we present the feasibility and the limitations of AdResS methodology for studying polyethylene glycol (PEG) in adaptive resolution water, for varying PEG length and architecture. We first validate the AdResS methodology for such systems, by comparing PEG and solvent structure with that from all-atom simulations. We elucidate the role of the atomistic zone size and the need for calculating thermodynamic force correction within this AdResS approach to correctly reproduce the structure of PEG and water. Lastly, by varying the PEG length and architecture, we study the hydration of PEG, and the effect of PEG architectures on the structural properties of water. Changing the architecture of PEG from linear to multiarm star, we observe reduction in the solvent accessible surface area of the PEG, and an increase in the order of water molecules in the hydration shells. PMID:27108869
Scattering studies of molecular dynamics of complex fluids
NASA Astrophysics Data System (ADS)
Liao, Ciya
The dynamics of complex fluids is studied by modeling the spectrum of density fluctuation: dynamic structure factor. The theoretic models are compared with experimental measurements by X-ray and molecular dynamics simulation results. In time scale, the dynamics of supercooled water can be well separated into short time and long time dynamics. While the long time dynamics is modeled well by a stretch exponential and explained as cage relaxations by mode coupling theory, the short time dynamics is under study in this thesis. We introduce two models for the short time dynamics. One model assumes that the short time movement of particles inside a cage is in a harmonic potential well with a vibrational frequency distribution function having a two-peak structure. The relationship of density of state with the single particle dynamic structure factor is employed to formulate the model. The other model treats the in-cage rattlings as collisions between hard sphere particles which can be modeled by a kinetic theory. A modification of the kinetic theory has to be used to account for the cage effect on the short time dynamics. The idea that the short time dynamics can be considered separately from long time dynamics is verified by the potential landscape view. The inherent structure which is defined as a local minimum in the potential function varies from time to time as the result of the crossing- basin of system in the potential landscape. The within basin movement regarded as short time rattlings can be eliminated by calculating the intermediate scattering function of the inherent structure, which shows an almost identical behavior as the long time part of original intermediate scattering function. A recent development of high resolution inelastic X-ray scattering technique brings a challenge on how to deal with the form factors of different atoms in the explanation of the measured dynamic structure factor. A generalized dynamic structure factor is defined to include the
Molecular dynamics of a water jet from a carbon nanotube.
Hanasaki, Itsuo; Yonebayashi, Toru; Kawano, Satoyuki
2009-04-01
A carbon nanotube (CNT) can be viewed as a molecular nozzle. It has a cylindrical shape of atomistic regularity, and the diameter can be even less than 1 nm. We have conducted molecular-dynamics simulations of water jet from a (6,6) CNT that confines water in a form of single-file molecular chain. The results show that the water forms nanoscale clusters at the outlet and they are released intermittently. The jet breakup is dominated by the thermal fluctuations, which leads to the strong dependence on the temperature. The cluster size n decreases and the release frequency f increases at higher temperatures. The f roughly follows the reaction kinetics by the transition state theory. The speed of a cluster is proportional to the 1/sqrt[n] because of the central limit theorem. These properties make great contrast with the macroscopic liquid jets. PMID:19518333
Dynamics in a supercooled molecular liquid: Theory and simulations
Rinaldi, Adele; Sciortino, Francesco; Tartaglia, Piero
2001-06-01
We report extensive simulations of liquid supercooled states for a simple three-site molecular model, introduced by Lewis and Wahnstrom [Phys. Rev. E >50, 3865 (1994)] to mimic the behavior of ortho-terphenyl. The large system size and the long simulation length allow us to calculate very precisely (in a large q-vector range) self-correlation and collective correlation functions, providing a clean and simple reference model for theoretical descriptions of molecular liquids in supercooled states. The time and wave-vector dependence of the site-site correlation functions are compared (neglecting the molecular constraints) with detailed ideal mode-coupling theory predictions. Except for the wave-vector region where the dynamics are controlled by the center of mass (around 9 nm{sup {minus}1}), the theoretical predictions compare very well with the simulation data.
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
Abdollahipour, Babak; Abouie, Jahanfar Ebrahimi, Navid
2015-09-15
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.
Dynamic Black-Level Correction and Artifact Flagging for Kepler Pixel Time Series
NASA Technical Reports Server (NTRS)
Kolodziejczak, J. J.; Clarke, B. D.; Caldwell, D. A.
2011-01-01
Methods applied to the calibration stage of Kepler pipeline data processing [1] (CAL) do not currently use all of the information available to identify and correct several instrument-induced artifacts. These include time-varying crosstalk from the fine guidance sensor (FGS) clock signals, and manifestations of drifting moire pattern as locally correlated nonstationary noise, and rolling bands in the images which find their way into the time series [2], [3]. As the Kepler Mission continues to improve the fidelity of its science data products, we are evaluating the benefits of adding pipeline steps to more completely model and dynamically correct the FGS crosstalk, then use the residuals from these model fits to detect and flag spatial regions and time intervals of strong time-varying black-level which may complicate later processing or lead to misinterpretation of instrument behavior as stellar activity.
Exploiting molecular dynamics in Nested Sampling simulations of small peptides
NASA Astrophysics Data System (ADS)
Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor
2016-04-01
Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.
Fast parallel algorithms for short-range molecular dynamics
Plimpton, S.
1993-05-01
Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a subset of atoms; the second assigns each a subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently -- those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 10,000,000 atoms on three parallel supercomputers, the nCUBE 2, Intel iPSC/860, and Intel Delta. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and the Intel Delta performs about 30 times faster than a single Y-MP processor and 12 times faster than a single C90 processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.
Applications of the molecular dynamics flexible fitting method.
Trabuco, Leonardo G; Schreiner, Eduard; Gumbart, James; Hsin, Jen; Villa, Elizabeth; Schulten, Klaus
2011-03-01
In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to landmark advances in experimental and computational techniques, resulting in sub-nanometer resolution structures being obtained routinely. The remaining gap between these data and revealing the mechanisms of molecular function can be closed through hybrid modeling tools that incorporate known atomic structures into the cryo-EM data. One such tool, molecular dynamics flexible fitting (MDFF), uses molecular dynamics simulations to combine structures from X-ray crystallography with cryo-EM density maps to derive atomic models of large biomolecular complexes. The structures furnished by MDFF can be used subsequently in computational investigations aimed at revealing the dynamics of the complexes under study. In the present work, recent applications of MDFF are presented, including the interpretation of cryo-EM data of the ribosome at different stages of translation and the structure of a membrane-curvature-inducing photosynthetic complex. PMID:20932910
Molecular dynamics simulations of solutions at constant chemical potential
NASA Astrophysics Data System (ADS)
Perego, C.; Salvalaglio, M.; Parrinello, M.
2015-04-01
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.
Molecular-level dynamics of refractory dissolved organic matter
NASA Astrophysics Data System (ADS)
Niggemann, J.; Gerdts, G.; Dittmar, T.
2012-04-01
Refractory dissolved organic matter (DOM) accounts for most of the global oceanic organic carbon inventory. Processes leading to its formation and factors determining its stability are still largely unknown. We hypothesize that refractory DOM carries a universal molecular signature. Characterizing spatial and temporal variability in this universal signature is a key to understanding dynamics of refractory DOM. We present results from a long-term study of the DOM geo-metabolome in the open North Sea. Geo-metabolomics considers the entity of DOM as a population of compounds, each characterized by a specific function and reactivity in the cycling of energy and elements. Ten-thousands of molecular formulae were identified in DOM by ultrahigh resolution mass spectrometry analysis (FT-ICR-MS, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry). The DOM pool in the North Sea was influenced by a complex interplay of processes that produced, transformed and degraded dissolved molecules. We identified a stable fraction in North Sea DOM with a molecular composition similar to deep ocean DOM. Molecular-level changes in this stable fraction provide novel information on dynamics and interactions of refractory DOM.
Dipietro, Laura; Poizner, Howard; Krebs, Hermano I.
2015-01-01
The ability to control online motor corrections is key to dealing with unexpected changes arising in the environment with which we interact. How the CNS controls online motor corrections is poorly understood, but evidence has accumulated in favor of a submovement-based model in which apparently continuous movement is segmented into distinct submovements. Although most studies have focused on submovements’ kinematic features, direct links with the underlying neural dynamics have not been extensively explored. This study sought to identify an electroencephalographic signature of submovements. We elicited kinematic submovements using a double-step displacement paradigm. Participants moved their wrist toward a target whose direction could shift mid-movement with a 50% probability. Movement kinematics and cortical activity were concurrently recorded with a low-friction robotic device and high-density electroencephalography. Analysis of spatiotemporal dynamics of brain activation and its correlation with movement kinematics showed that the production of each kinematic submovement was accompanied by (1) stereotyped topographic scalp maps and (2) frontoparietal ERPs time-locked to submovements. Positive ERP peaks from frontocentral areas contralateral to the moving wrist preceded kinematic submovement peaks by 220–250 msec and were followed by positive ERP peaks from contralateral parietal areas (140–250 msec latency, 0–80 msec before submovement peaks). Moreover, individual subject variability in the latency of frontoparietal ERP components following the target shift significantly predicted variability in the latency of the corrective submovement. Our results are in concordance with evidence for the intermittent nature of continuous movement and elucidate the timing and role of frontoparietal activations in the generation and control of corrective submovements. PMID:24564462
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.
Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A
2016-01-01
Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics. PMID:26013419
Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A
2013-03-21
The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio
NASA Astrophysics Data System (ADS)
McNeil, William J.; Madden, William G.; Haymet, A. D. J.; Rice, Stuart A.
1983-01-01
A recent theory of Haymet, Rice, and Madden (HRM) for the pair and triplet correlation functions is tested at liquid state densities against new molecular dynamics results for the Lennard-Jones (12,6) fluid. The HRM integral equation, based on the Born-Green equation and a topological reduction of the diagrammatic expansion of the triplet correlation function, has been solved for a high temperature state (T*=2.74, ρ*=0.80) and is found to give triplet correlation functions in good agreement with the molecular dynamics results. For a lower-temperature state (T*=0.73, ρ*=0.85), where numerical difficulties have thus far frustrated attempts to obtain a self-consistent solution of the HRM integral equation, direct tests of the HRM closure are made using molecular dynamics pair correlation functions to evaluate the diagrams. Although some striking qualitative features of the triplet correlations are correctly described by the HRM closure for this low-temperature state, the HRM approach is not in quantitative agreement with the molecular dynamics results. Test calculations indicate that the principle source of these errors is the neglect of important higher-order diagrams for the triplet correlation function. A reorganization of the diagrammatic series is suggested which may identify the most important of these neglected diagrams. Additional computer simulation results are also reported for the purely repulsive Weeks-Chandler-Andersen (WCA) ``reference'' fluid and for the underlying hard sphere fluid. The similarity of the pair structures of these fluids, noted by WCA, is also found to hold with high accuracy for the triplet structures. It is suggested that these similarities may be exploited in applying the methods of HRM to the hard sphere fluid.
Hall G. E.; Goncharov, V.
2012-05-29
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.
Hall, G.E.
2011-05-31
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.
Numerical methods for molecular dynamics. [Annual report, April 1, 1991--March 31, 1993
Not Available
1993-08-01
The objective is to find numerical algorithms suitable for large parallel computers that can much more efficiently model the dynamics of macromolecules such as proteins, DNA, and lipids. Emphasis is on the use of integration schemes, notably symplectic schemes, that can use large time steps to produce qualitatively correct simulations for long-time integrations. The goal is to obtain the desired information with the least computational effort, and the methodology is to use mathematical analysis and computational experiments on model problems. The techniques developed are to be tested on realistic molecular models as part of a different, complementary research project involving software development. Among the techniques to be considered, the better known ones are multiple time steps, constraint dynamics, and fast Coulomb solvers.
Correcting the dynamic response of a commercial esophageal balloon-catheter.
Cross, Troy J; Beck, Kenneth C; Johnson, Bruce D
2016-08-01
It is generally recommended that an esophageal balloon-catheter possess an adequate frequency response up to 15 Hz, such that parameters of respiratory mechanics may be quantified with precision. In our experience, however, we have observed that some commercially available systems do not display an ideal frequency response (<8-10 Hz). We therefore investigated whether the poor frequency response of a commercially available esophageal catheter may be adequately compensated using two numerical techniques: 1) an exponential model correction, and 2) Wiener deconvolution. These two numerical techniques were performed on a commercial balloon-catheter interfaced with 0, 1, and 2 lengths of extension tubing (90 cm each), referred to as configurations L0, L90, and L180, respectively. The frequency response of the balloon-catheter in these configurations was assessed by empirical transfer function analysis, and its "working" range was defined as the frequency beyond which more than 5% amplitude and/or phase distortion was observed. The working frequency range of the uncorrected balloon-catheter extended up to only 10 Hz for L0, and progressively worsened with additional tubing length (L90 = 3 Hz, L180 = 2 Hz). Although both numerical methods of correction adequately enhanced the working frequency range of the balloon-catheter to beyond 25 Hz for all length configurations (L0, L90, and L180), Wiener deconvolution consistently provided more accurate corrections. Our data indicate that Wiener deconvolution provides a superior correction of the balloon-catheter's dynamic response, and is relatively more robust to extensions in catheter tube length compared with the exponential correction method. PMID:27402558
Molecular Dynamics and Energy Minimization Based on Embedded Atom Method
Energy Science and Technology Software Center (ESTSC)
1995-03-01
This program performs atomic scale computer simulations of the structure and dynamics of metallic system using energetices based on the Embedded Atom Method. The program performs two types of calculations. First, it performs local energy minimization of all atomic positions to determine ground state and saddle point energies and structures. Second, it performs molecular dynamics simulations to determine thermodynamics or miscroscopic dynamics of the system. In both cases, various constraints can be applied to themore » system. The volume of the system can be varied automatically to achieve any desired external pressure. The temperature in molecular dynamics simulations can be controlled by a variety of methods. Further, the temperature control can be applied either to the entire system or just a subset of the atoms that would act as a thermal source/sink. The motion of one or more of the atoms can be constrained to either simulate the effects of bulk boundary conditions or to facilitate the determination of saddle point configurations. The simulations are performed with periodic boundary conditions.« less
Molecular interferometer to decode attosecond electron-nuclear dynamics.
Palacios, Alicia; González-Castrillo, Alberto; Martín, Fernando
2014-03-18
Understanding the coupled electronic and nuclear dynamics in molecules by using pump-probe schemes requires not only the use of short enough laser pulses but also wavelengths and intensities that do not modify the intrinsic behavior of the system. In this respect, extreme UV pulses of few-femtosecond and attosecond durations have been recognized as the ideal tool because their short wavelengths ensure a negligible distortion of the molecular potential. In this work, we propose the use of two twin extreme UV pulses to create a molecular interferometer from direct and sequential two-photon ionization processes that leave the molecule in the same final state. We theoretically demonstrate that such a scheme allows for a complete identification of both electronic and nuclear phases in the wave packet generated by the pump pulse. We also show that although total ionization yields reveal entangled electronic and nuclear dynamics in the bound states, doubly differential yields (differential in both electronic and nuclear energies) exhibit in addition the dynamics of autoionization, i.e., of electron correlation in the ionization continuum. Visualization of such dynamics is possible by varying the time delay between the pump and the probe pulses. PMID:24591647
Molecular interferometer to decode attosecond electron–nuclear dynamics
Palacios, Alicia; González-Castrillo, Alberto; Martín, Fernando
2014-01-01
Understanding the coupled electronic and nuclear dynamics in molecules by using pump–probe schemes requires not only the use of short enough laser pulses but also wavelengths and intensities that do not modify the intrinsic behavior of the system. In this respect, extreme UV pulses of few-femtosecond and attosecond durations have been recognized as the ideal tool because their short wavelengths ensure a negligible distortion of the molecular potential. In this work, we propose the use of two twin extreme UV pulses to create a molecular interferometer from direct and sequential two-photon ionization processes that leave the molecule in the same final state. We theoretically demonstrate that such a scheme allows for a complete identification of both electronic and nuclear phases in the wave packet generated by the pump pulse. We also show that although total ionization yields reveal entangled electronic and nuclear dynamics in the bound states, doubly differential yields (differential in both electronic and nuclear energies) exhibit in addition the dynamics of autoionization, i.e., of electron correlation in the ionization continuum. Visualization of such dynamics is possible by varying the time delay between the pump and the probe pulses. PMID:24591647
The dynamics of a correctable gyrocompass under conditions of the translational motion of the base
NASA Astrophysics Data System (ADS)
Ryzhkov, L. M.
1986-10-01
An analysis is made of the effect of the static unbalance of the sensitive element of a correctable gyrocompass on its precision under conditions of the translational motion of the base. An expression is obtained for determining the systematic error of the gyrocompass; the translational components of the disturbing moments are then determined by using the method of successive approximations. The additional dynamic error resulting from the static unbalance of the sensitive element of the gyrocompass is determined from the displacement along the oz axis. It is noted that the effect of this displacement cannot be diminished by increasing the time constant of the horizon indicator.
Temperature Effects on Soft Polymeric Nanoparticles: Molecular Dynamics Study
NASA Astrophysics Data System (ADS)
Maskey, Sabina; Grest, Gary S.; Perahia, Dvora
Luminescent polymers collapsed into soft nanoparticles or polydots have emerged as the potential candidates for biomedical applications such as drug delivery and biosensing. Here, using fully atomistic molecular dynamics simulation, the temperatures effects on the stability, internal structure and dynamics of polydots formed by substituted and bare dialkyl paraphenylene ethynylenes (PPEs) will be discussed. We find that with increasing temperature from 300 K to 600K both substituted and bare PPE polydots expand but do not fully unfold and remain in their confined state. As observed visually and by measurement of structure factor S(q), the overall shape of the both type of polydots changes from spherical to elongated with the increase in temperature. These effects are more pronounced for bare PPE polydots which show that interdigitation of side chains in substituted PPE polydots enhances stability. In addition, the side chains are more dynamic than the backbone.. NSF CHE 1308298 2013-2016.
The classical and quantum dynamics of molecular spins on graphene.
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2016-02-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices. PMID:26641019
Molecular dynamics studies of interfacial water at the alumina surface.
Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David
2011-01-01
Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.
The classical and quantum dynamics of molecular spins on graphene
NASA Astrophysics Data System (ADS)
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2016-02-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.
A molecular dynamics study of the ionic liquid, choline acetate.
Willcox, Jon A L; Kim, Hyunjin; Kim, Hyung J
2016-06-01
Structural and dynamic properties of the ionic liquid (IL) choline acetate are studied using molecular dynamics (MD) simulations. The hydroxyl group of choline shows significant hydrogen-bonding interactions with the oxygen atoms of acetate. Nearly all choline cations are found to form a hydrogen bond with acetate anions at 400 K, while about 67% of cations participate in hydrogen-bonding interactions at 600 K. At 400 K, subdiffusive and prominent non-Gaussian behavior persist for t > 10 ns. At 600 K, the usual diffusion regime is obtained after a few hundred ps of subdiffusive behavior. Analysis of reorientational motions of acetate ions, particularly those of their short axes, indicates a high degree of dynamic heterogeneity, in agreement with previous work on different IL systems. PMID:27188287
Rahimi, Mohammad; Arroyo, Marino
2012-07-01
Biological membranes are continuously brought out of equilibrium, as they shape organelles, package and transport cargo, or respond to external actions. Even the dynamics of plain lipid membranes in experimental model systems are very complex due to the tight interplay between the bilayer architecture, the shape dynamics, and the rearrangement of the lipid molecules. We formulate and numerically implement a continuum model of the shape dynamics and lipid hydrodynamics, which describes the bilayer by its midsurface and by a lipid density field for each monolayer. The viscoelastic response of bilayers is determined by the stretching and curvature elasticity, and by the inter-monolayer friction and the membrane interfacial shear viscosity. While the bilayer equilibria are well understood theoretically, dynamical calculations have relied on simplified continuum approaches of uncertain transferability, or on molecular simulations reaching very limited length and time scales. Our approach incorporates the main physics, is fully nonlinear, does not assume predefined shapes, and can access a wide range of time and length scales. We validate it with the well understood tether extension. We investigate the tubular lipid transport between cells, the dynamics of bud absorption by a planar membrane, and the fate of a localized lipid density asymmetry in vesicles. These axisymmetric examples bear biological relevance and highlight the diversity of dynamical regimes that bilayers can experience. PMID:23005476
Dong, Bing; Li, Yan; Han, Xin-Li; Hu, Bin
2016-01-01
For high-speed aircraft, a conformal window is used to optimize the aerodynamic performance. However, the local shape of the conformal window leads to large amounts of dynamic aberrations varying with look angle. In this paper, deformable mirror (DM) and model-based wavefront sensorless adaptive optics (WSLAO) are used for dynamic aberration correction of an infrared remote sensor equipped with a conformal window and scanning mirror. In model-based WSLAO, aberration is captured using Lukosz mode, and we use the low spatial frequency content of the image spectral density as the metric function. Simulations show that aberrations induced by the conformal window are dominated by some low-order Lukosz modes. To optimize the dynamic correction, we can only correct dominant Lukosz modes and the image size can be minimized to reduce the time required to compute the metric function. In our experiment, a 37-channel DM is used to mimic the dynamic aberration of conformal window with scanning rate of 10 degrees per second. A 52-channel DM is used for correction. For a 128 × 128 image, the mean value of image sharpness during dynamic correction is 1.436 × 10(-5) in optimized correction and is 1.427 × 10(-5) in un-optimized correction. We also demonstrated that model-based WSLAO can achieve convergence two times faster than traditional stochastic parallel gradient descent (SPGD) method. PMID:27598161
Extended Molecular Dynamics Methods for Vortex Dynamics in Nano-structured Superconductors
NASA Astrophysics Data System (ADS)
Kato, Masaru; Sato, Osamu
Using improved molecular dynamics simulation method, we study vortex dynamics in nano-scaled superconductors. Heat generations during vortex motion, heat transfer in superconductors, and entropy forces to vortices are incorporated. Also quasi-particle relaxations after vortex motion, and their attractive "retarded" forces to other vortices are incorporated using the condensation-energy field. We show the time development of formation of vortex channel flow in a superconducting Corbino-disk.
NASA Astrophysics Data System (ADS)
Yang, Peng
The focus of this dissertation is the Molecular Dynamics (MD) simulation study of two different systems. In thefirst system, we study the dynamic process of graphene exfoliation, particularly graphene dispersion using ionic surfactants (Chapter 2). In the second system, we investigate the mesoscopic structure of binary solute/ionic liquid (IL) mixtures through the comparison between simulations and corresponding experiments (Chapter 3 and 4). In the graphene exfoliation study, we consider two separation mechanisms: changing the interlayer distance and sliding away the relative distance of two single-layer graphene sheets. By calculating the energy barrier as a function of separation (interlayer or sliding-away) distance and performing sodium dodecyl sulfate (SDS) structure analysis around graphene surface in SDS surfactant/water + bilayer graphene mixture systems, we find that the sliding-away mechanism is the dominant, feasible separation process. In this process, the SDS-graphene interaction gradually replaces the graphene-graphene Van der Waals (VdW) interaction, and decreases the energy barrier until almost zero at critical SDS concentration. In solute/IL study, we investigate nonpolar (CS2) and dipolar (CH 3CN) solute/IL mixture systems. MD simulation shows that at low concentrations, IL is nanosegregated into an ionic network and nonpolar domain. It is also found that CS2 molecules tend to be localized into the nonpolar domain, while CH3CN interacts with nonpolar domain as well as with the charged head groups in the ionic network because of its amphiphilicity. At high concentrations, CH3CN molecules eventually disrupt the nanostructural organization. This dissertation is organized in four chapters: (1) introduction to graphene, ionic liquids and the methodology of MD; (2) MD simulation of graphene exfoliation; (3) Nanostructural organization in acetonitrile/IL mixtures; (4) Nanostructural organization in carbon disulfide/IL mixtures; (5) Conclusions. Results
Papaleo, Elena
2015-01-01
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210
Dynamic outflow tract obstruction in congenitally corrected transposition of the great arteries.
Zurick, Andrew O; Menon, Venu
2010-08-01
Congenitally corrected transposition of the great arteries (CCTGA) is a rare form of congenital heart disease, constituting 0.5% of all congenital heart defects. The incidence of left ventricle (non-systemic ventricle) outflow tract obstruction ranges between 44 and 57%. Herein, we present the case of a 45 year old woman with CCTGA with progressively worsening dyspnea who had been referred for surgical correction of severe systemic ventricle (morphologic right ventricle) atrio-ventricular valve (tricuspid valve) regurgitation. Cardiac magnetic resonance imaging (CMR) and transesophageal imaging (TEE) demonstrated severe systemic ventricle (morphologic right ventricle) contractile dysfunction, as well as dynamic non-systemic ventricle (morphologic left ventricle) outflow tract obstruction due to systolic anterior motion (SAM) of the non-systemic ventricle (morphologic left ventricle) atrio-ventricular valve (mitral valve) with a large membranous ventricular septal aneurysm that protrudes into the outflow tract of the non-systemic ventricle (morphologic left ventricle). Ultimately, our patient was felt to be too high-risk for surgical correction and a course of medical therapy has been pursued. PMID:20191324
Molecular dynamics modeling and characterization of graphene/polymer nanocomposites
NASA Astrophysics Data System (ADS)
Rahman, Rezwanur
The current work focuses on the characterization of graphene based nanocomposites using molecular dynamic simulation and multiscale modeling approaches. Both graphene-epoxy and graphene-cellulose nanocomposites were considered in this study. A hierarchical multiscale modeling approach has been proposed using peridynamics and molecular dynamics simulation. Firstly, the mechanical properties of crosslinked graphene/epoxy (G-Ep) nanocomposites were investigated by molecular mechanics (MM) and molecular dynamics (MD) simulations. The influence of graphene's weight concentration, aspect ratio and dispersion on stress-strain response and elastic properties were studied. The results show significant improvement in Young's modulus and shear modulus for the G-Ep system in comparison to the neat epoxy resin. It appears that the RDF, molecular energy and aspect ratios are influenced by both graphene concentrations and aspect ratios. The graphene concentrations in the range of 1-3% are seen to improve Young's modulus and shorter graphenes are observed to be more effective than larger ones. In addition, the dispersed graphene system is more promising in enhancing in-plane elastic modulus than the agglomerated graphene system. The cohesive and pullout forces versus displacements data were plotted under normal and shear modes in order to characterize interfacial properties. The cohesive force is significantly improved by attaching the graphene with a chemical bond at the graphene-epoxy interface. In the second part of the work, cellulose was considered to study the mechanical properties of graphene-cellulose bionanocomposite. Similar to graphene-epoxy systems, the effect of graphene dispersion and agglomeration were studied in the stress-strain plots of graphene-cellulose system. A pcff forcefield was used to define intermolecular and intramolecular interactions. The effect of graphene's aspect ratio and weight concentration on the structural property of each unitcell was
Molecular dynamics studies of protein folding and aggregation
NASA Astrophysics Data System (ADS)
Ding, Feng
This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism
Computational Studies on the Anharmonic Dynamics of Molecular Clusters
NASA Astrophysics Data System (ADS)
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 Simulation of Carbon Nanotube Based Gears
NASA Technical Reports Server (NTRS)
Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)
1996-01-01
We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.
Dynamical Simulations of Molecular Clouds in the Galactic Center
NASA Astrophysics Data System (ADS)
Salas, Jesus; Morris, Mark
2016-06-01
The formation of the central massive cluster of young stars orbiting the Galactic black hole, Sgr A*, has been modeled by several groups by invoking an almost radially infalling molecular cloud that interacts with the black hole and creates a dense, gaseous disk in which stars can then form. However, the dynamical origin of such a cloud remains an open question. We present simulations of the central 30-100 pc of the Milky Way, starting from a population of molecular clouds located in a disk with scale height of ~30 pc, using the N-body/smoothed-particle hydrodynamics code, Gadget2. We followed the dynamical evolution of clouds in a galactic potential that includes a bar to explore whether cloud collisions or a succession of cloud scatterings can remove sufficient angular momentum from a massive cloud to endow it with a predominantly radial orbit. Initial results illustrate the importance of tidal shear; while dense cloud cores remain identifiable for extended periods of time, much of the molecular mass ends up in tidal streams, so cannot be deflected onto low angular momentum orbits by their mutual interactions. At the completion of our ongoing computations, we will report on whether the cloud cores can undergo sufficient scattering to achieve low-angular-momentum orbits.
Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics
Yu, H.G.; Muckerman, J.T.
2010-06-01
The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.
Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics
Yu H. G.; Muckerman, J.T.
2012-05-29
The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.
Study of critical dynamics in fluids via molecular dynamics in canonical ensemble.
Roy, Sutapa; Das, Subir K
2015-12-01
With the objective of understanding the usefulness of thermostats in the study of dynamic critical phenomena in fluids, we present results for transport properties in a binary Lennard-Jones fluid that exhibits liquid-liquid phase transition. Various collective transport properties, calculated from the molecular dynamics (MD) simulations in canonical ensemble, with different thermostats, are compared with those obtained from MD simulations in microcanonical ensemble. It is observed that the Nosé-Hoover and dissipative particle dynamics thermostats are useful for the calculations of mutual diffusivity and shear viscosity. The Nosé-Hoover thermostat, however, as opposed to the latter, appears inadequate for the study of bulk viscosity. PMID:26687057
Recovering position-dependent diffusion from biased molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-01
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica® package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics. Given known free energy and D, the package can also generate diffusive trajectories.
Recovering position-dependent diffusion from biased molecular dynamics simulations
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-28
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.
Recovering position-dependent diffusion from biased molecular dynamics simulations.
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-28
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica(®) package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics. Given known free energy and D, the package can also generate diffusive trajectories. PMID:24588150
Validating clustering of molecular dynamics simulations using polymer models
2011-01-01
Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the
NASA Astrophysics Data System (ADS)
Gabdulkhakov, A. G.; Kljashtorny, V. G.; Dontsova, M. V.
2015-11-01
In thylakoids of cyanobacteria and other photosynthetic organisms, the light-induced production of molecular oxygen is catalyzed by the giant lipid-pigment-protein complex called photosystem II (PSII). The oxygen-evolving complex is buried deep in the lumenal part of PSII, and dioxygen molecules need to pass through the protein environment in order to leave the active site of the enzyme free. Previous studies aimed at finding oxygen channels in PSII were based on either an analysis of the cavities within is static structure or experiments on the insertion of noble gas molecules into PSII crystals under elevated pressure. In these studies, some possible exit pathways for the molecules were found and the static positions of molecular oxygen were determined. In the present work, the oxygen movement in the transport system of PSII is simulated by molecular dynamics.
2012-01-01
In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra. PMID:22904696
Giese, Timothy J; York, Darrin M
2016-06-14
A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed. PMID:27171914
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficientmore » as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.« less
Error and efficiency of replica exchange molecular dynamics simulations
Rosta, Edina; Hummer, Gerhard
2009-01-01
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977
Error and efficiency of replica exchange molecular dynamics simulations.
Rosta, Edina; Hummer, Gerhard
2009-10-28
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.
Femtosecond molecular dynamics of tautomerization in model base pairs
NASA Astrophysics Data System (ADS)
Douhal, A.; Kim, S. K.; Zewail, A. H.
1995-11-01
HYDROGEN bonds commonly lend robustness and directionality to molecular recognition processes and supramolecular structures1,2. In particular, the two or three hydrogen bonds in Watson-Crick base pairs bind the double-stranded DNA helix and determine the complementarity of the pairing. Watson and Crick pointed out3, however, that the possible tautomers of base pairs, in which hydrogen atoms become attached to the donor atom of the hydrogen bond, might disturb the genetic code, as the tautomer is capable of pairing with different partners. But the dynamics of hydrogen bonds in general, and of this tautomerization process in particular, are not well understood. Here we report observations of the femtosecond dynamics of tautomerization in model base pairs (7-azaindole dimers) containing two hydrogen bonds. Because of the femtosecond resolution of proton motions, we are able to examine the cooperativity of formation of the tautomer (in which the protons on each base are shifted sequentially to the other base), and to determine the characteristic timescales of the motions in a solvent-free environment. We find that the first step occurs on a timescale of a few hundred femtoseconds, whereas the second step, to form the full tautomer, is much slower, taking place within several picoseconds; the timescales are changed significantly by replacing hydrogen with deuterium. These results establish the molecular basis of the dynamics and the role of quantum tunnelling.
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.
2000-10-10
Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In most cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.
Towards imaging of ultrafast molecular dynamics using FELs
NASA Astrophysics Data System (ADS)
Rouzée, A.; Johnsson, P.; Rading, L.; Hundertmark, A.; Siu, W.; Huismans, Y.; Düsterer, S.; Redlin, H.; Tavella, F.; Stojanovic, N.; Al-Shemmary, A.; Lépine, F.; Holland, D. M. P.; Schlatholter, T.; Hoekstra, R.; Fukuzawa, H.; Ueda, K.; Vrakking, M. J. J.
2013-08-01
The dissociation dynamics induced by a 100 fs, 400 nm laser pulse in a rotationally cold Br2 sample was characterized by Coulomb explosion imaging (CEI) using a time-delayed extreme ultra-violet (XUV) FEL pulse, obtained from the Free electron LASer in Hamburg (FLASH). The momentum distribution of atomic fragments resulting from the 400 nm-induced dissociation was measured with a velocity map imaging spectrometer and used to monitor the internuclear distance as the molecule dissociated. By employing the simultaneously recorded in-house timing electro-optical sampling data, the time resolution of the final results could be improved to 300 fs, compared to the inherent 500 fs time-jitter of the FEL pulse. Before dissociation, the Br2 molecules were transiently ‘fixed in space’ using laser-induced alignment. In addition, similar alignment techniques were used on CO2 molecules to allow the measurement of the photoelectron angular distribution (PAD) directly in the molecular frame (MF). Our results on MFPADs in aligned CO2 molecules, together with our investigation of the dissociation dynamics of the Br2 molecules with CEI, show that information about the evolving molecular structure and electronic geometry can be retrieved from such experiments, therefore paving the way towards the study of complex non-adiabatic dynamics in molecules through XUV time-resolved photoion and photoelectron spectroscopy.
Molecular-dynamics simulations of void collapse in shocked model-molecular solids
NASA Astrophysics Data System (ADS)
Mintmire, J. W.; Robertson, D. H.; White, C. T.
1994-06-01
We have carried out a series of molecular-dynamics simulations on a model three-dimensional molecular solid to study the dynamics of shock-induced collapse of void defects. Molecular-dynamics methods were used for a model system of identical particles arranged as diatomic molecules aligned with the center of mass of each molecule at fcc lattice sites, using a \\{111\\} layering for the two-dimensional boundary conditions. The diatoms were internally coupled via a harmonic potential; all other interactions were modeled with Morse potentials between all particles other than the immediate diatomic partner. Using this model, we have investigated the effect of a cylindrical void at right angles to the direction of layering (and impact). Depending on the strength of the incident shock wave, the void is found to collapse either smoothly and symmetrically (like a balloon gradually losing air), or asymmetrically and turbulently. In the latter case, we note the transient formation (for periods of several hundreds of femtoseconds) of ``hot spots'' at the void location both in terms of the local effective temperature and the vibrational energies of the diatoms.
The integration of molecular dynamics simulations with imposed temperature and stress
NASA Astrophysics Data System (ADS)
Lill, J. V.
1994-04-01
Nonlinear molecular dynamics equations for the simulation of crystals under the conditions of imposed temperature and tensorial pressure are summarized. The physical effects included in these equations, but absent from previous linear and nonlinear theories, is the elastic response of the material being modeled. The physical effect is expressed through satisfaction of the nonlinear tensorial virial theorem. We transform these equations in Hamiltonian form to an equivalent set of Lagrangian equations, and present an algorithm for their numerical integration. The method uses a combination of Verlet and leap-frog algorithms to integrate the atomic positions and velocities as scaled by dynamical lattice vectors of the crystal, the elements of deformation gradient and its velocity, and the Nosé-Hoover time scale and generalized friction. A consistent error analysis is performed for the combined integration of each degree of freedom. A symmetrization procedure to eliminate rigid rotations of the crystal is introduced. Molecular dynamics simulations of a Martensitic tranformation are presented that demonstrate the validity of the nonlinear tensorial virial theorem throughout the transformation; complementary Metropolis Monte Carlo simulations verify that the correct distribution is sampled.
Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors
NASA Astrophysics Data System (ADS)
Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery
2015-05-01
Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.
Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.
Graziani, F R; Bauer, J D; Murillo, M S
2014-09-01
Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD
Molecular Dynamics Simulations of Fracture of Model Epoxies
STEVENS,MARK J.
2000-01-18
The failure of thermosetting polymer adhesives is an important problem which particularly lacks understanding from the molecular viewpoint. While linear elastic fracture mechanics works well for such polymers far from the crack tip, the method breaks down near the crack tip where large plastic deformation occurs and the molecular details become important [1]. Results of molecular dynamics simulations of highly crosslinked polymer networks bonded to a solid surface are presented here. Epoxies are used as the guide for modeling. The focus of the simulations is the network connectivity and the interfacial strength. In a random network, the bond stress is expected to vary, and the most stressed bonds will break first [2]. Crack initiation should occur where a cluster of highly constrained bonds exists. There is no reason to expect crack initiation to occur at the interface. The results to be presented show that the solid surface limits the interfacial bonding resulting in stressed interfacial bonds and interfacial fracture. The bonds in highly-crosslinked random networks do not become stressed as expected. The sequence of molecular structural deformations that lead to failure has been determined and found to be strongly dependent upon the network connectivity. The structure of these networks and its influence on the stress-strain behavior will be discussed in general. A set of ideal, ordered networks have been constructed to manipulate the deformation sequence to achieve different fracture modes (i.e. cohesive vs. adhesive).
Generalized master equations for exciton dynamics in molecular systems
NASA Astrophysics Data System (ADS)
Schreiber, Michael; May, V.
1995-02-01
The paper demonstrates the applicability of a special type of density matrix theory for the derivation of generalized Master equations. The density matrix theory has been formulated for the description of the dissipative electron transfer dynamics in molecular complexes. The theoretical approach is based on a representation of the density matrix in appropriately taken diabatic electron-vibrational states. Dissipative effects are taken into account by a coupling of these states to further vibrational modes of the molecular complex as well as to environmental degrees of freedom. The approach is applied to a two-center system as well as to a molecular chain. Memory kernels are derived in second order with respect to the inter-center coupling. The kernels are discussed under the assumption of a quick intra-center relaxation for a part of the vibrational modes as well as for all vibrational modes. Standard expressions for the transition rates between different sites are extended to include finite life times of the vibrational levels. Results which have been obtained in the study of the so-called spin boson model can be simply reproduced. The application of the derived generalized Master equations to the investigation of the motion of Frenkel excitons in molecular chains is also presented.
Nanochannel flow past permeable walls via molecular dynamics
NASA Astrophysics Data System (ADS)
Xie, Jian-Fei; Cao, Bing-Yang
2016-07-01
The nanochannel flow past permeable walls with nanopores is investigated by molecular dynamics (MD) simulations, including the density distribution, velocity field, molecular penetration mechanism and surface friction coefficient. A low density distribution has been found at the gas-wall interface demonstrating the low pressure region. In addition, there exists a jump of the gas density on the permeable surface, which indicates the discontinuity of the density distribution across the permeable surface. On the other hand, the nanoscale vortices are observed in nanopores of the permeable wall, and the reduced mass flux of the flow in nanopores results in a shifted hydrodynamic boundary above the permeable surface. Particularly the slip length of the gas flow on the permeable surface is pronounced a non-linear function of the molecular mean free path, which produces a large value of the tangential momentum accommodation coefficient (TMAC) and a big portion of the diffusive refection. Moreover, the gas-gas interaction and multi-collision among gas molecules may take place in nanopores, which contribute to large values of TMAC. Consequently the boundary friction coefficient on the permeable surface is increased because of the energy dissipation consumed by the nanoscale vortices in nanopores. The molecular boundary condition provides us with a new picture of the nanochannel flow past the permeable wall with nanopores.
Implementation of Green's function molecular dynamics: An extension to LAMMPS
NASA Astrophysics Data System (ADS)
Kong, Ling Ti; Bartels, Guido; Campañá, Carlos; Denniston, Colin; Müser, Martin H.
2009-06-01
The Green's function molecular dynamics method, which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only the surface atoms, was implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. This was done in the style of fixes. The first fix, FixGFC, measures the elastic stiffness coefficients for a (small) solid block of a given material by making use of the fluctuation-dissipation theorem. With the help of the second fix, FixGFMD, the coefficients obtained from FixGFC can then be used to compute the elastic forces for a (large) block of the same material. Both fixes are designed to be run in parallel and to exploit the functions provided by LAMMPS. Program summaryProgram title: FixGFC/FixGFMD Catalogue identifier: AECW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 33 469 No. of bytes in distributed program, including test data, etc.: 1 383 631 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Parallelized via MPI RAM: Depends on the problem Classification: 7.7 External routines: MPI, FFTW 2.1.5 ( http://www.fftw.org/), LAMMPS version May 21, 2008 ( http://lammps.sandia.gov/) Nature of problem: Using molecular dynamics to study elastically deforming solids imposes very high computational costs because portions of the solid far away from the interface or contact points need to be included in the simulation to reproduce the effects of long-range elastic deformations. Green's function molecular dynamics (GFMD) incorporates the full elastic response of semi-infinite solids so that only surface atoms have to be considered in molecular dynamics simulations, thus
Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation
NASA Technical Reports Server (NTRS)
Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.
2007-01-01
The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.
Molecular Dynamics Simulations of Homogeneous Crystallization in Polymer Melt
NASA Astrophysics Data System (ADS)
Kong, Bin
2015-03-01
Molecular mechanisms of homogeneous nucleation and crystal growth from the melt of polyethylene-like polymer were investigated by molecular dynamics simulations. The crystallinity was determined by using the site order parameter method (SOP), which described local order degree around an atom. Snapshots of the simulations showed evolution of the nucleation and the crystal growth through SOP images clearly. The isothermal crystallization kinetics was determined at different temperatures. The rate of crystallization, Kc, and the Avrami exponents, n, were determined as a function of temperature. The forming of nucleis was traced to reveal that the nucleis were formed with more ordered cores and less ordered shells. A detailed statistical analysis of the MD snapshots and trajectories suggested conformations of the polymer chains changed smoothly from random coil to chain folded lamella in the crystallization processes.
Molecular encryption and reconfiguration for remodeling of dynamic hydrogels.
Li, Shihui; Gaddes, Erin R; Chen, Niancao; Wang, Yong
2015-05-11
Dynamic materials have been widely studied for regulation of cell adhesion that is important to a variety of biological and biomedical applications. These materials can undergo changes mainly through one of the two mechanisms: ligand release in response to chemical, physical, or biological stimuli, and ligand burial in response to mechanical stretching or the change of electrical potential. This study demonstrates an encrypted ligand and a new hydrogel that are capable of inducing and inhibiting cell adhesion, which is controlled by molecular reconfiguration. The ligand initially exhibits an inert state; it can be reconfigured into active and inert states by using unblocking and recovering molecules in physiological conditions. Since molecular reconfiguration does not require the release of the ligand from the hydrogels, inhibiting and inducing cell adhesion on the hydrogels can be repeated for multiple cycles. PMID:25808026
Spotting the difference in molecular dynamics simulations of biomolecules.
Sakuraba, Shun; Kono, Hidetoshi
2016-08-21
Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (LDA-ITER) to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the "difference" between two trajectories. PMID:27544096
Permeance of H2 through porous graphene from molecular dynamics
NASA Astrophysics Data System (ADS)
Liu, Hongjun; Dai, Sheng; Jiang, De-en
2013-12-01
A recent experiment (Koenig et al., 2012 [15]) demonstrated the capability of porous graphene as one-atom-thin membrane to separate gases by molecular sieving. A quantitative connection between the measured leak rate and the simulated gas permeance has yet to be established. Using H2 as a model gas, here we determine its permeance through porous graphene from molecular dynamics (MD) simulations. Trajectories are used to directly obtain H2 flux, pressure drop across the graphene membrane, and subsequently, H2 permeance. The permeance is determined to be on the order of 105 GPU (gas permeance unit) for pressure driving forces ranging from 2 to 163 atm. By relating to the experimental leak rate, we then use the permeation data to estimate the pore density in the experimentally created porous graphene.
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane
NASA Astrophysics Data System (ADS)
Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping
2012-12-01
We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.
Structure factor and rheology of chain molecules from molecular dynamics
NASA Astrophysics Data System (ADS)
Castrejón-González, Omar; Castillo-Tejas, Jorge; Manero, Octavio; Alvarado, Juan F. J.
2013-05-01
Equilibrium and non-equilibrium molecular dynamics were performed to determine the relationship between the static structure factor, the molecular conformation, and the rheological properties of chain molecules. A spring-monomer model with Finitely Extensible Nonlinear Elastic and Lennard-Jones force field potentials was used to describe chain molecules. The equations of motion were solved for shear flow with SLLOD equations of motion integrated with Verlet's algorithm. A multiple time scale algorithm extended to non-equilibrium situations was used as the integration method. Concentric circular patterns in the structure factor were obtained, indicating an isotropic Newtonian behavior. Under simple shear flow, some peaks in the structure factor were emerged corresponding to an anisotropic pattern as chains aligned along the flow direction. Pure chain molecules and chain molecules in solution displayed shear-thinning regions. Power-law and Carreau-Yasuda models were used to adjust the generated data. Results are in qualitative agreement with rheological and light scattering experiments.
NASA Technical Reports Server (NTRS)
Kiselev, V. V.; Rodionov, B. N.
1974-01-01
The linear and angular motions of the Zond 6 and Zond 8 spacecraft imaging camera during the exposure cause displacements of the optical image points. In the case of instantaneous exposure of each individual point and the nonsimultaneous exposure of the complete frame, this leads to finite geometric shifts of the points without causing blurring of the photographic image. Therefore, when measuring the resulting photographic pictures, the problem arises of reducing the picture point positions to a common instant of time. This reduction is performed by means of dynamic corrections to the measured picture point coordinates. These corrections are found by using formulas of dynamic photogrammetry. Their use with the Zond space probe photographs is described.
Finite-N corrections to Vlasov dynamics and the range of pair interactions
NASA Astrophysics Data System (ADS)
Gabrielli, Andrea; Joyce, Michael; Morand, Jules
2014-12-01
We explore the conditions on a pair interaction for the validity of the Vlasov equation to describe the dynamics of an interacting N -particle system in the large N limit. Using a coarse graining in phase space of the exact Klimontovich equation for the N -particle system, we evaluate, neglecting correlations of density fluctuations, the scalings with N of the terms describing the corrections to the Vlasov equation for the coarse-grained one-particle phase space density. Considering a generic interaction with radial pair force F (r ) , with F (r ) ˜1 /rγ at large scales, and regulated to a bounded behavior below a "softening" scale ɛ , we find that there is an essential qualitative difference between the cases γ
Discrete Molecular Dynamics Distinguishes Nativelike Binding Poses from Decoys in Difficult Targets
Proctor, Elizabeth A.; Yin, Shuangye; Tropsha, Alexander; Dokholyan, Nikolay V.
2012-01-01
Virtual screening is one of the major tools used in computer-aided drug discovery. In structure-based virtual screening, the scoring function is critical to identifying the correct docking pose and accurately predicting the binding affinities of compounds. However, the performance of existing scoring functions has been shown to be uneven for different targets, and some important drug targets have proven especially challenging. In these targets, scoring functions cannot accurately identify the native or near-native binding pose of the ligand from among decoy poses, which affects both the accuracy of the binding affinity prediction and the ability of virtual screening to identify true binders in chemical libraries. Here, we present an approach to discriminating native poses from decoys in difficult targets for which several scoring functions failed to correctly identify the native pose. Our approach employs Discrete Molecular Dynamics simulations to incorporate protein-ligand dynamics and the entropic effects of binding. We analyze a collection of poses generated by docking and find that the residence time of the ligand in the native and nativelike binding poses is distinctly longer than that in decoy poses. This finding suggests that molecular simulations offer a unique approach to distinguishing the native (or nativelike) binding pose from decoy poses that cannot be distinguished using scoring functions that evaluate static structures. The success of our method emphasizes the importance of protein-ligand dynamics in the accurate determination of the binding pose, an aspect that is not addressed in typical docking and scoring protocols. PMID:22225808
Molecular dynamics study of V 2O 5 glass
NASA Astrophysics Data System (ADS)
Seshasayee, M.; Muruganandam, K.
1998-01-01
Structure of V 2O 5 glass has been simulated by constant volume molecular dynamics technique. It was found that the glass is made up of a mixture of corner sharing VO 4, VO 5 and VO 6 polyhedra with VO 5 dominating the matrix, having a 75% share of the total. Angular distribution of OVO bond angle shows VO 4 to be a tetrahedron, VO 5 to be square pyramidal and VO 6 to be an octahedron. Extensive bridging amongst the VO n polyhedra in all directions is observed.
Using collective variables to drive molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme
2013-12-01
A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.
Molecular dynamics simulation of threshold displacement energies in zircon
Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.
2009-10-15
Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different interatomic potentials. For each sublattice, the simulation was repeated from different initial conditions to estimate the uncertainty in the calculated value of Ed. The displacement threshold energies vary considerably with crystallographic direction and sublattice. The average displacement energy calculated with a recently developed transferable potential is about 120 and 60 eV for cations and anions, respectively. The oxygen displacement energy shows good agreement with experimental estimates in ceramics.
Multiple Point Dynamic Gas Density Measurements Using Molecular Rayleigh Scattering
NASA Technical Reports Server (NTRS)
Seasholtz, Richard; Panda, Jayanta
1999-01-01
A nonintrusive technique for measuring dynamic gas density properties is described. Molecular Rayleigh scattering is used to measure the time-history of gas density simultaneously at eight spatial locations at a 50 kHz sampling rate. The data are analyzed using the Welch method of modified periodograms to reduce measurement uncertainty. Cross-correlations, power spectral density functions, cross-spectral density functions, and coherence functions may be obtained from the data. The technique is demonstrated using low speed co-flowing jets with a heated inner jet.
Optimized explicit-solvent replica exchange molecular dynamics from scratch.
Nadler, Walter; Hansmann, Ulrich H E
2008-08-28
Replica exchange molecular dynamics (REMD) simulations have become an important tool to study proteins and other biological molecules in silico. However, such investigations require considerable, and often prohibitive, numerical effort when the molecules are simulated in explicit solvents. In this communication we show that in this case the cost can be minimized by choosing the number of replicas as N(opt) approximately 1+0.594 radical C ln(Tmax/Tmin), where C is the specific heat, and the temperatures distributed according to Ti(opt) approximately T min(Tmax/Tmin)(i-1)/(N-1). PMID:18671362
Molecular dynamics simulation of bicrystalline metal surface treatment
Nikonov, A. Yu.
2015-10-27
The paper reports the molecular dynamics simulation results on the behavior of a copper crystallite in local frictional contact. The crystallite has a perfect defect-free structure and contains a high-angle grain boundary of type Σ5. The influence of the initial structure on the specimen behavior under loading was analyzed. It is shown that nanoblocks are formed in the subsurface layer. The atomic mechanism of nanofragmentation was studied. A detailed analysis of atomic displacements in the blocks showed that the displacements are rotational. Calculations revealed that the misorientation angle of formed nanoblocks along different directions does not exceed 2 degrees.
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
Mugnai, Mauro L.; Elber, Ron
2015-01-07
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.
The A = 8 isotriplet in Fermionic Molecular Dynamics
NASA Astrophysics Data System (ADS)
Henninger, KR
2016-06-01
Nuclear structure of the A = 8 isotriplet is investigated in the Fermionic Molecular Dynamics (FMD) model. All three nuclei have importance to astrophysics, and exhibit clustering or haloes. FMD uses a wave-packet basis and is well-suited for modelling such structures. For a multiconfiguration treatment we construct the many-body Hilbert space from antisymmetrised angular-momentum projected 8-particle states. First results show formation of a proton halo in 8B, and reasonable reproduction of the T =1 states in 8Be.
EPR, NMR and molecular dynamics in fluoride glasses
NASA Astrophysics Data System (ADS)
Silly, G.; Buzaré, J. Y.; Bureau, B.; Legein, C.; Boulard, B.
1999-11-01
This paper deals with the method of investigation of local order in Transition Metal Fluoride Glasses that has been developed in the past few years using magnetic resonance techniques associated to molecular dynamics calculations. The results presented here will concern lead fluoride PZG (PbF2-ZnF2-GaF3) glasses of the PbF2-MtIIF2-MtIIIF3 family, but the method remains valid for any other disordered compound. The only limitations are that the sample may be doped with transition metal ions (S⩾1) for EPR measurements or contain quadrupolar nuclei (I⩾1) to perform NMR investigations.
Molecular Dynamics Trajectory Compression with a Coarse-Grained Model
Cheng, Yi-Ming; Gopal, Srinivasa Murthy; Law, Sean M.; Feig, Michael
2012-01-01
Molecular dynamics trajectories are very data-intensive thereby limiting sharing and archival of such data. One possible solution is compression of trajectory data. Here, trajectory compression based on conversion to the coarse-grained model PRIMO is proposed. The compressed data is about one third of the original data and fast decompression is possible with an analytical reconstruction procedure from PRIMO to all-atom representations. This protocol largely preserves structural features and to a more limited extent also energetic features of the original trajectory. PMID:22025759
Higher-order symplectic Born-Oppenheimer molecular dynamics
Niklasson, Anders; Bock, Nicolas; Challacombe, Matt; Odell, Anders; Delin, Anna; Johansson, Borje
2009-01-01
The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics (TR-BOMD) enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the 6th order have been adapted and optimized to TR-BOMD in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements.
Easy creation of polymeric systems for molecular dynamics with Assemble!
NASA Astrophysics Data System (ADS)
Degiacomi, Matteo T.; Erastova, Valentina; Wilson, Mark R.
2016-05-01
We present Assemble!, a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. The program is controlled either via command line or an intuitive Graphical User Interface, and runs on all major operating systems. Assemble! allows the creation of a desired system of polymer chains from constituent monomers, packs the chains into a box according to the required concentration and returns all the files needed for simulation with Gromacs. We illustrate the capabilities of Assemble! by demonstrating the easy preparation of a 300 monomers-long polyisoprene in hexane, and a heterogeneous mixture of polybutadiene.
Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics
NASA Astrophysics Data System (ADS)
Mathiazhagan, S.; Anup, S.
2016-08-01
Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.
Field-free molecular alignment for probing collisional relaxation dynamics
NASA Astrophysics Data System (ADS)
Vieillard, Th.; Chaussard, F.; Billard, F.; Sugny, D.; Faucher, O.; Ivanov, S.; Hartmann, J.-M.; Boulet, C.; Lavorel, B.
2013-02-01
We report the experimental study of field-free molecular alignment in CO2 gas mixtures induced by intense femtosecond laser pulses in the presence of collisional processes. We demonstrate that the alignment signals exhibit specific features due to nontrivial collisional propensity rules that tend to preserve the orientation of the rotational angular momentum of the molecules. The analysis is performed with a quantum approach based on the modeling of rotational J- and M-dependent state-to-state transfer rates. The present work paves the way for strong-field spectroscopy of collisional dynamics.
Molecular dynamics study of temperature behavior in a graphene nanoribbon
NASA Astrophysics Data System (ADS)
Wang, Xianqiao
2014-01-01
Unlike an independent variable in classical continuum mechanics, temperature at molecular dynamics simulation is perceived as a spatiotemporal averaged quantity from the velocity field of atoms in system of interest. Following this definition, an intriguing correlation between displacement and temperature in graphene nanoribbon under impulsive loading has been captured at the early stage of simulation to demonstrate that temperature variation along a specific direction behaves like a wave motion, while at the end of simulation temperature field reaches to a steady state like a classical diffusion equation of temperature. This riveting phenomenon offers insights into the thermal-mechanical coupling phenomena of nanodevices.
Molecular dynamics simulation of hollow thick-walled cylinder collapse
Nikonov, A. Yu.
2015-10-27
The generation and evolution of plastic deformation in a hollow single-crystal cylinder under high-rate axisymmetric loading were studied. An advantage of the proposed loading scheme is that all loading modes are applied simultaneously within the chosen crystallographic plane of the cylinder base and different strain degrees are achieved along the specimen cross section. Molecular dynamics simulation was performed to show that the achievement of a certain strain causes the formation of structural defects on the inner surface of the specimen. The obtained results can be used to explain the main plastic deformation mechanisms of crystalline solids.
Molecular Dynamics Simulations Of Nanometer-Scale Feature Etch
Vegh, J. J.; Graves, D. B.
2008-09-23
Molecular dynamics (MD) simulations have been carried out to examine fundamental etch limitations. Beams of Ar{sup +}, Ar{sup +}/F and CF{sub x}{sup +} (x = 2,3) with 2 nm diameter cylindrical confinement were utilized to mimic 'perfect' masks for small feature etching in silicon. The holes formed during etch exhibit sidewall damage and passivation as a result of ion-induced mixing. The MD results predict a minimum hole diameter of {approx}5 nm after post-etch cleaning of the sidewall.
A molecular dynamics study of freezing in a confined geometry
NASA Technical Reports Server (NTRS)
Ma, Wen-Jong; Banavar, Jayanth R.; Koplik, Joel
1992-01-01
The dynamics of freezing of a Lennard-Jones liquid in narrow channels bounded by molecular walls is studied by computer simulation. The time development of ordering is quantified and a novel freezing mechanism is observed. The liquid forms layers and subsequent in-plane ordering within a layer is accompanied by a sharpening of the layer in the transverse direction. The effects of channel size, the methods of quench, the liquid-wall interaction and the roughness of walls on the freezing mechanism are elucidated. Comparison with recent experiments on freezing in confined geometries is presented.
Generalized extended Lagrangian Born-Oppenheimer molecular dynamics
Niklasson, Anders M. N. Cawkwell, Marc J.
2014-10-28
Extended Lagrangian Born-Oppenheimer molecular dynamics based on Kohn-Sham density functional theory is generalized in the limit of vanishing self-consistent field optimization prior to the force evaluations. The equations of motion are derived directly from the extended Lagrangian under the condition of an adiabatic separation between the nuclear and the electronic degrees of freedom. We show how this separation is automatically fulfilled and system independent. The generalized equations of motion require only one diagonalization per time step and are applicable to a broader range of materials with improved accuracy and stability compared to previous formulations.
Molecular Dynamics Simulations of Hexadecane/Silicalite Interfaces
Grest, G.S.; Webb, E.B.
1999-01-20
The interface between liquid hexadecane and the (010) surface of silicalite was studied by molecular dynamics. The structure of molecules in the interracial region is influenced by the presence of pore mouths on the silicalite surface. For this surface, whose pores are the entrances to straight channels, the concentration profile for partially absorbed molecules is peaked around 10 monomers inside the zeolite. No preference to enter or exit the zeolite based on absorption length is observed except for very small or very large absorption lengths. We also found no preferential conformation of the unabsorbed tails for partially absorbed molecules.
Molecular dynamics of adsorption and segregation from an Alkane mixture
Xia, T.K.; Landman, U. )
1993-09-03
Adsorption and segregation of n-hexadecane molecules from an equal by weight mixture of n-hexadecane and n-hexane to an Au(001) surface at 315 kelvin are studied with the use of molecular dynamics simulations. Preferential adsorption of n-hexadecane at the solid-to-liquid interface together with subsequent layer-by-layer growth of an ordered, wetting interface were observed. The long chains penetrate and adsorb at the interfacial layer by means of a sequential segmental mechanism involving end-segment anchoring and displacive desorption of preadsorbed n-hexane molecules.
Tight-binding molecular-dynamics simulation of buckyball collisions
Zhang, B.L.; Wang, C.Z.; Chan, C.T.; Ho, K.M. )
1993-04-01
The collisions between C[sub 60] molecules are studied by tight-binding molecular-dynamics simulations. We observe three different regimes of behavior as the collisions become more and more energetic: bouncing, fusion, and fragmentation. The critical energies for fusion and fragmentation as well as details of the energy transfer during the collision process for the bouncing regime are investigated. The collisions at several specific energies and orientations produce interesting novel molecules, such as small baby cages, caps, and even a Russian-Doll molecule in which a small cage is trapped in a bigger one. 28 refs., 5 figs., 2 tabs.
Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems.
Ceotto, Michele; Ayton, Gary S; Voth, Gregory A
2008-04-01
An extension of superposition state molecular dynamics (SSMD) [Venkatnathan and Voth J. Chem. Theory Comput. 2005, 1, 36] is presented with the goal to accelerate timescales and enable the study of "long-time" phenomena for condensed phase systems. It does not require any a priori knowledge about final and transition state configurations, or specific topologies. The system is induced to explore new configurations by virtue of a fictitious (free-particle-like) accelerating potential. The acceleration method can be applied to all degrees of freedom in the system and can be applied to condensed phases and fluids. PMID:26620930
A sampling problem in molecular dynamics simulations of macromolecules.
Clarage, J B; Romo, T; Andrews, B K; Pettitt, B M; Phillips, G N
1995-01-01
Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled. Images Fig. 1 Fig. 2 Fig. 3 PMID:7724554
Large scale molecular dynamics modeling of materials fabrication processes
Belak, J.; Glosli, J.N.; Boercker, D.B.; Stowers, I.F.
1994-02-01
An atomistic molecular dynamics model of materials fabrication processes is presented. Several material removal processes are shown to be within the domain of this simulation method. Results are presented for orthogonal cutting of copper and silicon and for crack propagation in silica glass. Both copper and silicon show ductile behavior, but the atomistic mechanisms that allow this behavior are significantly different in the two cases. The copper chip remains crystalline while the silicon chip transforms into an amorphous state. The critical stress for crack propagation in silica glass was found to be in reasonable agreement with experiment and a novel stick-slip phenomenon was observed.
Molecular dynamics simulations of nanoidentation of silicon nitride
Walsh, P.; Omeltchenko, A.; Kikuchi, Hideaki; Kalia, R.K.; Nakano, Aiichiro; Vashishta, P.
1999-08-01
This is a report of work in progress on 10 million atom Molecular Dynamics (MD) simulations of nanoindentation of crystalline and amorphous silicon nitride (Si{sub 3}N{sub 4}). Nanoindentation is used to determine mechanical properties of extremely thin films such as hardness and elastic moduli. The authors report load-displacement curves for several Si{sub 3}N{sub 4} configurations using an idealized non-deformable indenter and analyze the local stress distributions in the vicinity of the indenter tip. Preliminary results for surface adhesion using Si{sub 3}N{sub 4} for both tip and substrate are also reported.
Molecular dynamic study of pressure fluctuations spectrum in plasma
NASA Astrophysics Data System (ADS)
Bystryi, R. G.
2015-11-01
Pressure of plasma is calculated by using classical molecular dynamics method. The formula based on virial theorem was used. Spectrum pressure's fluctuations of singly ionized non-ideal plasma are studied. 1/f-like spectrum behavior is observed. In other words, flicker noise is observed in fluctuations of pressure equilibrium non-ideal plasma. Relations between the obtained result and pressure fluctuations within the Gibbs and Einstein approaches are discussed. Special attention is paid to features of calculating the pressure in strongly coupled systems.
NASA Astrophysics Data System (ADS)
Saiz, Fernan; Gamero-Castaño, Manuel
2016-06-01
The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile's energy that is transferred to the target, as well as the fraction of this energy that is dissipated.
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
Wei Gu; Garcia, A.E.; Schoenborn, B.P.
1994-12-31
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.
Molecular Dynamics Simulation on Stability of Insulin on Graphene
NASA Astrophysics Data System (ADS)
Liang, Li-jun; Wang, Qi; Wu, Tao; Shen, Jia-wei; Kang, Yu
2009-12-01
The adsorption dynamics of a model protein (the human insulin) onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some α-helices in non-fixed systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.
Micellar crystals in solution from molecular dynamics simulations
Anderson, J.; Lorenz, C.; Travesset, A.
2008-05-14
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers.
Molecular dynamics simulation of radiation damage cascades in diamond
Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.
2015-06-28
Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
Vashishta, Priya; Kalia, Rajiv
2005-02-24
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report.
High temperature phonon dispersion in graphene using classical molecular dynamics
Anees, P. Panigrahi, B. K.; Valsakumar, M. C.
2014-04-24
Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 K the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.
Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes
Chen, Rui; Mias, George I.; Li-Pook-Than, Jennifer; Jiang, Lihua; Lam, Hugo Y. K.; Chen, Rong; Miriami, Elana; Karczewski, Konrad J.; Hariharan, Manoj; Dewey, Frederick E.; Cheng, Yong; Clark, Michael J.; Im, Hogune; Habegger, Lukas; Balasubramanian, Suganthi; O'Huallachain, Maeve; Dudley, Joel T.; Hillenmeyer, Sara; Haraksingh, Rajini; Sharon, Donald; Euskirchen, Ghia; Lacroute, Phil; Bettinger, Keith; Boyle, Alan P.; Kasowski, Maya; Grubert, Fabian; Seki, Scott; Garcia, Marco; Whirl-Carrillo, Michelle; Gallardo, Mercedes; Blasco, Maria A.; Greenberg, Peter L.; Snyder, Phyllis; Klein, Teri E.; Altman, Russ B.; Butte, Atul; Ashley, Euan A.; Nadeau, Kari C.; Gerstein, Mark; Tang, Hua; Snyder, Michael
2012-01-01
SUMMARY Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here we present an integrative Personal Omics Profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14-month period. Our iPOP analysis revealed various medical risks, including Type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high coverage genomic and transcriptomic data, which provide the basis of our iPOP, discovered extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and disease states by connecting genomic information with additional dynamic omics activity. PMID:22424236
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
NASA Astrophysics Data System (ADS)
Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
2016-05-01
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from