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.
Xin, Yao; Doshi, Urmi; Hamelberg, Donald
2010-06-14
Accelerated molecular dynamics simulations are routinely being used to recover the correct canonical probability distributions corresponding to the original potential energy landscape of biomolecular systems. However, the limits of time reweighting, based on transition state theory, in obtaining true kinetic rates from accelerated molecular dynamics for biomolecular systems are less obvious. Here, we investigate this issue by studying the kinetics of cis-trans isomerization of peptidic omega bond by accelerated molecular dynamics. We find that time reweighting is valid for obtaining true kinetics when the original potential is not altered at the transition state regions, as expected. When the original potential landscape is modified such that the applied boost potential alters the transition state regions, time reweighting fails to reproduce correct kinetics and the reweighted rate is much slower than the true rate. By adopting the overdamped limit of Kramers' rate theory, we are successful in recovering correct kinetics irrespective of whether or not the transition state regions are modified. Furthermore, we tested the validity of the acceleration weight factor from the path integral formalism for obtaining the correct kinetics of cis-trans isomerization. It was found that this formulation of the weight factor is not suitable for long time scale processes such as cis-trans isomerization with high energy barriers.
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.
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.
Cheng, Xiaolin; Ivanov, Ivaylo
2012-01-01
Molecular dynamics (MD) simulation holds the promise of revealing the mechanisms of biological processes in their ultimate detail. It is carried out by computing the interaction forces acting on each atom and then propagating the velocities and positions of the atoms by numerical integration of Newton's equations of motion. In this review, we present an overview of how the MD simulation can be conducted to address computational toxicity problems. The study cases will cover a standard MD simulation performed to investigate the overall flexibility of a cytochrome P450 (CYP) enzyme and a set of more advanced MD simulations to examine the barrier to ion conduction in a human α7 nicotinic acetylcholine receptor (nAChR).
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.
Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A
2015-01-01
Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.
McGrath, Matthew J; Kuo, I-Feng William; Siepmann, J Ilja
2011-11-28
Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.
NASA Astrophysics Data System (ADS)
Kahros, Argyris
Incorporating quantum mechanics into an atomistic simulation necessarily involves solving the Schrodinger equation. Unfortunately, the computational expense associated with solving this equation scales miserably with the number of included quantum degrees of freedom (DOF). The situation is so dire, in fact, that a molecular dynamics (MD) simulation cannot include more than a small number of quantum DOFs before it becomes computationally intractable. Thus, if one were to simulate a relatively large system, such as one containing several hundred atoms or molecules, it would be unreasonable to attempt to include the effects of all of the electrons associated with all of the components of the system. The mixed quantum/classical (MQC) approach provides a way to circumvent this issue. It involves treating the vast majority of the system classically, which incurs minimal computational expense, and reserves the consideration of quantum mechanical effects for only the few degrees of freedom more directly involved in the chemical phenomenon being studied. For example, if one were to study the bonding of a single diatomic molecule in the gas phase, one could employ a MQC approach by treating the nuclei of the molecule's two atoms classically---including the deeply bound, low-energy electrons that change relatively little---and solving the Schrodinger equation only for the high energy electron(s) directly involved in the bonding of the classical cores. In such a way, one could study the bonding of this molecule in a rigorous fashion while treating only the directly related degrees of freedom quantum mechanically. Pseudopotentials are then responsible for dictating the interactions between the quantum and classical degrees of freedom. As these potentials are the sole link between the quantum and classical DOFs, their proper development is of the utmost importance. This Thesis is concerned primarily with my work on the development of novel, rigorous and dynamical
Laasonen, Kari
2013-01-01
In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.
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.
Inertial corrections by dynamic estimation
NASA Technical Reports Server (NTRS)
Sonnabend, David
1989-01-01
The highlights are presented of an Engineering Memorandum, Dynamic Estimation for Floated Gradiometers. The original impetus for the work was that gradiometers, in principle, measure components of the gravity gradient tensor, plus rotation effects, similar to centrifugal and Coriolis effects in accelerometers. The problem is that the rotation effects are often quite large, compared to the gradient, and that available inertial instruments can't measure them to adequate accuracy. The paper advances the idea that, if the instruments can be floated in a package subject to very low disturbances, a dynamic estimation, based on the Euler and translational equations of motion, plus models of all the instruments, can be used to greatly strengthen the estimates of the gradient and the rotation parameters. Moreover, symmetry constraints can be imposed directly in the filter, further strengthening the solution.
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 simulations.
Lindahl, Erik
2015-01-01
Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.
Molecular dynamics simulations.
Lindahl, Erik R
2008-01-01
Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.
QED Corrections to the Dynamic Polarizability
Haas, M.; Jentschura, U.D.; Keitel, C.H.
2005-10-26
In a relatively weak laser field, atoms interacting with one-photon off-resonant laser fields are dynamically polarized. This perturbation manifests itself in a shift of the atomic energy levels called the 'dynamic Stark effect' or 'AC-Stark effect', which is intensity dependent. The AC-Stark coefficients are therefore of particular importance for high-precision spectroscopy experiments which rely on two-photon processes like the 1S-2S transition in hydrogen, hydrogenlike ions, antihydrogen or similar composite matter-antimatter systems. In addition, the imaginary part of the dynamic polarizability determines the resonant one-photon ionization width for the excited level.Up to now, the dynamic polarizability has been investigated only up to the level of relativistic corrections. In this contribution, we present results for several experimentally relevant transitions in hydrogenlike systems and the leading-order QED radiative corrections.
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
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.
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.
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.
NASA Astrophysics Data System (ADS)
Moultos, Othonas A.; Zhang, Yong; Tsimpanogiannis, Ioannis N.; Economou, Ioannis G.; Maginn, Edward J.
2016-08-01
Molecular dynamics simulations were carried out to study the self-diffusion coefficients of CO2, methane, propane, n-hexane, n-hexadecane, and various poly(ethylene glycol) dimethyl ethers (glymes in short, CH3O-(CH2CH2O)n-CH3 with n = 1, 2, 3, and 4, labeled as G1, G2, G3, and G4, respectively) at different conditions. Various system sizes were examined. The widely used Yeh and Hummer [J. Phys. Chem. B 108, 15873 (2004)] correction for the prediction of diffusion coefficient at the thermodynamic limit was applied and shown to be accurate in all cases compared to extrapolated values at infinite system size. The magnitude of correction, in all cases examined, is significant, with the smallest systems examined giving for some cases a self-diffusion coefficient approximately 15% lower than the infinite system-size extrapolated value. The results suggest that finite size corrections to computed self-diffusivities must be used in order to obtain accurate results.
Moultos, Othonas A; Zhang, Yong; Tsimpanogiannis, Ioannis N; Economou, Ioannis G; Maginn, Edward J
2016-08-21
Molecular dynamics simulations were carried out to study the self-diffusion coefficients of CO2, methane, propane, n-hexane, n-hexadecane, and various poly(ethylene glycol) dimethyl ethers (glymes in short, CH3O-(CH2CH2O)n-CH3 with n = 1, 2, 3, and 4, labeled as G1, G2, G3, and G4, respectively) at different conditions. Various system sizes were examined. The widely used Yeh and Hummer [J. Phys. Chem. B 108, 15873 (2004)] correction for the prediction of diffusion coefficient at the thermodynamic limit was applied and shown to be accurate in all cases compared to extrapolated values at infinite system size. The magnitude of correction, in all cases examined, is significant, with the smallest systems examined giving for some cases a self-diffusion coefficient approximately 15% lower than the infinite system-size extrapolated value. The results suggest that finite size corrections to computed self-diffusivities must be used in order to obtain accurate results. PMID:27544089
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
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 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)
Body mass-corrected molecular rate for bird mitochondrial DNA.
Nabholz, Benoit; Lanfear, Robert; Fuchs, Jérome
2016-09-01
Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species' body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.
State-dependent molecular dynamics.
Yang, Ciann-Dong; Weng, Hung-Jen
2014-01-01
This paper proposes a new mixed quantum mechanics (QM)-molecular mechanics (MM) approach, where MM is replaced by quantum Hamilton mechanics (QHM), which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
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
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.
Thomas-Fermi molecular dynamics
Clerouin, J.; Pollock, E.L. ); Zerah, G. )
1992-10-15
A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello (Phys. Rev. Lett. 55, 2471 (1985)), the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker (Phys. Rev. A 38, 2205 (1988)). As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated.
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
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
From molecular dynamics to Brownian dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane. PMID:25002825
NMR investigations of molecular dynamics
NASA Astrophysics Data System (ADS)
Palmer, Arthur
2011-03-01
NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.
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 δ-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
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
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 of polymer growth
NASA Astrophysics Data System (ADS)
Akkermans, Reinier L. C.; Toxvaerd, Søren; Briels, W. J.
1998-08-01
The irreversible polymerization of a monomer liquid has been studied by molecular-dynamics simulation in two and three dimensions. The growth process is studied under good solvent conditions in the dilute regime and up to semidilute and concentrated regimes. In the dilute regime we observe a reaction limitation due to trapping of the growing centers, which is more pronounced in the lower dimension. At higher concentrations the presence of other chains decreases the monomer mobility and reaction rate. Conformational properties are studied by scaling analysis of end-to-end and gyration radii. A crossover from swollen conformations towards screened conformations is observed as growth proceeds.
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.
Molecular dynamics of interface rupture
NASA Technical Reports Server (NTRS)
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
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
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.
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
A novel method of dynamic correction in the time domain
NASA Astrophysics Data System (ADS)
Hessling, J. P.
2008-07-01
The dynamic error of measured signals is sometimes unacceptably large. If the dynamic properties of the measurement system are known, the true physical signal may to some extent be re-constructed. With a parametrized characterization of the system and sampled signals, time-domain digital filters may be utilized for correction. In the present work a general method for synthesizing such correction filters is developed. It maps the dynamic parameters of the measurement system directly on to the filter coefficients and utilizes time reversed filtering. This avoids commonly used numerical optimization in the filter synthesis. The method of correction is simple with absolute repeatability and stability, and results in a low residual error. Explicit criteria to control both the horizontal (time) and vertical (amplitude) discretization errors are presented in terms of the utilization of bandwidth and noise gain, respectively. To evaluate how close to optimal the correction is, these errors are also formulated in relation to the signal-to-noise ratio of the original measurement system. For purposes of illustration, typical mechanical and piezo-electric transducer systems for measuring force, pressure or acceleration are simulated and dynamically corrected with such dedicated digital filters.
Shear flow by molecular dynamics
NASA Astrophysics Data System (ADS)
Heyes, D. M.
1985-08-01
A detailed comparison is made between a number of methods for generating shear flow in Molecular Dynamics computer simulation. Algorithms which closely mimic most experimental methods for producing shear flow are those by Trozzi and Ciccotti, and Ashurst and Hoover. They employ hard wall boundaries and fluid walls respectively (with sheared cell periodicity being only in two dimensions). The sheared fluid properties are therefore inextricably linked with interfacial effects. These problems are largely eliminated by the Lees and Edwards scheme which creates a pseudo-infinite sheared material. There are a number of derivatives of this model including one favoured by the author for investigating non-linear viscoelastic phenomena. A number of results from this scheme pertaining to the Lennard-Jones liquid are presented.
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
Emergent Phenomena via Molecular Dynamics
NASA Astrophysics Data System (ADS)
Rapaport, D. C.
Emergent phenomena are unusual because they are not obvious consequences of the design of the systems in which they appear, a feature no less relevant when they are being simulated. Several systems that exhibit surprisingly rich emergent behavior, each studied by molecular dynamics (MD) simulation, are described: (i) Modeling self-assembly processes associated with virus growth reveals the ability to achieve error-free assembly, where paradoxically, near-maximum yields are due to reversible bond formation. (ii) In fluids studied at the atomistic level, complex hydrodynamic phenomena in rotating and convecting fluids - the Taylor- Couette and Rayleigh-Bénard instabilities - can be reproduced, despite the limited length and time scales accessible by MD. (iii) Segregation studies of granular mixtures in a rotating drum reproduce the expected, but counterintuitive, axial and radial segregation, while for the case of a vertically vibrated layer a novel form of horizontal segregation is revealed.
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.
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.
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.
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
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.
A correction method suitable for dynamical seasonal prediction
NASA Astrophysics Data System (ADS)
Chen, H.; Lin, Z. H.
2006-05-01
Based on the hindcast results of summer rainfall anomalies over China for the period 1981-2000 by the Dynamical Climate Prediction System (IAP-DCP) developed by the Institute of Atmospheric Physics, a correction method that can account for the dependence of model's systematic biases on SST anomalies is proposed. It is shown that this correction method can improve the hindcast skill of the IAP-DCP for summer rainfall anomalies over China, especially in western China and southeast China, which may imply its potential application to real-time seasonal prediction.
Localised distributions and criteria for correctness in complex Langevin dynamics
NASA Astrophysics Data System (ADS)
Aarts, Gert; Giudice, Pietro; Seiler, Erhard
2013-10-01
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.
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.
Beam dynamics in rf guns and emittance correction techniques
NASA Astrophysics Data System (ADS)
Serafini, Luca
1994-02-01
In this paper we present a general review of beam dynamics in a laser-driven rf gun. The peculiarity of such an accelerating structure versus other conventional multi-cell linac structures is underlined on the basis of the Panofsky-Wenzel theorem, which is found to give a theoretical background for the well known Kim's model. A basic explanation for some proposed methods to correct rf induced emittance growth is also derived from the theorem. We also present three emittance correction techniques for the recovery of space-charge induced emittance growth, namely the optimum distributed disk-like bunch technique, the use of rf spatial harmonics to correct spherical aberration induced by space charge forces and the technique of emittance filtering by clipping the electron beam. The expected performances regarding the beam quality achievable with different techniques, as predicted by scaling laws and simulations, are analyzed, and, where available, compared to experimental results.
Time-Dependent Molecular Reaction Dynamics
NASA Astrophysics Data System (ADS)
Öhrn, Yngve
2007-11-01
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.
Voter, A.F.; Doll, J.D.; Cohen, J.M.
1989-02-01
A method is presented for computing the classically exact, surface or bulk diffusion constant of a point defect at arbitrary temperature. The thermal diffusion constant is expressed using the squared jump length averaged over all possible final states to which the atom can jump. The rate constants that weight this sum are computed using transition state theory and molecular dynamics within a recently developed many-state dynamical corrections formalism. While these rate constants are valid only in the rare-event regime (i.e., at low temperature), it is shown that for a periodic lattice of equivalent binding sites, the resulting diffusion contants is valid at any temperature for which the lattice sites remain well defined. It is thus possible to compute classically exact surface or bulk diffusion constant for an arbitrary interatomic potential, without the time scale limitations of direct molecular dynamics.
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.
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.
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.
Protein dynamics: Moore's law in molecular biology.
Vendruscolo, Michele; Dobson, Christopher M
2011-01-25
The millisecond barrier has been broken in molecular dynamics simulations of proteins. Such simulations are increasingly revealing the inner workings of biological systems by generating atomic-level descriptions of their behaviour that make testable predictions about key molecular processes.
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.
Parallel Molecular Dynamics Program for Molecules
Plimpton, Steve
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.
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. PMID:26604800
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
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.
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.
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
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.
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.
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.
Molecular Exchange Dynamics in Block Copolymer Micelles
NASA Astrophysics Data System (ADS)
Bates, Frank; Lu, Jie; Choi, Soohyung; Lodge, Timothy
2012-02-01
Poly(styrene-b-ethylene propylene) (PS-PEP) diblock copolymers were mixed with squalane (C30H62) at 1% by weight resulting in the formation of spherical micelles. The structure and dynamics of molecular exchange were characterized by synchrotron small-angle x-ray scattering (SAXS) and time resolved small-angle neutron scattering (TR-SANS), respectively, between 100 C and 160 C. TR-SANS measurements were performed with solutions initially containing deuterium labeled micelle cores and normal cores dispersed in a contrast matched squalane. Monitoring the reduction in scattering intensity as a function of time at various temperatures revealed molecular exchange dynamics highly sensitive to the core molecular weight and molecular weight distribution. Time-temperature superposition of data acquired at different temperatures produced a single master curve for all the mixtures. Experiments conducted with isotopically labeled micelle cores, each formed from two different but relatively mondisperse PS blocks, confirmed a simple dynamical model based on first order kinetics and core Rouse single chain relaxation. These findings demonstrate a dramatic transition to nonergodicity with increasing micelle core molecular weight and confirm the origins of the logarithmic exchange kinetics in such systems.
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.
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.
Multiscale coupling of molecular dynamics and peridynamics
NASA Astrophysics Data System (ADS)
Tong, Qi; Li, Shaofan
2016-10-01
We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.
MDMovie: a molecular dynamics viewing tool.
Greenberg, J P
1996-10-01
The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.
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.
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.
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.
Polar solvation dynamics of lysozyme from molecular dynamics studies
NASA Astrophysics Data System (ADS)
Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
2012-05-01
The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the α-helices and β-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.
Thermostats and thermostat strategies for molecular dynamics simulations of nanofluidics.
Yong, Xin; Zhang, Lucy T
2013-02-28
The thermostats in molecular dynamics (MD) simulations of highly confined channel flow may have significant influences on the fidelity of transport phenomena. In this study, we exploit non-equilibrium MD simulations to generate Couette flows with different combinations of thermostat algorithms and strategies. We provide a comprehensive analysis on the effectiveness of three thermostat algorithms Nosé-Hoover chain (NHC), Langevin (LGV) and dissipative particle dynamics (DPD) when applied in three thermostat strategies, thermostating either walls (TW) or fluid (TF), and thermostating both the wall and fluid (TWTF). Our results of thermal and mechanical properties show that the TW strategy more closely resembles experimental conditions. The TF and TWTF systems also produce considerably similar behaviors in weakly sheared systems, but deviate the dynamics in strongly sheared systems due to the isothermal condition. The LGV and DPD thermostats used in the TF and TWTF systems provide vital ways to yield correct dynamics in coarse-grained systems by tuning the fluid transport coefficients. Using conventional NHC thermostat to thermostat fluid only produces correct thermal behaviors in weakly sheared systems, and breaks down due to significant thermal inhomogeneity in strongly sheared systems.
Dynamic strength of molecular adhesion bonds.
Evans, E; Ritchie, K
1997-01-01
In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale
Dynamical quenching of tunneling in molecular magnets
NASA Astrophysics Data System (ADS)
José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.
2015-12-01
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation.
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
Molecular dynamic simulation methods for anisotropic liquids.
Aoki, Keiko M; Yoneya, Makoto; Yokoyama, Hiroshi
2004-03-22
Methods of molecular dynamics simulations for anisotropic molecules are presented. The new methods, with an anisotropic factor in the cell dynamics, dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under constant hydrostatic pressure or constant volume. The methods are especially effective for anisotropic liquids, such as smectic liquid crystals and membranes, of which the stacks of layers are compressible (elastic in direction perpendicular to the layers) while the layer itself is liquid and only elastic under uniform compressive force. The methods can also be used for crystals and isotropic liquids as well.
Molecular Dynamics Simulations of Alpha-synuclein
NASA Astrophysics Data System (ADS)
Sammalkorpi, Maria; Schreck, Carl; Nath, Abhinav; Dewitt, David; Rhoades, Elizabeth; O'Hern, Corey
2011-03-01
We investigate the conformational dynamics of single alpha-synuclein proteins, which have been implicated in amyloid diseases such as Parkinson's and Alzheimer's disease, in solution using unconstrained and constrained all-atom, explicit solvent molecular dynamics simulations. The constraints on inter-residue separations are obtained from our single-molecule FRET measurements of eleven FRET pairs that span the protein. By comparing the simulation data satisfying different combinations of FRET constraints, we are able to identify those constraints that are most important in determining the radius of gyration and key features of the contact map of the protein.
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
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.
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.
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.
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
Control-volume representation of molecular dynamics.
Smith, E R; Heyes, D M; Dini, D; Zaki, T A
2012-05-01
A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑ(i) for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [Todd et al., Phys. Rev. E 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.
Control-volume representation of molecular dynamics
NASA Astrophysics Data System (ADS)
Smith, E. R.; Heyes, D. M.; Dini, D.; Zaki, T. A.
2012-05-01
A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys.JCPSA60021-960610.1063/1.1747782 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds’ transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑi for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys.JAPIAU0021-897910.1063/1.341877 64, 1152 (1988)] techniques and the method of planes [Todd , Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.52.1627 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.
Molecular dynamics simulation study of methanesulfonic acid.
Canales, Manel; Alemán, Carlos
2014-03-27
A molecular dynamics simulation study of methanesulfonic acid has been carried out using a reliable force field in a large range of temperatures. Several thermodynamic, structural, and dynamical properties have been calculated and compared with the available experimental data. The density, the shear viscosity, the heat of vaporization, and the melting temperature results, calculated from this force field, are in a good agreement with the experimental data. Analysis of the influence of the hydrogen bonds in structural and dynamical properties has also been performed. The continuous and interrupted methodologies to compute hydrogen bonding lifetimes have been applied. The interrupted hydrogen bond lifetimes values are consistent with the diffusion and viscosity coefficients. The activation energies of the self-diffusion, the reorientational motions, and the hydrogen bonding lifetimes are coincident.
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
Voter, A.F.; Doll, J.D.
1985-01-01
We derive an expression for the classical rate constant between any two states of a multistate system. The rate is given as the transition state theory rate of escape from the originating state, multiplied by a dynamical correction factor in the form of a time-correlation function which is evaluated using molecular dynamics techniques. This method is desiged to treat cases in which reactive state-change events are so infrequent (e.g., at low temperature) that direct molecular dynamics calculations are unfeasible. In this regime where dynamical recrossings occur much more quickly than the average time between reactive state changes, the concept of a rate between two nonadjacent states becomes meaningful. We apply the method to the surface diffusion of Rh on Rh(100) at the temperatures employed in field ion microscope experiments.
Dynamic compression system for the correction of pectus carinatum.
Martinez-Ferro, Marcelo; Fraire, Carlos; Bernard, Silvia
2008-08-01
Between April 2001 and 2007, we treated 208 patients with pectus carinatum by using a specially designed dynamic compression system (DCS) that uses a custom-made aluminum brace. Recently, an electronic pressure measuring device was added to the brace. Results were evaluated by using a double-blinded subjective scale (1 to 10). A total of 208 patients were treated over 6 years; 154 were males (74%) and the mean age was 12.5 years (range 3 to 18 years). Mean utilization time was 7.2 hours daily for 7 months (range 3 to 20 months). A total of 28 (13.4%) patients abandoned treatment and were not evaluated for final results. Of the 180 remaining patients, 112 completed treatment. A total of 99 of 112 (88.4%) had good to excellent results scoring between 7 and 10 points, and 13 (11.6%) patients scored 1 to 6 points and were judged as poor or failed results. The "Pressure for Initial Correction" (PIC) in pounds per square inch (PSI) proved that starting treatment with less than 2.5 PSI avoids skin lesions. Patients who require pressures higher than 7.5 PSI should not be treated with this method. We found a good correlation between PIC versus treatment duration and outcome. DCS is an effective treatment for pectus carinatum with minimal morbidity. We suggest that patients with pectus carinatum have a trial of compression therapy before recommending surgical resection. The use of pressure measurement avoids complications such as skin lesions, partial or poor results, and patient noncompliance.
Molecular Dynamics Simulation of Dynamic Response of Beryllium
NASA Astrophysics Data System (ADS)
Thompson, Aidan P.; Lane, J. Matthew D.; Baskes, Michael I.; Desjarlais, Michael P.
2009-06-01
The response of beryllium to dynamic loading has been extensively studied, both experimentally and theoretically, due to its importance in several technological areas. Compared to other metals, it is quite challenging to accurately represent the various anomalous behaviors of beryllium using classical interatomic potentials. The spherically-symmetric EAM potential can not reproduce the observed c/a ratio for α-Be under ambient conditions, which is significantly smaller than the ideal HCP value. The directional-dependence of the MEAM potential overcomes this problem, but introduces additional complexity. We will compare predictions of these classical potentials to experimental measurements of beryllium at ambient conditions, and also to theoretical calculations at high temperatures and pressures. Finally, we will present initial results from non-equilibrium molecular dynamics simulations of beryllium under dynamic loading. This work is supported by the Laboratory Directed Research and Development program at Sandia National Laboratories.
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.
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.
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
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.
Cohen, J.M.; Voter, A.F. , Los Alamos National Laboratory, Los Alamos, New Mexico 87545 )
1989-10-15
Surface self-diffusion constants have been calculated for the single component Lennard-Jones fcc(111) system using the dynamical corrections formalism for transition state theory (TST). At high temperatures, these results are found to be in agreement with previous molecular dynamics calculations. Over the extended temperature range in which this method is valid, deviations from Arrhenius behavior are observed. At lower temperatures, a noticeable contribution to the diffusion constant stems from trajectories in which the adatom recrosses the TST boundary, often due to a direction-reversing collision with the substrate atom on the far side of the binding site. This produces a dip in the dynamical correction factor centered around a reduced temperature of {ital T}=0.038. At higher temperatures, the expected multiple-jump effects are observed.
Molecular Dynamics: New Frontier in Personalized Medicine.
Sneha, P; Doss, C George Priya
2016-01-01
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. PMID:26827606
Molecular Dynamics: New Frontier in Personalized Medicine.
Sneha, P; Doss, C George Priya
2016-01-01
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine.
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
Voter, A.F.
1997-05-01
I derive a general method for accelerating the molecular-dynamics (MD) simulation of infrequent events in solids. A bias potential ({Delta}V{sub b}) raises the energy in regions other than the transition states between potential basins. Transitions occur at an accelerated rate and the elapsed time becomes a statistical property of the system. {Delta}V{sub b} can be constructed without knowing the location of the transition states and implementation requires only first derivatives. I examine the diffusion mechanisms of a 10-atom Ag cluster on the Ag(111) surface using a 220 {mu}s hyper-MD simulation. {copyright} {ital 1997} {ital The American Physical Society}
[Oligoglycine surface structures: molecular dynamics simulation].
Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V
2010-01-01
The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.
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.
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.
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
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.
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.
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.
MDLab: a molecular dynamics simulation prototyping environment.
Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R; Izaguirre, Jesús A
2010-05-01
Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net.
Molecular dynamics of the excitatory synapse.
Okabe, Shigeo
2012-01-01
Molecular dynamics of synapses are one of the most important factors that control the remodeling of synaptic connection and efficacy of transmission. This chapter focuses on the dynamics of postsynaptic molecular machinery and describes the imaging technologies important for quantitative analyses of synapses, their application to the postsynaptic molecules, and the insights obtained from these analyses. New visualization techniques, such as super-resolution microscopy, will become an indispensable approach to reveal submicron changes of synaptic molecules. New methods of monitoring protein interactions will also be integrated with experimental paradigms of synaptic plasticity. Cell biological analyses, together with cutting-edge imaging technologies, have been applied to the studies of nascent synapse formation, synapse maintenance, and activity-dependent synapse remodeling. From these studies, a variety of new concepts emerged, such as local assembly of postsynaptic scaffolds, presence of "transport packets" of postsynaptic receptors, heterogeneity of actin movement within spines, and activity-free fluctuation of PSD/spine sizes. These new concepts are useful in understanding specific properties of postsynaptic functions and should be integrated in future to build a realistic model of the postsynaptic organization that can explain its remarkable stability and tunability. PMID:22351054
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.
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.
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
Molecular dynamics simulations of wear processes
NASA Astrophysics Data System (ADS)
Yu, Hualiang
Wear has been recognized as a vital problem in many industries. It results in a loss of durability, reliability, and efficiency and costs tens of billions of dollars annually. Significant effort has been devoted in both experimental and theoretical studies. However, the mechanisms of wear are still poorly understood and therefore wear control is far behind its demand. One way to study wear process is via computer simulation, which has become more powerful with the rapid development in computer facilities and efficient algorithms. It allows observation of atomic scale deformation and therefore it is a very good tool to study wear mechanisms at the nano-scale. This study presents a series of molecular dynamic simulation of some nano-scale wear processes, such as indentation and plowing, with the goal of exploring the factors that affect wear and predicting wear for different conditions. Molecular Dynamics simulations were carried out on a system that includes an aluminum substrate and a hard tip. Embedded atom method (EAM) and Lennard-Jones potentials were used to describe interactions between atoms. For nano-indentation simulations, both constant indent force and constant loading speed were applied to study the wear mechanisms as well as material properties. Some phenomenon, such as jump-to-contact, local melting, and dislocation nucleation were observed. More importantly, the effects of system temperature, indent force, substrate orientation, tip-substrate bond, indenter shape, boundary condition, and defect concentrations of the substrate were systematically investigated during indentation. The results are in qualitative agreement with limited experimental data. Similar simulations were carried out for plowing. The effects of plowing force, substrate orientation, the tip-substrate bond, and alloy elements are discussed based on the simulation results. In addition, a simple analytic model of plowing behavior is provided. The model reveals two parameters, static
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.
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.
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.
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
Detecting Allosteric Networks Using Molecular Dynamics Simulation.
Bowerman, S; Wereszczynski, J
2016-01-01
Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. PMID:27497176
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.
NASA Astrophysics Data System (ADS)
2012-09-01
The feature article "Material advantage?" on the effects of technology and rule changes on sporting performance (July pp28-30) stated that sprinters are less affected by lower oxygen levels at high altitudes because they run "aerobically". They run anaerobically. The feature about the search for the Higgs boson (August pp22-26) incorrectly gave the boson's mass as roughly 125 MeV it is 125 GeV, as correctly stated elsewhere in the issue. The article also gave a wrong value for the intended collision energy of the Superconducting Super Collider, which was designed to collide protons with a total energy of 40 TeV.
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
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..
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.
Effects of Dynamic Corrective Feedback on ESL Writing Accuracy
ERIC Educational Resources Information Center
Hartshorn, K. James; Evans, Norman W.; Merrill, Paul F.; Sudweeks, Richard R.; Strong-Krause, Diane; Anderson, Neil J.
2010-01-01
Though recent research has shown that written corrective feedback (WCF) may improve aspects of writing accuracy in some English as a second language (ESL) contexts, many teachers continue to be confused about the practical steps they should utilize to help their students improve their writing. Moreover, some have raised concerns as to whether…
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.
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
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.
Classical Molecular Dynamics Simulation of Nuclear Fuel
Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie
2015-10-10
Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.
Molecular Dynamics Studies of Gold Surfaces
NASA Astrophysics Data System (ADS)
Ercolessi, F.; Bartolini, A.; Garofalo, M.; Parrinello, M.; Tosatti, E.
1987-01-01
In the glue model the total cohesion of a metal is determined by a pairwise atom-atom effective interaction plus a many-body force (the "glue") which is introduced to ensure optimal coordination. Using parameters optimized for gold, we have studied the structural behaviour of the low index surfaces Au(100), Au(110) and Au(111). We have used a simulated annealing strategy based on molecular dynamics to search the lowest surface energy configuration. In all cases the optimal structures are found to be reconstructed, and remarkably similar to some experimentally suggested reconstruction models. The main driving mechanism is the formation of close-packed triangular surface layers favoured by the glue term.
Extended Lagrangian free energy molecular dynamics.
Niklasson, Anders M N; Steneteg, Peter; Bock, Nicolas
2011-10-28
Extended free energy Lagrangians are proposed for first principles molecular dynamics simulations at finite electronic temperatures for plane-wave pseudopotential and local orbital density matrix-based calculations. Thanks to the extended Lagrangian description, the electronic degrees of freedom can be integrated by stable geometric schemes that conserve the free energy. For the local orbital representations both the nuclear and electronic forces have simple and numerically efficient expressions that are well suited for reduced complexity calculations. A rapidly converging recursive Fermi operator expansion method that does not require the calculation of eigenvalues and eigenfunctions for the construction of the fractionally occupied density matrix is discussed. An efficient expression for the Pulay force that is valid also for density matrices with fractional occupation occurring at finite electronic temperatures is also demonstrated.
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.
Nonequilibrium molecular dynamics of liquid crystals
NASA Astrophysics Data System (ADS)
Sarman, S. S.; Cummings, P. T.; Evans, D. J.
1994-11-01
During the last 15 years, noneyuilibrium molecular dynamics (NEMD) has been successfully applied to study transport phenomena in fluids that are isotropic at equilibrium. A natural extension is therefore to study liquid crystals, which are anisotropic al equilibrium. The lower symmetry of these systems means that the linear transport coefficients are considerably more complicated than in an isotropic system. Part of the reason for this is that there are crosscouplings between tensors of different rank and parity. Such couplings arc symmetry-forbidden in isotropic phases. In this paper. we review some of fundamental theoretical results we have derived concerning the rheology of liquid crystals. report NEMD simulations of thermal conductivity and shear viscosity of liquid crystals, and present NEMD simulations of shear cessation phenomena. All of the NEMD results are presented for a model liquid crystal fluid which is a modification of the Gay-Borne fluid. The results obtained are in qualitative agreement with experimental measurements on liquid crystal systems.
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
Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy
2015-04-30
The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.
Molecular dynamics studies of metallic glasses
NASA Astrophysics Data System (ADS)
Lee, Hyon-Jee
The thermodynamic, structural, and mechanical properties of metallic glasses are studied using molecular dynamics simulations. Molecular dynamics provides a computational framework to simulate the movement of interacting atoms in response to external perturbations, such as changes in temperature or pressure. In this thesis, a Sutton-Chen potential was chosen to describe the many-body interactions in metals and alloys. Our first application for this approach is to develop a simple model to derive the thermodynamic properties of metallic alloys (Chapter 2). Based on this model, we demonstrate that the glass transition is thermodynamically sensitive to differences between atomic radii and that there is an optimal difference for glass formation. Next, we extend these simulations to elucidate the details of structural organization in the glass (Chapter 3). We find that the liquid phase is characterized by a local five-fold symmetry, which becomes more prominent as the glass phase forms. This five-fold symmetry is related to the formation of icosahedral structures. The mechanical properties of glasses are also investigated and it is found that shear localization, which accompanies a sharp drop in the stress-strain curve, occurs at 45 degree with respect to the loading axis (Chapter 4). The generation of free volume is found to be the dominant mechanism that leads to shear localization, rather than adiabatic heating. Finally, generic first principle potentials are constructed to guide the experimental development of AlTiNi based metallic glasses (Chapter 5). Together, the results from these simulations improve our understanding of the thermodynamic, structural, and mechanical properties of metallic glasses and will aid computer-driven materials design.
Molecular Docking of Balanol to Dynamics Snapshots of Protein Kinase A
Wong, Chung F.; Kua, Jeremy S.; Zhang, Yingkai; Straatsma, TP; McCammon, J A.
2005-10-21
Even if the structure of a receptor has been determined experimentally, it may not be a conformation to which a ligand would bind when induced fit effects are significant. Here we evaluate the use of an ensemble of receptor conformations generated from a molecular dynamics simulation for molecular docking. Two molecular dynamics simulations were carried out to generate snapshots for protein kinase A (PKA): one with the ligand bound, the other without. The ligand, balanol, was then docked to conformations of the receptors presented by these trajectories. The Larmarkian genetic algorithm in Autodock1,2 was used in the docking. Three ligand models were used: rigid, flexible, and flexible with torsional potentials. When the snapshots were taken from the molecular dynamics simulation of the protein-ligand complex, the correct docking structure was found in all cases. On the other hand, when the snapshots were taken from the apo simulation, several clusters of structures were found. Out of the ten docking runs for each snapshot, at least one structure was close to the correctly docked structure when the flexible ligand models were used. However, the lowest energy structures, according to Autodock1,2, did not always correspond to the correctly docked structure. Rescoring using a more sophisticated Generalized Born electrostatics model did not improve the identification of the correctly docked structure. On the other hand, the correctly docked structure appeared more frequently as the lowest energy structures with the Autodock1,2 scoring function. This can provide a useful criterion for selecting the correctly docked structure from clusters of structures obtained from molecular docking experiments.
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.
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-dynamic study of liquid ethylenediamine
NASA Astrophysics Data System (ADS)
Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.
2016-10-01
Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.
NASA Astrophysics Data System (ADS)
Yang, Kaike
FOR MOLECULES WEAKLY COUPLED TO LEADS THE EXACT ZERO-BIAS KOHN-SHAM CONDUCTANCE CAN BE ORDERS OF MAGNITUDE LARGER THAN THE TRUE CONDUCTANCE DUE TO THE LACK OF DYNAMICAL EXCHANGE-CORRELATION (XC) EFFECTS. RECENTLY, IT HAS BEEN SHOWN HOW THESE DYNAMICAL XC CORRECTIONS CAN BE CALCULATED USING ONLY QUANTITIES OBTAINED FROM STATIC DENSITY FUNCTIONAL THEORY. HERE, WE INVESTIGATE THE THERMOELECTRIC TRANSPORT AND DERIVE THE XC CORRECTION TO THE SEEBECK COEFFICIENT. WE FIND THAT THE DYNAMICAL CORRECTION TO THE SEEBECK COEFFICIENT IS DETERMINANT IN EVALUATING THE THERMOPOWER: THE ABSOLUTE VALUE OF THE DYNAMICAL CORRECTION FOR THE SEEBECK COEFFICIENT IS, FOR CERTAIN VALUES OF GATE VOLTAGE, MUCH LARGER THAN THAT OF THE KOHN-SHAM TERM. FINALLY, WE COMPARE OUR DENSITY FUNCTIONAL CALCULATIONS TO THE RATE EQUATION AND THE EXPERIMENTAL RESULTS
[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
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.
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
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
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
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.
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.
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…
NASA Astrophysics Data System (ADS)
Harding, Michael E.; Vázquez, Juana; Stanton, John F.; Diezemann, Gregor; Gauss, Jürgen
2011-06-01
For a small set of linear and non-linear molecules, a detailed comparison of two different procedures for predicting vibrationally averaged molecular properties, i.e., second-order vibrational perturbation theory (VPT2) and a variational approach, is carried out. Results for vibrational corrections to dipole and quadrupole moments, nuclear quadrupole moments, static electric-dipole polarizabilities, NMR chemical shielding tensors, nuclear spin-rotation tensors, magnetizabilities, and rotational g-tensors are reported.
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.
Rempi Studies of Molecular Reaction Dynamics.
NASA Astrophysics Data System (ADS)
Black, John Forbes
Available from UMI in association with The British Library. Requires signed TDF. Resonance-Enhanced Multi-Photon Ionisation (REMPI qv.) is used to prepare and probe systems undergoing unimolecular decomposition. It is shown that the highly efficient state selective nature of the REMPI process is well suited to both highly dynamical situations such as the "A-Band" dissociation of MeI at around 280nm and to the slower "Quasi-statistical" dissociations of the mainifold of states of the MeI(+) cation. In the study of the neutral dissociation we attempt to extract the population distributions of the quantum states "by implication" as has been done previously. We demonstrate the failings of the time-of-flight technique in being unable to do this effectively. A comparison with previous studies is made. We report the first rotationally resolved spectrum of a polyatomic (N atoms > 2) photofragment (Me from the "A-Band" photodissociation of MeI) and propose a mechanism to account for the observed differences of the rotational populations in the different dissociation channels. Two-photon linestrength theory incorporating alignment effects is extended to symmetric tops to analyse the data. The pre-dissociation dynamics of a high lying Rydberg state of the methyl radical have been extracted as part of a spectroscopic study performed on CH _3 and CD_3. The dynamics are compared to existing studies on the near-neighbours NH_3 and ND_3 with some apparent correlation. In the dissociations of the A and B states of the MeI(+) cation we are able to provide some more evidence for existing ideas that the A state dissociates by rapid inter-conversion to highly excited levels of the ground state whereas the B state dissociates in a more direct manner. We identify two existing features in the REMPI spectrum of MeI in the "A-Band" region as molecular Rydberg resonances and show that an interesting competition exists between the direct photodissociation and the "virtual" state involved in
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
Molecular dynamics simulations of unsaturated lipid bilayers
NASA Astrophysics Data System (ADS)
Rabinovich, Alexander L.; Balabaev, Nikolay K.
2001-02-01
Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -SCH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.
Molecular dynamics simulations of unsaturated lipid bilayers
NASA Astrophysics Data System (ADS)
Rabinovich, Alexander L.; Balabaev, Nikolay K.
2000-02-01
Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -SCH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.
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
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.
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
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 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.
Fracture simulations via massively parallel molecular dynamics
Holian, B.L.; Abraham, F.F.; Ravelo, R.
1993-09-01
Fracture simulations at the atomistic level have heretofore been carried out for relatively small systems of particles, typically 10,000 or less. In order to study anything approaching a macroscopic system, massively parallel molecular dynamics (MD) must be employed. In two spatial dimensions (2D), it is feasible to simulate a sample that is 0.1 {mu}m on a side. We report on recent MD simulations of mode I crack extension under tensile loading at high strain rates. The method of uniaxial, homogeneously expanding periodic boundary conditions was employed to represent tensile stress conditions near the crack tip. The effects of strain rate, temperature, material properties (equation of state and defect energies), and system size were examined. We found that, in order to mimic a bulk sample, several tricks (in addition to expansion boundary conditions) need to be employed: (1) the sample must be pre-strained to nearly the condition at which the crack will spontaneously open; (2) to relieve the stresses at free surfaces, such as the initial notch, annealing by kinetic-energy quenching must be carried out to prevent unwanted rarefactions; (3) sound waves emitted as the crack tip opens and dislocations emitted from the crack tip during blunting must be absorbed by special reservoir regions. The tricks described briefly in this paper will be especially important to carrying out feasible massively parallel 3D simulations via MD.
Molecular dynamics simulations of gold nanomaterials
NASA Astrophysics Data System (ADS)
Wang, Yanting
We have carried out Molecular Dynamics simulations to study the thermal stability and melting behavior of gold nanoclusters and gold nanorods. The surface is found to play a very important role in both gold nanomaterials. Upon cooling from the liquid, we find that gold nanoclusters with 600-3000 atoms crystallize into a Mackay icosahedron. Upon heating, the {111} facets on the surface of the Mackay icosahedral gold nanoclusters soften but do not premelt below the bulk melting temperature. We attribute this surface softening to the increasing mobility of vertex and edge atoms with temperature, which leads to inter-layer and intra-layer diffusion, and a shrinkage of the average facet size. Upon heating, our simulated gold nanorods undergo a shape transformation preceding the melting transition. The shape transformation is induced by a minimization of the surface free energy, and is accompanied by a complete reconstruction of the internal structure driven by the surface change. During the transformation, the atoms on the end caps of the rod move to the sides of the rods, leading the rods to be shorter and wider. After the transformation, the surface of the stable intermediate state rod is mostly covered by the more stable {111} facets, other than the less stable {110} and {100} facets covering the sides of the initial constructed rod.
Molecular dynamics studies of lanthanum chloride solutions
Meier, W.; Bopp, Ph. ); Probst, M.M. ); Spohr, E. ); Lin, J.L. )
1990-05-31
Molecular dynamics studies are reported for LaCl{sub 3} solutions at two different concentrations and temperatures, and for isolated aqueous La{sup 3+} ions. Ion-water clusters La(H{sub 2}O){sub n}{sup 3+} with n = 61 and n = 100 and systems consisting of one ion and 100 or 200 water molecules in the usual periodic box, as well as solutions of 7 (4) cations and 21 (12) anions in 190 (200) water molecules, corresponding to 2 and 1.1 m solutions, respectively, were investigated. The 2 m solution was investigated at two different temperatures. The results for the static structure, with special emphasis on the hydration structure of the La{sup 3+} ion, are discussed in terms of radial distribution functions and resulting hydration numbers, and various other correlations. These results are compared with X-ray data and discussed in light of the hydration numbers observed for aqueous ions in general.
Efficient compression of molecular dynamics trajectory files.
Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James
2012-10-15
We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases.
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.
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.
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.
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.
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.
Molecular dynamics of biaxial nematic liquid crystals
NASA Astrophysics Data System (ADS)
Sarman, Sten
1996-01-01
We devise a constraint algorithm that makes the angular velocity of the director of a liquid crystal a constant of motion. When the angular velocity is set equal to zero, a director based coordinate system becomes an inertial frame. This is a great advantage because most thermodynamic properties and time correlation functions of a liquid crystal are best expressed relative to a director based coordinate system. One also prevents the director reorientation from interfering with the tails of the time correlation functions. When the angular velocity is forced to be zero the constraints do not do any work on the system. This makes it possible to prove that ensemble averages of phase functions and time correlation functions are unaffected by the director constraint torques. The constraint algorithm also facilitates generalization of nonequilibrium molecular dynamics algorithms to liquid crystal phases. In order to test the algorithm numerically we have simulated a biaxial nematic phase of a variant of the Gay-Berne fluid [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)]. The director constraint algorithm works very well. We have calculated the velocity autocorrelation functions and the self diffusion coefficients. In a biaxial nematic liquid crystal there are three independent components of the self-diffusion tensor. They have been found to be finite and different thus proving that we really simulate a liquid rather than a solid and that the symmetry is biaxial. Simulation of biaxial liquid crystals requires fairly large systems. We have therefore developed an algorithm that we run on a parallel computer instead of an ordinary work station.
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 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.
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
Object image correction using an X-ray dynamical diffraction Fraunhofer hologram.
Balyan, Minas K
2014-03-01
Taking into account background correction and using Fourier analysis, a numerical method of an object image correction using an X-ray dynamical diffraction Fraunhofer hologram is presented. An example of the image correction of a cylindrical beryllium wire is considered. A background correction of second-order iteration leads to an almost precise reconstruction of the real part of the amplitude transmission coefficient and improves the imaginary part compared with that without a background correction. Using Fourier analysis of the reconstructed transmission coefficient, non-physical oscillations can be avoided. This method can be applied for the determination of the complex amplitude transmission coefficient of amplitude as well as phase objects, and can be used in X-ray microscopy.
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
NASA Astrophysics Data System (ADS)
Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; Schwegler, Eric
2016-10-01
Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na+, K+, and Cl- ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.
Frontiers in molecular dynamics simulations of DNA.
Pérez, Alberto; Luque, F Javier; Orozco, Modesto
2012-02-21
It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global
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.
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.
Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids.
Voulgarakis, Nikolaos K; Chu, Jhih-Wei
2009-04-01
A new multiscale coarse-graining (CG) methodology is developed to bridge molecular and hydrodynamic models of a fluid. The hydrodynamic representation considered in this work is based on the equations of fluctuating hydrodynamics (FH). The essence of this method is a mapping from the position and velocity vectors of a snapshot of a molecular dynamics (MD) simulation to the field variables on Eulerian cells of a hydrodynamic representation. By explicit consideration of the effective lengthscale d(mol) that characterizes the volume of a molecule, the computed density fluctuations from MD via our mapping procedure have volume dependence that corresponds to a grand canonical ensemble of a cold liquid even when a small cell length (5-10 A) is used in a hydrodynamic representation. For TIP3P water at 300 K and 1 atm, d(mol) is found to be 2.4 A, corresponding to the excluded radius of a water molecule as revealed by its center-of-mass radial distribution function. By matching the density fluctuations and autocorrelation functions of momentum fields computed from solving the FH equations with those computed from MD simulation, the sound velocity and shear and bulk viscosities of a CG hydrodynamic model can be determined directly from MD. Furthermore, a novel staggered discretization scheme is developed for solving the FH equations of an isothermal compressive fluid in a three dimensional space with a central difference method. This scheme demonstrates high accuracy in satisfying the fluctuation-dissipation theorem. Since the causative relationship between field variables and fluxes is captured, we demonstrate that the staggered discretization scheme also predicts correct physical behaviors in simulating transient fluid flows. The techniques presented in this work may also be employed to design multiscale strategies for modeling complex fluids and macromolecules in solution. PMID:19355721
Trudell, J R; Bertaccini, E
1998-11-23
(1) Successful application of molecular mechanics and molecular dynamics calculations to the binding of halogenated anesthetics requires forcefields with correct parameters for halocarbons. (2) Unfortunately, our survey of six popular forcefields revealed that some of them provide a very poor representation of electrostatic interactions for the halogens. (3) This problem is due to poor or missing assignments of partial atomic charges to the halogen atoms. (4) We describe the forcefields most appropriate for use with halogenated anesthetics and suggest a general method for editing the assignment of partial atomic charges by performing an initial quantum mechanics calculation. PMID:10049174
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.
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
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...
Attosecond molecular dynamics: fact or fiction?
NASA Astrophysics Data System (ADS)
Lépine, Franck; Ivanov, Misha Y.; Vrakking, Marc J. J.
2014-03-01
The emerging application of attosecond techniques to molecular systems allows the role of electronic coherence in the control of chemical reactions to be investigated. Prompt ionization of molecules by an attosecond pulse may induce charge migration across a molecular structure on attosecond to few-femtosecond timescales, thereby possibly determining the subsequent relaxation pathways that a molecule may take. We discuss how proposals for this 'charge-directed reactivity' fit within the current understanding of quantum control and review the current state of the art of attosecond molecular science. Specifically, we review the role of electronic coherence and coupling of the electronic and nuclear degrees of freedom in high-harmonic spectroscopy and in the first attosecond pump-probe experiments on molecular systems.
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
Error suppression and error correction in adiabatic quantum computation: non-equilibrium dynamics
NASA Astrophysics Data System (ADS)
Sarovar, Mohan; Young, Kevin C.
2013-12-01
While adiabatic quantum computing (AQC) has some robustness to noise and decoherence, it is widely believed that encoding, error suppression and error correction will be required to scale AQC to large problem sizes. Previous works have established at least two different techniques for error suppression in AQC. In this paper we derive a model for describing the dynamics of encoded AQC and show that previous constructions for error suppression can be unified with this dynamical model. In addition, the model clarifies the mechanisms of error suppression and allows the identification of its weaknesses. In the second half of the paper, we utilize our description of non-equilibrium dynamics in encoded AQC to construct methods for error correction in AQC by cooling local degrees of freedom (qubits). While this is shown to be possible in principle, we also identify the key challenge to this approach: the requirement of high-weight Hamiltonians. Finally, we use our dynamical model to perform a simplified thermal stability analysis of concatenated-stabilizer-code encoded many-body systems for AQC or quantum memories. This work is a companion paper to ‘Error suppression and error correction in adiabatic quantum computation: techniques and challenges (2013 Phys. Rev. X 3 041013)’, which provides a quantum information perspective on the techniques and limitations of error suppression and correction in AQC. In this paper we couch the same results within a dynamical framework, which allows for a detailed analysis of the non-equilibrium dynamics of error suppression and correction in encoded AQC.
Gao, Peng-fei; Yang, Rui; Ji, Jiang; Guo, Han-ming; Hu, Qi; Zhuang, Song-lin
2015-05-01
The baseline correction is an, extremely important spectral preprocessing step and can significantly improve the accuracy of the subsequent spectral analysis algorithm. At present most of the baseline correction algorithms are manual and semi-automated. The manual baseline correction depends on the user experience and its accuracy is greatly affected by the subjective factor. The semi-automated baseline correction needs to set different optimizing parameters for different Raman spectra, which will be inconvenient to users. In this paper, a locally.dynamically moving average algorithm (LDMA) for the fully automated baseline correction is presented and its basic ideas.and steps are demonstrated in detail. In the LDMA algorithm the modified moving averaging algorithm (MMA) is used to strip the Raman peaks. By automatically finding the baseline subintervals of the raw Raman spectrum to divide the total spectrum range into multi Raman peak subintervals, the LDMA algorithm succeed in dynamically changing the window half width of the MA algorithm and controlling the numbers of the smoothing iterations in each Raman peak subinterval. Hence, the phenomena of overcorrection and under-correction are avoided to the most degree. The LDMA algorithm has achieved great effect not only to the synthetic Raman spectra with the convex, exponential, or sigmoidal baseline but also to the real Raman spectra.
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
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
Jiang, Cheng; Cui, Yuanshun; Chen, Guibin
2016-01-01
We explore theoretically the dynamics of an optomechanical system in which a resonantly driven cavity mode is quadratically coupled to the displacement of a mechanical resonator. Considering the first order correction to adiabatic elimination, we obtain the analytical expression of optomechanical damping rate which is negative and depends on the position of the mechanical resonator. After comparing the numerical results between the full simulation of Langevin equations, adiabatic elimination, and first order correction to adiabatic elimination, we explain the dynamics of the system in terms of overall mechanical potential and optomechanical damping rate. The antidamping induced by radiation pressure can result in self-sustained oscillation of the mechanical resonator. Finally, we discuss the time evolution of the intracavity photon number, which also shows that the effect of first order correction cannot be neglected when the ratio of the cavity decay rate to the mechanical resonance frequency becomes smaller than a critical value. PMID:27752125
Dynamic and Inherent B0 Correction for DTI Using Stimulated Echo Spiral Imaging
Avram, Alexandru V.; Guidon, Arnaud; Truong, Trong-Kha; Liu, Chunlei; Song, Allen W.
2013-01-01
Purpose To present a novel technique for high-resolution stimulated echo (STE) diffusion tensor imaging (DTI) with self-navigated interleaved spirals (SNAILS) readout trajectories that can inherently and dynamically correct for image artifacts due to spatial and temporal variations in the static magnetic field (B0) resulting from eddy currents, tissue susceptibilities, subject/physiological motion, and hardware instabilities. Methods The Hahn spin echo formed by the first two 90° radio-frequency pulses is balanced to consecutively acquire two additional images with different echo times (TE) and generate an inherent field map, while the diffusion-prepared STE signal remains unaffected. For every diffusion-encoding direction, an intrinsically registered field map is estimated dynamically and used to effectively and inherently correct for off-resonance artifacts in the reconstruction of the corresponding diffusion-weighted image (DWI). Results After correction with the dynamically acquired field maps, local blurring artifacts are specifically removed from individual STE DWIs and the estimated diffusion tensors have significantly improved spatial accuracy and larger fractional anisotropy. Conclusion Combined with the SNAILS acquisition scheme, our new method provides an integrated high-resolution short-TE DTI solution with inherent and dynamic correction for both motion-induced phase errors and off-resonance effects. PMID:23630029
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
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.
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)
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.
NASA Astrophysics Data System (ADS)
Pavese, Marc; Berard, Daniel R.; Voth, Gregory A.
1999-01-01
A fully quantum molecular dynamics method is presented which combines ab initio Car-Parrinello molecular dynamics with centroid molecular dynamics. The first technique allows the forces on the atoms to be obtained from ab initio electronic structure. The second technique, given the forces on the atoms, allows one to calculate an approximate quantum time evolution for the nuclei. The combination of the two, therefore, represents the first feasible approach to simulating the fully quantum dynamics of a many-body system. An application to excess proton translocation along a model water wire will be presented.
Molecular Dynamics in Self-Assembled Monolayers
NASA Astrophysics Data System (ADS)
Bochinski, Jason; Stevens, Derrick; Scott, Mary; Guy, Laura; Dedeugd, Casey; Clarke, Laura
2007-03-01
Silane self-assembled monolayers (SAMs) are an important tool for both scientific research and technological applications. Despite their widespread use, few experimental investigations have addressed molecular motion within these films, which offer a unique and useful physical system for fundamental scientific studies, such as observing dipolar and other glass transitions in two-dimensions. In addition, relaxations such as ``rotator'' phases where molecular groups rotate in a plane parallel to the surface have been correlated with film conductivity, adhesive, and wetting properties. We utilize surface-sensitive, dielectric relaxation spectroscopy to probe molecular motion as a function of temperature within silane chemistry-based monolayers formed upon interdigitated electrodes. Our latest results exploring a previously published motion as well as comparisons to linear polymer films will be discussed.
On electronic representations in molecular reaction dynamics
NASA Astrophysics Data System (ADS)
Killian, Benjamin J.
For many decades, the field of chemical reaction dynamics has utilized computational methods that rely on potential energy surfaces that are constructed using stationary-state calculations. These methods are typically devoid of dynamical couplings between the electronic and nuclear degrees of freedom, a fact that can result in incorrect descriptions of dynamical processes. Often, non-adiabatic coupling expressions are included in these methodologies. The Electron-Nuclear Dynamics (END) formalism, in contrast, circumvents these deficiencies by calculating all intermolecular forces directly at each time step in the dynamics and by explicitly maintaining all electronic-nuclear couplings. The purpose of this work is to offer two new frameworks for implementing electronic representations in dynamical calculations. Firstly, a new schema is proposed for developing atomic basis sets that are consistent with dynamical calculations. Traditionally, basis sets have been designed for use in stationary-state calculations of the structures and properties of molecules in their ground states. As a consequence of common construction techniques that utilize energy optimization methods, the unoccupied orbitals bear little resemblance to physical virtual atomic orbitals. We develop and implement a method for basis set construction that relies upon physical properties of atomic orbitals and that results in meaningful virtual orbitals. These basis sets are shown to provide a significant improvement in the accuracy of calculated dynamical properties such as charge transfer probabilities. Secondly, the theoretical framework of END is expanded to incorporate a multi-configurational representation for electrons. This formalism, named Vector Hartree-Fock, is based in the theory of vector coherent states and utilizes a complete active space electronic representation. The Vector Hartree-Fock method is fully disclosed, with derivation of the equations of motion. The expressions for the equation
Optimal control of molecular motion expressed through quantum fluid dynamics
NASA Astrophysics Data System (ADS)
Dey, Bijoy K.; Rabitz, Herschel; Askar, Attila
2000-04-01
A quantum fluid-dynamic (QFD) control formulation is presented for optimally manipulating atomic and molecular systems. In QFD the control quantum system is expressed in terms of the probability density ρ and the quantum current j. This choice of variables is motivated by the generally expected slowly varying spatial-temporal dependence of the fluid-dynamical variables. The QFD approach is illustrated for manipulation of the ground electronic state dynamics of HCl induced by an external electric field.
Single Molecule Spectroscopy Illuminating the Molecular Dynamics of Life
NASA Astrophysics Data System (ADS)
Webb, Watt W.
This chapter summarizes a series of new single-molecule spectroscopy investigations in the life sciences at Cornell University that began with our invention of Fluorescence Correlation Spectroscopy (FCS) about 1970. Our invention of FCS became my first focus on the "Molecular Dynamics of Life." It motivated my transition from research on quantum fluctuations and transport in condensed matter physics including superconductivity and in the molecular dynamics of coherent fluctuations and nano-transport in inanimate physical and chemical systems subject to the nonlinear dynamics of continuous phase transitions. These interdisciplinary transitions exemplify the productivity of such interdisciplinary interactions in science.
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.
Josa, Daniela; Rodríguez-Otero, Jesús; Cabaleiro-Lago, Enrique M
2015-05-28
In 2007, Sygula and co-workers introduced a novel type of molecular tweezers with buckybowl pincers that have attracted the substantial interest of researchers due to their ideal architecture for recognizing fullerenes by concave-convex π∙∙∙π interactions (A. Sygula et al., J. Am. Chem. Soc., 2007, 129, 3842). Although in recent years some modifications have been performed on these original molecular tweezers to improve their ability for catching fullerenes, very few improvements were achieved to date. For that reason, in the present work a series of molecular tweezers have been devised and their supramolecular complexes with C60 studied at the B97-D2/TZVP//SCC-DFTB-D and B97-D2/TZVP levels. Three different strategies have been tested: (1) changing the corannulene pincers to other buckybowls, (2) replacing the tetrabenzocyclooctatetraene tether by a buckybowl, and (3) adding methyl groups on the molecular tweezers. According to the results, all the three approaches are effective, in such a way that a combination of the three strategies results in buckycatchers with complexation energies (with C60) up to 2.6 times larger than that of the original buckycatcher, reaching almost -100 kcal mol(-1). The B97-D2/TZVP//SCC-DFTB-D approach can be a rapid screening tool for testing new molecular tweezers. However, since this approach does not reproduce correctly the deformation energy and this energy represents an important contribution to the total complexation energy of complexes, subsequent higher-level re-optimization is compulsory to achieve reliable results (the full B97-D2/TZVP level is used herein). This re-optimization could be superfluous when quite rigid buckycatchers are studied.
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.
NASA Astrophysics Data System (ADS)
Valentini, Paolo; Schwartzentruber, Thomas E.
2009-12-01
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 ρ=10-4 kg/m and ρ=10-1 kg/m, 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.
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.
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
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.
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
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
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.
Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
Luchko, T.; Simmerling, C.; Gusarov, S.; Roe, D.R., Case, D.A.; Tuszynski, J.; Kovalenko, A.
2010-02-01
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 multiple 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.
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
Dynamic distortions in the HARP TPC: observations, measurements, modelling and corrections
NASA Astrophysics Data System (ADS)
Bagulya, A.; Blondel, A.; Borghi, S.; Catanesi, G.; Chimenti, P.; Gastaldi, U.; Giani, S.; Grichine, V.; Ivanchenko, V.; Kolev, D.; Panman, J.; Radicioni, E.; Tsenov, R.; Tsukerman, I.
2009-11-01
The HARP experiment was designed to study hadron production in proton-nucleus collisions in the energy range of 1.5 GeV/c-15 GeV/c. The experiment was made of two spectrometers, a forward dipole spectrometer and a large-angle solenoid spectrometer. In the large-angle spectrometer the main tracking and particle identification is performed by a cylindrical Time Projection Chamber (TPC) which suffered a number of shortcomings later addressed in the analysis. In this paper we discuss the effects of time-dependent (dynamic) distortions of the position measurements in the TPC which are due to a build-up of ion charges in the chamber during the accelerator spill. These phenomena have been studied both by modelling and by experiment, and a correction procedure has been developed. The effects of the time-dependent distortions have been measured experimentally by means of recoil protons in elastic scattering reactions, where the track coordinates are precisely predictable from simple kinematical considerations. The dynamics of the positive ion cloud and of the electrostatics of the field-cage system have been modelled with a phenomenological approach providing an understanding of the features. Using the elastic scattering data a general correction procedure has been developed and applied to all data settings. After application of the corrections for dynamic distortions the corrected data have a performance equal to data where the dynamic distortions are absent. We describe the phenomenological model, the comparison with the measurements, the distortion correction method and the results obtained with experimental data.
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.
Combining Molecular Dynamics and Density Functional Theory
NASA Astrophysics Data System (ADS)
Kaxiras, Efthimios
2015-03-01
The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.
Pseudorotational Dynamics of Small Molecular Systems
NASA Astrophysics Data System (ADS)
Hagelberg, Frank
2001-03-01
A variety of dynamic effects related to the pseudorotation of triatomic singly charged species is explored using the Electron Nuclear Dynamics(END)Theory. The concepts relevant to the motion studied are developed through the analysis of the simplest polyatomic molecule, namely H3+. It is shown that the limiting situation of circular pseudorotation is unattainable for this case. This observation is explained by the anisotropy of the ground state potential energy surface caused by the interaction between the D3h ground state of the molecule and its twofold degenerate first excited state. Further, pseudorotational motion is demonstrated to induce a rotational mode which in turn couples the two shape oscillation modes by action of the Coriolis force. Analogous phenomena are found for Li3+. The Jahn-Teller system C3+ exhibits a range of new motional effects. Particularly, a characteristic frequency shift between the two shape oscillation modes is obtained, resulting from the anisotropy in the curvature of the C2v minimum of C3+. The Jahn-Teller parameters of the system are determined from Electron Nuclear Dynamics simulations.
Hydrolysis of Al3+ from constrained molecular dynamics
NASA Astrophysics Data System (ADS)
Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi
2006-02-01
We investigated the hydrolysis reactions of Al3+ in AlCl3 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 ΔG0≃8.0kcalmol-1 the hydrolysis constant pKa1 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 Al3+ in acidic conditions is at least 4kcalmol-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.
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
Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors
Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem
2015-01-01
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. PMID:25688287
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.
Thermal Conductivity of Natural Rubber Using Molecular Dynamics Simulation.
He, Yan; Ma, Lian-Xiang; Tang, Yuan-Zheng; Wang, Ze-Peng; Li, Wei; Kukulka, David
2015-04-01
Thermal conductivity of natural rubber has been studied by classic molecular dynamics simulations. These simulations are performed on natural rubber models using the adaptive intermolecular reactive empirical bond order (AIREBO) and the Green-Kubo molecular dynamics (MD) simulations. Thermal conductivity results are found to be very sensitive to the time step used in the simulations. For a time step of 0.1 fs, the converged thermal conductivity is 0.35 W/mK. Additionally the anisotropic thermal conductivity of a specially-modeled natural rubber model with straight molecular chains was studied and values of thermal conductivity parallel to the molecular chains was found to be 1.71 W/mK and the anisotropy, 2Kz/(Kx + Ky), was 2.67.
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
Molecular Dynamics Simulations of Liquid-Crystalline Dendritic Architectures
NASA Astrophysics Data System (ADS)
Bourgogne, C.; Bury, I.; Gehringer, L.; Zelcer, A.; Cukiernik, F.; Terazzi, E.; Donnio, B.; Guillon, D.
We report here a few examples of the self-organization behaviour of some novel materials based on liquid-crystalline dendritic architectures. The original design of the molecules imposes the use of all-atomic methods to model correctly every intra- and intermolecular effects. The selected materials are octopus dendrimers with block anisotropic side-arms, segmented amphiphilic block codendrimers, multicore and star-shaped oligomers, and multi-functionalized manganese clusters. The molecular organization in lamellar or columnar phases occurs due to soft/rigid parts self-recognition, hydrogen-bonding networks or from the molecular shape intrinsically.
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
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).
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.
AceCloud: Molecular Dynamics Simulations in the Cloud.
Harvey, M J; De Fabritiis, G
2015-05-26
We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.
NASA Astrophysics Data System (ADS)
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.
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
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.
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.
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.
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
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.
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.
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
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.
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.
Input File Creation for the Molecular Dynamics Program LAMMPS.
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.
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.
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.
Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics
Holian, B.L.; Voter, A.F.; Ravelo, R.
1995-09-01
The Nose-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ``demon,`` which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature. We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations.
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
Quantum dynamics of light-driven chiral molecular motors.
Yamaki, Masahiro; Nakayama, Shin-ichiro; Hoki, Kunihito; Kono, Hirohiko; Fujimura, Yuichi
2009-03-21
The results of theoretical studies on quantum dynamics of light-driven molecular motors with internal rotation are presented. Characteristic features of chiral motors driven by a non-helical, linearly polarized electric field of light are explained on the basis of symmetry argument. The rotational potential of the chiral motor is characterized by a ratchet form. The asymmetric potential determines the directional motion: the rotational direction is toward the gentle slope of the asymmetric potential. This direction is called the intuitive direction. To confirm the unidirectional rotational motion, results of quantum dynamical calculations of randomly-oriented molecular motors are presented. A theoretical design of the smallest light-driven molecular machine is presented. The smallest chiral molecular machine has an optically driven engine and a running propeller on its body. The mechanisms of transmission of driving forces from the engine to the propeller are elucidated by using a quantum dynamical treatment. The results provide a principle for control of optically-driven molecular bevel gears. Temperature effects are discussed using the density operator formalism. An effective method for ultrafast control of rotational motions in any desired direction is presented with the help of a quantum control theory. In this method, visible or UV light pulses are applied to drive the motor via an electronic excited state. A method for driving a large molecular motor consisting of an aromatic hydrocarbon is presented. The molecular motor is operated by interactions between the induced dipole of the molecular motor and the electric field of light pulses. PMID:19290336
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.
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.
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.
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
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
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…
Molecular dynamics simulation of size segregation in three dimensions
NASA Astrophysics Data System (ADS)
Gallas, Jason A. C.; Herrmann, Hans J.; Pöschel, Thorsten; Sokołowski, Stefan
1996-01-01
We report the first three-dimensional molecular dynamics simulation of particle segregation by shaking. Two different containers are considered: one cylindrical and another with periodic boundary conditions. The dependence of the time evolution of a test particle inside the material is studied as a function of the shaking frequency and amplitude, damping coefficients, and dispersivity.
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.
Clustering molecular dynamics trajectories for optimizing docking experiments.
De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C
2015-01-01
Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.
Clustering molecular dynamics trajectories for optimizing docking experiments.
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
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
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.
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
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
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
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
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
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
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.
Correcting sequencing errors in DNA coding regions using a dynamic programming approach
Xu, Y.; Mural, R.J.; Uberbacher, E.C.
1994-12-01
This paper presents an algorithm for detecting and ``correcting`` sequencing errors that occur in DNA coding regions. The types of sequencing error addressed include insertions and deletions (indels) of DNA bases. The goal is to provide a capability which makes single-pass or low-redundancy sequence data more informative, reducing the need for high-redundancy sequencing for gene identification and characterization purposes. The algorithm detects sequencing errors by discovering changes in the statistically preferred reading frame within a putative coding region and then inserts a number of ``neutral`` bases at a perceived reading frame transition point to make the putative exon candidate frame consistent. The authors have implemented the algorithm as a front-end subsystem of the GRAIL DNA sequence analysis system to construct a version which is very error tolerant and also intend to use this as a testbed for further development of sequencing error-correction technology. On a test set consisting of 68 Human DNA sequences with 1% randomly generated indels in coding regions, the algorithm detected and corrected 76% of the indels. The average distance between the position of an indel and the predicted one was 9.4 bases. With this subsystem in place, GRAIL correctly predicted 89% of the coding messages with 10% false message on the ``corrected`` sequences, compared to 69% correctly predicted coding messages and 11% falsely predicted messages on the ``corrupted`` sequences using standard GRAIL II method. The method uses a dynamic programming algorithm, and runs in time and space linear to the size of the input sequence.
Ab initio molecular dynamics: Concepts, recent developments, and future trends
Iftimie, Radu; Minary, Peter; Tuckerman, Mark E.
2005-01-01
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
Molecular Dynamics Simulations of Lignin Peroxidase in Solution
Francesca Gerini, M.; Roccatano, Danilo; Baciocchi, Enrico; Nola, Alfredo Di
2003-01-01
The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel. PMID:12770894
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.
Li, Jianwei; Nowak, Piotr; Otto, Sijbren
2013-06-26
Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.
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.
Wen, C; Smith, David J
2016-10-01
Aberration-corrected transmission electron microscope images taken under optimum-defocus conditions or processed offline can correctly reflect the projected crystal structure with atomic resolution. However, dynamical scattering, which will seriously influence image contrast, is still unavoidable. Here, the multislice image simulation approach was used to quantify the impact of dynamical scattering on the contrast of aberration-corrected images for a 3C-SiC specimen with changes in atomic occupancy and thickness. Optimum-defocus images with different spherical aberration (CS) coefficients, and structure images restored by deconvolution processing, were studied. The results show that atomic-column positions and the atomic occupancy for SiC 'dumbbells' can be determined by analysis of image contrast profiles only below a certain thickness limit. This limit is larger for optimum-defocus and restored structure images with negative CS coefficient than those with positive CS coefficient. The image contrast of C (or Si) atomic columns with specific atomic occupancy changes differently with increasing crystal thickness. Furthermore, contrast peaks for C atomic columns overlapping with neighboring peaks of Si atomic columns with varied Si atomic occupancy, which is enhanced with increasing crystal thickness, can be neglected in restored structure images, but the effect is substantial in optimum-defocus images.
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.
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
Lauve, A D; Siebers, J V; Crimaldi, A J; Hagan, M P; Kealla, P J
2006-06-01
Traditionally, pretreatment detected patient-positioning errors have been corrected by repositioning the couch to align the patient to the treatment beam. We investigated an alternative strategy: aligning the beam to the patient by repositioning the dynamic multileaf collimator and adjusting the beam weights, termed dynamic compensation. The purpose of this study was to determine the geometric range of positioning errors for which the dynamic compensation method is valid in prostate cancer patients treated with three-dimensional conformal radiotherapy. Twenty-five previously treated prostate cancer patients were replanned using a four-field technique to deliver 72 Gy to 95% of the planning target volume (PTV). Patient-positioning errors were introduced by shifting the patient reference frame with respect to the treatment isocenter. Thirty-six randomly selected isotropic displacements with magnitudes of 1.0, 2.0, 4.0, 6.0, 8.0, and 10.0 cm were sampled for each patient, for a total of 5400 errors. Dynamic compensation was used to correct each of these errors by conforming the beam apertures to the new target position and adjusting the monitor units using inverse-square and off-axis factor corrections. The dynamic compensation plans were then compared with the original treatment plans via dose-volume histogram (DVH) analysis. Changes of more than 5% of the prescription dose, 3.6 Gy, were deemed significant. Compared with the original treatment plans, dynamic compensation produced small discrepancies in isodose distributions and DVH analyses. These differences increased with the magnitudes of the initial patient-positioning errors. Coverage of the PTV was excellent: D95 and Dmean were not increased or decreased by more than 5% of the prescription dose, and D5 was not decreased by more than 5% of the prescription dose for any of the 5400 simulated positioning errors. D5 was increased by more than 5% of the prescription dose in only three of the 5400 positioning errors
Lauve, A. D.; Siebers, J. V.; Crimaldi, A. J.; Hagan, M. P.; Keall, P. J.
2006-06-15
Traditionally, pretreatment detected patient-positioning errors have been corrected by repositioning the couch to align the patient to the treatment beam. We investigated an alternative strategy: aligning the beam to the patient by repositioning the dynamic multileaf collimator and adjusting the beam weights, termed dynamic compensation. The purpose of this study was to determine the geometric range of positioning errors for which the dynamic compensation method is valid in prostate cancer patients treated with three-dimensional conformal radiotherapy. Twenty-five previously treated prostate cancer patients were replanned using a four-field technique to deliver 72 Gy to 95% of the planning target volume (PTV). Patient-positioning errors were introduced by shifting the patient reference frame with respect to the treatment isocenter. Thirty-six randomly selected isotropic displacements with magnitudes of 1.0, 2.0, 4.0, 6.0, 8.0, and 10.0 cm were sampled for each patient, for a total of 5400 errors. Dynamic compensation was used to correct each of these errors by conforming the beam apertures to the new target position and adjusting the monitor units using inverse-square and off-axis factor corrections. The dynamic compensation plans were then compared with the original treatment plans via dose-volume histogram (DVH) analysis. Changes of more than 5% of the prescription dose, 3.6 Gy, were deemed significant. Compared with the original treatment plans, dynamic compensation produced small discrepancies in isodose distributions and DVH analyses. These differences increased with the magnitudes of the initial patient-positioning errors. Coverage of the PTV was excellent: D{sub 95} and D{sub mean} were not increased or decreased by more than 5% of the prescription dose, and D{sub 5} was not decreased by more than 5% of the prescription dose for any of the 5400 simulated positioning errors. D{sub 5} was increased by more than 5% of the prescription dose in only three of the
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.
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.
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.
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.
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.
Liu, Qixin; Cai, Zhiyong
2014-01-01
This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745
Molecular dynamics simulation: A tool for exploration and discovery
NASA Astrophysics Data System (ADS)
Rapaport, Dennis C.
2009-03-01
The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).
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
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
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.
Improving structure-based function prediction using molecular dynamics
Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.
2009-01-01
Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472
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.
ICESat Receiver Signal Dynamic Range Assessment and Correction of Range Bias due to Saturation
NASA Astrophysics Data System (ADS)
Sun, X.; Abshire, J. B.; Yi, D.; Fricker, H. A.
2005-12-01
The laser echo pulse signals for Earth orbiting laser altimeters have a large dynamic range due to the variabilities in the Earth's surface reflectivity, scattering angles, and atmosphere conditions. The echo pulse energies received by the Geoscience Laser Altimeter System (GLAS) on the ICESat mission vary over 4 orders of magnitude. Echo pulse energies measured over ice and snow surfaces are 2 to 3 times stronger than those expected, which were based on prior passive measurements and by assuming Lambertian scattering surfaces. Echo pulse energies from still water surfaces are several hundred times stronger, due to the narrow solid angle of the specular reflections. Attenuation by clouds and aerosols also cause a large and rapid variation in the received signal. As a result, many of the echo pulses exceed the linear dynamic range of the GLAS altimeter receiver and partially saturate the detector electronics. The recorded pulse waveform is distorted when the receiver is saturated, causing a significant bias in the GLAS range, surface slope, and surface reflectance measurements. We have characterized the properties of the GLAS altimetry detector beyond its linear dynamic range. We did this in the laboratory using a flight spare detector assembly and a calibrated laser diode test source. The results show the highly reproducible effects of detector saturation on the range measurements. A simple algorithm can be used to correct the range bias to within 5 cm for signals from flat ice and snow surfaces. The algorithm was tested using the GLAS measurements over Salar de Uyuni, Bolivia, where the surface elevation of the dry salt-lake had been surveyed with cm-level resolution with GPS receivers. The results show that the GLAS range measurements with the range bias correction agree with surface elevations to within 2 cm in absolute range and 3 cm in standard deviation. The algorithm is being incorporated into the GLAS data products. We are currently extending the approach
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.
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.
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
Basconi, Joseph E; Shirts, Michael R
2013-07-01
Temperature control algorithms in molecular dynamics (MD) simulations are necessary to study isothermal systems. However, these thermostatting algorithms alter the velocities of the particles and thus modify the dynamics of the system with respect to the microcanonical ensemble, which could potentially lead to thermostat-dependent dynamical artifacts. In this study, we investigate how six well-established thermostat algorithms applied with different coupling strengths and to different degrees of freedom affect the dynamics of various molecular systems. We consider dynamic processes occurring on different times scales by measuring translational and rotational self-diffusion as well as the shear viscosity of water, diffusion of a small molecule solvated in water, and diffusion and the dynamic structure factor of a polymer chain in water. All of these properties are significantly dampened by thermostat algorithms which randomize particle velocities, such as the Andersen thermostat and Langevin dynamics, when strong coupling is used. For the solvated small molecule and polymer, these dampening effects are reduced somewhat if the thermostats are applied to the solvent alone, such that the solute's temperature is maintained only through thermal contact with solvent particles. Algorithms which operate by scaling the velocities, such as the Berendsen thermostat, the stochastic velocity rescaling approach of Bussi and co-workers, and the Nosé-Hoover thermostat, yield transport properties that are statistically indistinguishable from those of the microcanonical ensemble, provided they are applied globally, i.e. coupled to the system's kinetic energy. When coupled to local kinetic energies, a velocity scaling thermostat can have dampening effects comparable to a velocity randomizing method, as we observe when a massive Nose-Hoover coupling scheme is used to simulate water. Correct dynamical properties, at least those studied in this paper, are obtained with the Berendsen
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.
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
NASA Astrophysics Data System (ADS)
Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto
Molecular crystal structure prediction has posed a substantial challenge to first-principles methods and requires sophisticated electronic structure methods to determine the stabilities of nearly degenerate polymorphs. In this work, we demonstrate that the anharmonicity from van der Waals interactions is relevant to the finite-temperature structures of pyridine and pyridine-like molecular crystals. Using such an approach, we find that the equilibrium structures are well captured with classical ab initio molecular dynamics (AIMD), despite the presence of light atoms such as hydrogen. Employing path integral AIMD simulations, we demonstrate that the success of classical AIMD results from a separation of nuclear quantum effects between the intermolecular and intramolecular degrees of freedom. In this separation, the quasiclassical and anharmonic intermolecular degrees of freedom determine the equilibrium structure, while the quantum and harmonic intramolecular degrees of freedom are averaging to the correct intramolecular structure. This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.
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,…
Dong, Bing; Li, Yan; Han, Xin-Li; Hu, Bin
2016-09-02
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.
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
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
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.
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.
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.
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.
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.
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.
Nissen, Felix; Keeling, Jonathan
2010-06-15
We apply a many-body Wentzel-Kramers-Brillouin (WKB) approach to determine the leading quantum corrections to the semiclassical dynamics of the Josephson model, describing interacting bosons able to tunnel between two localized states. The semiclassical dynamics is known to divide between regular oscillations and self-trapped oscillations where the sign of the imbalance remains fixed. In both cases, the WKB wave functions are matched to Airy functions, yielding a modified Bohr-Sommerfeld quantization condition. At the critical energy dividing normal and self-trapped oscillations, the WKB wave functions should instead be matched to parabolic cylinder functions, leading to a quantization formula that is not just the Bohr-Sommerfeld formula, and recovering the known logarithmic quantum break times at this energy. This work thus provides another illustration of the usefulness of the WKB approach in certain many-body problems.
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
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.
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.
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
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
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.
Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics
Mücksch, Christian; Urbassek, Herbert M.
2013-01-01
The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ( s) and experiment (up to hours), and the accordingly different ‘final’ adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces. PMID:23755156
Adiabatic molecular-dynamics-simulation-method studies of kinetic friction
NASA Astrophysics Data System (ADS)
Zhang, J.; Sokoloff, J. B.
2005-06-01
An adiabatic molecular-dynamics method is developed and used to study the Muser-Robbins model for dry friction (i.e., nonzero kinetic friction in the slow sliding speed limit). In this model, dry friction between two crystalline surfaces rotated with respect to each other is due to mobile molecules (i.e., dirt particles) adsorbed at the interface. Our adiabatic method allows us to quickly locate interface potential-well minima, which become unstable during sliding of the surfaces. Since dissipation due to friction in the slow sliding speed limit results from mobile molecules dropping out of such unstable wells, our method provides a way to calculate dry friction, which agrees extremely well with results found by conventional molecular dynamics for the same system, but our method is more than a factor of 10 faster.
Coherent Amplification of Ultrafast Molecular Dynamics in an Optical Oscillator.
Aharonovich, Igal; Pe'er, Avi
2016-02-19
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.
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 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
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.
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.
Long Timestep Molecular Dynamics on the Graphical Processing Unit
Sweet, James C.; Nowling, Ronald J.; Cickovski, Trevor; Sweet, Christopher R.; Pande, Vijay S.; Izaguirre, Jesús A.
2013-01-01
Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 μs/day using implicit solvent models. PMID:24436689
Correct diagnosis of Warthin tumor in the parotid gland with dynamic MRI.
Ogawa, Takenori; Suzuki, Takahiro; Sakamoto, Maya; Watanabe, Mika; Tateda, Yutaka; Oshima, Takeshi; Kato, Kengo; Sagai, Shun; Kobayashi, Toshimitsu; Shiga, Kiyoto
2012-01-01
Warthin tumor (WT) is a benign tumor of the salivary gland primarily affecting middle-aged men. WT is almost exclusively located in the parotid gland and tend to grow slowly without symptoms. Although fine needle aspiration cytology (FNAC) often correctly diagnoses these tumors, they are occasionally misdiagnosed as malignant. Our study sought to distinguish between WT and non-WT using dynamic MRI. In dynamic MRI, a series of images are taken over time measuring the intensity of gadolinium uptake by the parotid. We examined two patients for this study. The first was a 53-year old male, heavy smoker, experiencing manic-depressive episodes. He received a brain MRI at which time his parotid tumor was discovered. Parotid FNAC indicated a squamous cell carcinoma. The second patient was a 76-year old male, moderate smoker and drinker, who had been complaining about swelling in the neck. FNAC of the parotid indicated acinic cell carcinoma and gadolinium-enhanced MRI suggested the tumor was malignant. Prior to surgically extracting of these masses, we performed dynamic MRI on each patient. Both tumors exhibited a pattern consisting of rapid enhancement and rapid attenuation, the pattern of which is characteristic of WT. The surgical specimens confirmed that both were WTs without malignant transformation. Our findings indicate that dynamic MRI is a useful tool for preoperative diagnosis of WT, where other examinations indicate malignancy. Early and correct diagnosis of WT can minimize the use of invasive procedures, and eliminate the stress placed on the patient from a diagnosis of cancer.
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
Molecular dynamics analysis on impact behavior of carbon nanotubes
NASA Astrophysics Data System (ADS)
Seifoori, Sajjad
2015-01-01
Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler-Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation.
Molecular 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.
Quantum tunneling splittings from path-integral molecular dynamics
NASA Astrophysics Data System (ADS)
Mátyus, Edit; Wales, David J.; Althorpe, Stuart C.
2016-03-01
We illustrate how path-integral molecular dynamics can be used to calculate ground-state tunnelling splittings in molecules or clusters. The method obtains the splittings from ratios of density matrix elements between the degenerate wells connected by the tunnelling. We propose a simple thermodynamic integration scheme for evaluating these elements. Numerical tests on fully dimensional malonaldehyde yield tunnelling splittings in good overall agreement with the results of diffusion Monte Carlo calculations.
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.
Phase transitions of methane using molecular dynamics simulations
NASA Astrophysics Data System (ADS)
El-Sheikh, S. M.; Barakat, K.; Salem, N. M.
2006-03-01
Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.
Phase transitions of methane using molecular dynamics simulations.
El-Sheikh, S M; Barakat, K; Salem, N M
2006-03-28
Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4 under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256 molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Molecular dynamics simulations of ordering of polydimethylsiloxane under uniaxial extension
Lacevic, N M; Gee, R H
2005-03-11
Molecular dynamics simulations of a bulk melts of polydimethylsiloxane (PDMS) are utilized to study chain conformation and ordering under constant uniaxial tension. We find that large extensions induce chain ordering in the direction of applied tension. We also find that voids are created via a cavitation mechanism. This study represents a validation of the current model for PDMS and benchmark for the future study of mechanical properties of PDMS melts enriched with fillers under tension.
A molecular dynamics study on sI hydrogen hydrate.
Mondal, S; Ghosh, S; Chattaraj, P K
2013-07-01
A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.
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
Molecular dynamics simulation of shocks in porous TATB crystals
Fried, L.E.; Tarver, C.
1995-08-01
We report molecular dynamics results on the shock structure of 2-D crystals of triaminotrinitrobenzene (TATB). We find that the shock front broadens to approx. 30 nm in materials with a 20% random void distribution. As expected from bulk experiments, the shock velocity decreases with increasing porosity and the temperature behind the shock front increases with increasing porosity. Shock equilibration times increase from 1 ps to greater than 10 ps.
Molecular Dynamics study of Pb overlayer on Cu(100)
NASA Technical Reports Server (NTRS)
Karimi, M.; Tibbits, P.; Ila, D.; Dalins, I.; Vidali, G.
1991-01-01
Isothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2x2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.
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.
Molecular Dynamics Simulation of a Microvillus in a Cross Flow
NASA Astrophysics Data System (ADS)
Chen, X. Y.; Liu, Y.; So, R. M. C.; Yang, J. M.
One of the functions of microvilli in the microvessel endothelial glycocalyx is molecular filtering. The microvillus behaves as a mechanosensory system which may sense the fluid shear and drag forces. The permeability of small particles in microvessel is crucial for drug design and drug delivery. Therefore a better understanding of flow field around microvillus is important to simulate accurately the particle penetration in microvessel. Since the dimension of the microvilli is about ~10 nm, the conventional Navier-Stokes equation may not be good enough to simulate the fluid flow in such microscale and nanoscale structures. Molecular dynamics (MD) simulation is a powerful method to simulate the fluid flow at the molecular level. As a first attempt, the microvillus is reduced as a two-dimensional cylinder which is in a cross flow. The detailed drag and lift together with flow field are obtained and compared with available data.
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.
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.
Ultrafast Molecular Dynamics probed by Vacuum Ultraviolet Pulses
NASA Astrophysics Data System (ADS)
Cryan, James; Champenois, Elio; Shivaram, Niranjan; Wright, Travis; Yang, Chan-Shan; Falcone, Roger; Belkacem, Ali
2014-05-01
We present time-resolved measurements of the relaxation dynamics in small molecular systems (CO2 and C2H4) following ultraviolet (UV) photo-excitation. We probe these excitations through photoionization and velocity map imaging (VMI) spectroscopy. Vacuum and extreme ultraviolet (VUV/XUV) pump and probe pulses are created by exploiting strong-field high harmonic generation (HHG) from our state-of-the-art 30 mJ, 1 kHz laser system. Three dimensional photoelectron and photoion momentum images recorded with our VMI spectrometer reveal non-Born Oppenheimer dynamics in the vicinity of a conical intersection, and allow us track the state of the system as a function of time. We also present initial experiments with the goal of controlling the dynamics near a conical intersection using a strong-field IR pulse. Finally, we will show progress towards measurements of time-resolved molecular frame photoelectron angular distributions (TRMFPADs) by applying our VUV/XUV pulse sequence to an aligned molecular ensemble. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.
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.
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.
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.
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.
Molecular Dynamics and Energy Minimization Based on Embedded Atom Method
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 dynamics simulations of lysozyme in water/sugar solutions
NASA Astrophysics Data System (ADS)
Lerbret, A.; Affouard, F.; Bordat, P.; Hédoux, A.; Guinet, Y.; Descamps, M.
2008-04-01
Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.
A rotary nano ion pump: a molecular dynamics study.
Lohrasebi, A; Feshanjerdi, M
2012-09-01
The dynamics of a rotary nano ion pump, inspired by the F (0) part of the F(0)F(1)-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation.
Molecular View on Supramolecular Chain and Association Dynamics
NASA Astrophysics Data System (ADS)
Monkenbusch, M.; Krutyeva, M.; Pyckhout-Hintzen, W.; Antonius, W.; Hövelmann, C. H.; Allgaier, J.; Brás, A.; Farago, B.; Wischnewski, A.; Richter, D.
2016-09-01
The chain and association dynamics of supramolecular polymer ensembles decisively determines their properties. Using neutron spin echo (NSE) spectroscopy we present molecular insight into the space and time evolution of this dynamics. Studying a well characterized ensemble of linearly associating telechelic poly(ethylene glycol) melts carrying triple H-bonding end groups, we show that H-bond breaking significantly impacts the mode spectrum of the associates. The breaking affects the mode contributions and not the relaxation times as was assumed previously. NSE spectra directly reveal the so far intangible H-bond lifetimes in the supramolecular melt and demonstrate that for both the microscopic and the macroscopic dynamics of the supramolecular ensemble the instantaneous average of the Mw distribution governs the system response at least as long as the Rouse picture applies.
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
(Artificial intelligence and molecular dynamics simulations of polymers)
Noid, D.W.
1990-08-27
The traveler participated in planning a new methodology for performing molecular dynamics simulation of polymers. Current computer polymer dynamics programs are either capable of very general calculations and are extremely inefficient or are very efficiently written for a particular computer architecture to study a specific polymer system. Both of these approaches involve tremendous efforts in FORTRAN programming. A combined effort of computer scientists and myself hope to develop an expert system to produce efficient FORTRAN codes for any polymer and be optimized on computer architectures ranging from TRANSPUTERS to CRAY. The result of this collaboration will be an efficient way to model polymer dynamics for an arbitrary polymer structure. The subsidiary purpose was to present a seminar at the University of Newcastle and discussions with several other departments at Oxford University.
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.
Acceleration of dynamic fluorescence molecular tomography with principal component analysis
Zhang, Guanglei; He, Wei; Pu, Huangsheng; Liu, Fei; Chen, Maomao; Bai, Jing; Luo, Jianwen
2015-01-01
Dynamic fluorescence molecular tomography (FMT) is an attractive imaging technique for three-dimensionally resolving the metabolic process of fluorescent biomarkers in small animal. When combined with compartmental modeling, dynamic FMT can be used to obtain parametric images which can provide quantitative pharmacokinetic information for drug development and metabolic research. However, the computational burden of dynamic FMT is extremely huge due to its large data sets arising from the long measurement process and the densely sampling device. In this work, we propose to accelerate the reconstruction process of dynamic FMT based on principal component analysis (PCA). Taking advantage of the compression property of PCA, the dimension of the sub weight matrix used for solving the inverse problem is reduced by retaining only a few principal components which can retain most of the effective information of the sub weight matrix. Therefore, the reconstruction process of dynamic FMT can be accelerated by solving the smaller scale inverse problem. Numerical simulation and mouse experiment are performed to validate the performance of the proposed method. Results show that the proposed method can greatly accelerate the reconstruction of parametric images in dynamic FMT almost without degradation in image quality. PMID:26114027
Confinement of conjugated polymers into soft nanoparticles: molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Wijesinghe, Sidath; Perahia, Dvora; Grest, Gary S.
2013-03-01
The structure and dynamics of conjugated polymers confined into soft nanoparticles (SNPs) have been studies by molecular dynamic simulations. This new class of tunable luminescent SNPs exhibits an immense potential as bio-markers as well as targeted drug delivery agents where tethering specific groups to the surface particles offers a means to target specific applications. Of particular interest are SNPs that consist of non- crosslinked polymers, decorated with polar groups. These SNPs are potentially tunable through the dynamics of the polymer chains, whereas the polar entity serves as internal stabilizer and surface encore. Confinement of a polymer whose inherent conformation is extended impacts not only their dynamics and as a result their optical properties. Here we will present insight into the structure and dynamics of dialkyl poly para phenylene ethynylene (PPE), decorated by a carboxylate groups, confined into a soft particle. The conformation and dynamics of polymer within SNP will be discussed and compared with that of the linear chain in solution. This work in partially supported by DOE grant DE-FG02-12ER46843
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
NASA Astrophysics Data System (ADS)
Boek, E. S.; Jusufi, A.; Löwen, H.; Maitland, G. C.
2002-10-01
Understanding how macroscopic properties depend on intermolecular interactions for complex fluid systems is an enormous challenge in statistical mechanics. This issue is of particular importance for designing optimal industrial fluid formulations such as responsive oilfield fluids, based on viscoelastic surfactant solutions. We have carried out extensive molecular dynamics simulations, resolving the full chemical details in order to study how the structure of the lamellar phase of viscoelastic surfactant solutions depends on the head group (HG) chemistry of the surfactant. In particular, we consider anionic carboxylate and quaternary ammonium HGs with erucyl tails in aqueous solutions together with their sodium and chloride counterions at room temperature. We find a strong HG dependence of the lamellar structure as characterized by suitable pair correlation functions and density distributions. The depth of penetration of water into the bilayer membrane, the nature of counterion condensation on the HGs and even the order and correlation of the tails in the lamellae depend sensitively on the chemical details of the HG. We also determine the compressibility of the lamellar system as a first step to using atom-resolved molecular dynamics in order to link the molecular and macroscopic scales of length and time. The results give important insight into the links between molecular details and surfactant phase structure which is being exploited to develop more systematic procedures for the molecular design and formulation of industrial systems.
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.
Hall,G.E.; Sears, T.J.
2009-04-03
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.
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.
Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies
NASA Astrophysics Data System (ADS)
St. John, Alexander; Wexler, Carlos
2015-03-01
Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.
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
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.
Fault Detection and Correction for the Solar Dynamics Observatory Attitude Control System
NASA Technical Reports Server (NTRS)
Starin, Scott R.; Vess, Melissa F.; Kenney, Thomas M.; Maldonado, Manuel D.; Morgenstern, Wendy M.
2007-01-01
The Solar Dynamics Observatory is an Explorer-class mission that will launch in early 2009. The spacecraft will operate in a geosynchronous orbit, sending data 24 hours a day to a devoted ground station in White Sands, New Mexico. It will carry a suite of instruments designed to observe the Sun in multiple wavelengths at unprecedented resolution. The Atmospheric Imaging Assembly includes four telescopes with focal plane CCDs that can image the full solar disk in four different visible wavelengths. The Extreme-ultraviolet Variability Experiment will collect time-correlated data on the activity of the Sun's corona. The Helioseismic and Magnetic Imager will enable study of pressure waves moving through the body of the Sun. The attitude control system on Solar Dynamics Observatory is responsible for four main phases of activity. The physical safety of the spacecraft after separation must be guaranteed. Fine attitude determination and control must be sufficient for instrument calibration maneuvers. The mission science mode requires 2-arcsecond control according to error signals provided by guide telescopes on the Atmospheric Imaging Assembly, one of the three instruments to be carried. Lastly, accurate execution of linear and angular momentum changes to the spacecraft must be provided for momentum management and orbit maintenance. In thsp aper, single-fault tolerant fault detection and correction of the Solar Dynamics Observatory attitude control system is described. The attitude control hardware suite for the mission is catalogued, with special attention to redundancy at the hardware level. Four reaction wheels are used where any three are satisfactory. Four pairs of redundant thrusters are employed for orbit change maneuvers and momentum management. Three two-axis gyroscopes provide full redundancy for rate sensing. A digital Sun sensor and two autonomous star trackers provide two-out-of-three redundancy for fine attitude determination. The use of software to maximize
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
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
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.
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.
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.
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.
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.
Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Lu, Yan; Salsbury, Freddie R.
2015-01-01
ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.
Karp, Jerome M.; Erylimaz, Ertan
2015-01-01
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder. PMID:25416617
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.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo.
White, Alexander J; Gorshkov, Vyacheslav N; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-01
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. PMID:26156473
Quantum mechanical molecular dynamics studies of chemical systems
NASA Astrophysics Data System (ADS)
Pavese, Marc
Methods for including quantum mechanical effects in molecular dynamics (MD) simulations are discussed in this thesis. The thesis focuses on the path integral centroid molecular dynamics (CMD) algorithm. This algorithm is first described and then used in simulations of low temperature para-hydrogen, and also in simulations of the excess proton in water clusters and in the bulk. The CMD method allows one to include the effects of nuclear quantization approximately while still maintaining a quasi-classical, trajectory based, description of the dynamics. The effects of quantization of the electronic degrees of freedom are also discussed. These effects are usually taken into account implicitly through parameterized potential functions. However, methods for including the quantum electronic degrees of freedom explicitly in a MD simulation are also discussed in this thesis. Most notably, the Car-Parrinello method, which combines density functional theory (DFT) with MD, is employed with the CMD algorithm. This yields a method which takes explicit account of the quantum electrons and nuclei. Thus, this work represents one feasible approach for considering the quantum nature of all the degrees of freedom of the system while still maintaining an MD framework. In the concluding remarks, future directions and possibilities for this type of approach are discussed.
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
Collisional deactivation of CF 3I - a molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Svedung, Harald; Marković, Nikola; Nordholm, Sture
1999-10-01
The detailed mechanisms of ro-vibrational energy transfer in collisions between CF 3I and argon or propane are investigated. Molecular dynamics simulations of collisions between a reactant CF 3I molecule at energies from 50 to 200 kJ/mol with medium argon or propane at selected initial temperatures are interpreted in terms of ergodic collision limits. The intramolecular potential used for CF 3I is a Morse-stretch/harmonic-bend type function with parameters fitted to equilibrium structure, normal mode frequencies and dissociation energies. Simple generic Buckingham type pair-potentials are used for intermolecular atom-atom interactions. Energy transfer is related to (i) geometry of collision, (ii) impact parameter, (iii) number of atom-atom encounters, (iv) average dynamical hardness of interaction at atom-atom collisions, (v) number of minima in the center of mass separation and (vi) lifetime of the collisional complex. The energy transfer in our molecular dynamics calculations is compared with experimental results for the same colliders. The observed trends are interpreted in terms of detailed collisional mechanisms. Our results highlight the importance of rotational excitation and the repulsive part of the intermolecular potential.
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.
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.
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
Protons in polar media: An ab initio molecular dynamics study
NASA Astrophysics Data System (ADS)
von Rosenvinge, Tycho
1998-10-01
The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations
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 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.
Omelyan, Igor P; Kovalenko, Andriy
2012-01-10
We propose and validate a new multiscale technique, the extrapolative isokinetic Nóse-Hoover chain orientational (EINO) motion multiple time step algorithm for rigid interaction site models of molecular liquids. It nontrivially combines the multiple time step decomposition operator method with a specific extrapolation of intermolecular interactions, complemented by an extended isokinetic Nosé-Hoover chain approach in the presence of translational and orientational degrees of freedom. The EINO algorithm obviates the limitations on time step size in molecular dynamics simulations. While the best existing multistep algorithms can advance from a 5 fs single step to a maximum 100 fs outer step, we show on the basis of molecular dynamics simulations of the TIP4P water that our EINO technique overcomes this barrier. Specifically, we have achieved giant time steps on the order of 500 fs up to 5 ps, which now become available in the study of equilibrium and conformational properties of molecular liquids without a loss of stability and accuracy.
Implementation of Dynamically Corrected Gates on a Single Electron Spin in Diamond
NASA Astrophysics Data System (ADS)
Rong, Xing; Geng, Jianpei; Wang, Zixiang; Zhang, Qi; Ju, Chenyong; Shi, Fazhan; Duan, Chang-Kui; Du, Jiangfeng
2014-02-01
Precise control of an open quantum system is critical to quantum information processing but is challenging due to inevitable interactions between the quantum system and the environment. We demonstrated experimentally a type of dynamically corrected gates using only bounded-strength pulses on the nitrogen-vacancy centers in diamond. The infidelity of quantum gates caused by a nuclear-spin bath is reduced from being the second order to the sixth order of the noise-to-control-field ratio, which offers greater efficiency in reducing infidelity. The quantum gates have been protected to the limit essentially set by the spin-lattice relaxation time T1. Our work marks an important step towards fault-tolerant quantum computation in realistic systems.
Commissioning of a beta* knob for dynamic IR correction at RHIC
Robert-Demolaize G.; Marusic, A.; Tepikian, S.; White, S.
2012-05-20
In addition to the recent optics correction technique demonstrated at CERN and applied at RHIC, it is important to have a separate tool to control the value of the beta functions at the collision point ({beta}*). This becomes even more relevant when trying to reach high level of integrated luminosity while dealing with emittance blow-up over the length of a store, or taking advantage of compensation processes like stochastic cooling. Algorithms have been developed to allow modifying independently the beta function in each plane for each beam without significant increase in beam losses. The following reviews the principle of such algorithms and their experimental implementation as a dynamic {beta}-squeeze procedure.
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.
Application of torsion angle molecular dynamics for efficient sampling of protein conformations.
Chen, Jianhan; Im, Wonpil; Brooks, Charles L
2005-11-30
We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.
Analysis and Correction of Dynamic Geometric Misalignment for Nano-Scale Computed Tomography at BSRF
Fu, Jian; Li, Chen; Liu, Zhenzhong
2015-01-01
Due to its high spatial resolution, synchrotron radiation x-ray nano-scale computed tomography (nano-CT) is sensitive to misalignments in scanning geometry, which occurs quite frequently because of mechanical errors in manufacturing and assembly or from thermal expansion during the time-consuming scanning. Misalignments degrade the imaging results by imposing artifacts on the nano-CT slices. In this paper, the geometric misalignment of the synchrotron radiation nano-CT has been analyzed by partial derivatives on the CT reconstruction algorithm and a correction method, based on cross correlation and least-square sinusoidal fitting, has been reported. This work comprises a numerical study of the method and its experimental verification using a dataset measured with the full-field transmission x-ray microscope nano-CT at the beamline 4W1A of the Beijing Synchrotron Radiation Facility. The numerical and experimental results have demonstrated the validity of the proposed approach. It can be applied for dynamic geometric misalignment and needs neither phantom nor additional correction scanning. We expect that this method will simplify the experimental operation of synchrotron radiation nano-CT. PMID:26509552
Rodríguez-Reyes, Gerardo; López-Gavito, Eduardo; Pérez-Sanpablo, Alberto Isaac; Galván Duque-Gastélum, Carlos; Alvarez-Camacho, Michelín; Mendoza-Cruz, Felipe; Parra-Téllez, Patricia; Vázquez-Escamilla, Jesús; Quiñones-Urióstegui, Ivett
2014-07-01
Percutaneous surgical techniques are suitable for the correction of the hallux valgus deformity. Satisfactory aesthetic and functional results obtained with the Reverdin- Isham osteotomy have been reported. The aim of this study was to describe dynamic plantar pressure redistribution after the correction of the deformity using this technique. A sample of 20 feet with mild or moderate hallux valgus was conformed and surgically treated using the Reverdin-Isham osteotomy. Clinical, radiological, surface and pressure assessments were performed pre and postoperatively. Postoperative mean (± SD) values of the American Orthopaedic Foot and Ankle Society (AOFAS) score, metatarsophalangeal, first intermetatarsal and proximal articular sect angles were 95.7 (3.3), 15.5° (5.4), 9.5° (1.5) y 5.3° (3.0), respectively. A significant decrease was observed in surface values of both lateral (P = 0.003) and medial (P = 0.001) masks of the forefoot. Mean pressure values of the lateral forefoot region denoted a significant increase (P < 0.001) while the medial forefoot region showed no change (P = 0.137). There is evidence that this particular surgical technique promotes a new plantar pressure pattern in the foot that might significantly favour the increase of the pressure observed under the lesser metatarsal heads and might not induce meaningful changes in the mean pressure registered under the first metatarsal head and hallux. PMID:25264801
Dynamic Black-Level Correction and Artifact Flagging in the Kepler Data Pipeline
NASA Technical Reports Server (NTRS)
Clarke, B. D.; Kolodziejczak, J. J.; Caldwell, D. A.
2013-01-01
Instrument-induced artifacts in the raw Kepler pixel data include time-varying crosstalk from the fine guidance sensor (FGS) clock signals, manifestations of drifting moiré pattern as locally correlated nonstationary noise and rolling bands in the images which find their way into the calibrated pixel time series and ultimately into the calibrated target flux time series. Using a combination of raw science pixel data, full frame images, reverse-clocked pixel data and ancillary temperature data the Keplerpipeline models and removes the FGS crosstalk artifacts by dynamically adjusting the black level correction. By examining the residuals to the model fits, the pipeline detects and flags spatial regions and time intervals of strong time-varying blacklevel (rolling bands ) on a per row per cadence basis. These flags are made available to downstream users of the data since the uncorrected rolling band artifacts could complicate processing or lead to misinterpretation of instrument behavior as stellar. This model fitting and artifact flagging is performed within the new stand-alone pipeline model called Dynablack. We discuss the implementation of Dynablack in the Kepler data pipeline and present results regarding the improvement in calibrated pixels and the expected improvement in cotrending performances as a result of including FGS corrections in the calibration. We also discuss the effectiveness of the rolling band flagging for downstream users and illustrate with some affected light curves.
Rodríguez-Reyes, Gerardo; López-Gavito, Eduardo; Pérez-Sanpablo, Alberto Isaac; Galván Duque-Gastélum, Carlos; Alvarez-Camacho, Michelín; Mendoza-Cruz, Felipe; Parra-Téllez, Patricia; Vázquez-Escamilla, Jesús; Quiñones-Urióstegui, Ivett
2014-07-01
Percutaneous surgical techniques are suitable for the correction of the hallux valgus deformity. Satisfactory aesthetic and functional results obtained with the Reverdin- Isham osteotomy have been reported. The aim of this study was to describe dynamic plantar pressure redistribution after the correction of the deformity using this technique. A sample of 20 feet with mild or moderate hallux valgus was conformed and surgically treated using the Reverdin-Isham osteotomy. Clinical, radiological, surface and pressure assessments were performed pre and postoperatively. Postoperative mean (± SD) values of the American Orthopaedic Foot and Ankle Society (AOFAS) score, metatarsophalangeal, first intermetatarsal and proximal articular sect angles were 95.7 (3.3), 15.5° (5.4), 9.5° (1.5) y 5.3° (3.0), respectively. A significant decrease was observed in surface values of both lateral (P = 0.003) and medial (P = 0.001) masks of the forefoot. Mean pressure values of the lateral forefoot region denoted a significant increase (P < 0.001) while the medial forefoot region showed no change (P = 0.137). There is evidence that this particular surgical technique promotes a new plantar pressure pattern in the foot that might significantly favour the increase of the pressure observed under the lesser metatarsal heads and might not induce meaningful changes in the mean pressure registered under the first metatarsal head and hallux.
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).
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.
Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.
Fennen, J; Torda, A E; van Gunsteren, W F
1995-09-01
Time-averaging restraints in molecular dynamics simulations were introduced to account for the averaging implicit in spectroscopic data. Space- or molecule-averaging restraints have been used to overcome the fact that not all molecular conformations can be visited during the finite time of a simulation of a single molecule. In this work we address the issue of using the correct Boltzmann weighting for each member of an ensemble, both in time and in space. It is shown that the molecular- or space-averaging method is simple in theory, but requires a priori knowledge of the behaviour of a system. This is illustrated using a five-atom model system and the small cycle peptide analogue somatostatin. When different molecular conformers that are separated by energy barriers insurmountable on the time scale of a simulation contribute significantly to a measured NOE intensity, the use of space- or molecule-averaged distance restraints yields a more appropriate description of the measured data than conventional single-molecule refinement with or without application of time averaging.
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
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.
Thermal Transport in Carbon Nanotubes using Molecular Dynamics
NASA Astrophysics Data System (ADS)
Moore, Andrew; Khatun, Mahfuza
2011-10-01
We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.
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.
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.
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
Spotting the difference in molecular dynamics simulations of biomolecules
NASA Astrophysics Data System (ADS)
Sakuraba, Shun; Kono, Hidetoshi
2016-08-01
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.
Gao, Yi; Neuhauser, Daniel
2013-05-14
We show how to obtain the correct electronic response of a large system by embedding; a small region is propagated by TDDFT (time-dependent density functional theory) simultaneously with a classical electrodynamics evolution using the Near-Field method over a larger external region. The propagations are coupled through a combined time-dependent density yielding a common Coulomb potential. We show that the embedding correctly describes the plasmonic response of a Mg(0001) slab and its influence on the dynamical charge transfer between an adsorbed H2O molecule and the substrate, giving the same spectral shape as full TDDFT (similar plasmon peak and molecular-dependent differential spectra) with much less computational effort. The results demonstrate that atomistic embedding electrodynamics is promising for nanoplasmonics and nanopolaritonics.
Gao Yi; Neuhauser, Daniel
2013-05-14
We show how to obtain the correct electronic response of a large system by embedding; a small region is propagated by TDDFT (time-dependent density functional theory) simultaneously with a classical electrodynamics evolution using the Near-Field method over a larger external region. The propagations are coupled through a combined time-dependent density yielding a common Coulomb potential. We show that the embedding correctly describes the plasmonic response of a Mg(0001) slab and its influence on the dynamical charge transfer between an adsorbed H{sub 2}O molecule and the substrate, giving the same spectral shape as full TDDFT (similar plasmon peak and molecular-dependent differential spectra) with much less computational effort. The results demonstrate that atomistic embedding electrodynamics is promising for nanoplasmonics and nanopolaritonics.
NASA Astrophysics Data System (ADS)
Robinson, Andrew P.; Tipping, Jill; Cullen, David M.; Hamilton, David
2016-07-01
Accurate activity quantification is the foundation for all methods of radiation dosimetry for molecular radiotherapy (MRT). The requirements for patient-specific dosimetry using single photon emission computed tomography (SPECT) are challenging, particularly with respect to scatter correction. In this paper data from phantom studies, combined with results from a fully validated Monte Carlo (MC) SPECT camera simulation, are used to investigate the influence of the triple energy window (TEW) scatter correction on SPECT activity quantification for {{}1 7 7} Lu MRT. Results from phantom data show that; (1) activity quantification for the total counts in the SPECT field-of-view demonstrates a significant overestimation in total activity recovery when TEW scatter correction is applied at low activities (≤slant 200 MBq). (2) Applying the TEW scatter correction to activity quantification within a volume-of-interest with no background activity provides minimal benefit. (3) In the case of activity distributions with background activity, an overestimation of recovered activity of up to 30% is observed when using the TEW scatter correction. Data from MC simulation were used to perform a full analysis of the composition of events in a clinically reconstructed volume of interest. This allowed, for the first time, the separation of the relative contributions of partial volume effects (PVE) and inaccuracies in TEW scatter compensation to the observed overestimation of activity recovery. It is shown, that even with perfect partial volume compensation, TEW scatter correction can overestimate activity recovery by up to 11%. MC data is used to demonstrate that even a localized and optimized isotope-specific TEW correction cannot reflect a patient specific activity distribution without prior knowledge of the complete activity distribution. This highlights the important role of MC simulation in SPECT activity quantification.
Estimation of atomic hydrophobicities using molecular dynamics simulation of peptides
NASA Astrophysics Data System (ADS)
Held, Marie; Nicolau, Dan V.
2007-12-01
The hydrophobic force is one of the main driving forces in protein folding and binding. However, its nature is not yet well understood and consequently there are more than 80 different scales published trying to quantify it. Most of the hydrophobicity scales are amino acid-based, but the interaction between the molecular surface of the proteins (and DNA) and surfaces they are immobilized on, e.g., on biomedical micro/nanodevices, occurs on fractions of, rather than whole amino acids. This fragmented structure of the biomolecular surface requires the derivation of atom-level hydrophobicity. Most attempts for the evaluation of atomic hydrophobicities are derived from amino acid-based values, which ignore dynamic and steric factors. This contribution reports on the Molecular Dynamics simulations that aim to overcome this simplification. The calculations examine various tripeptides in an aqueous solution and the analysis focuses on the distance of the nearest water molecules to the individual atoms in the peptides. Different environments result in a variation of average distances for similar atoms in different tripeptides. Comparison with the atomic hydrophobicities derived from the amino acid-based hydrophobicity obtained from peptide partition in water-octanol (Dgoct) and transport through the membrane interface (Dgwif) shows a similar trend to the calculated distances. The variations are likely due to the steric differences of similar types of atoms in different geometric contexts. Therefore, Molecular Dynamics simulations proved convenient for the evaluation of atomic hydrophobicities and open new research avenues. The atomic hydrophobicities can be used to design surfaces that mimic the biomolecular surfaces and therefore elicit an expected biomolecular activity from the immobilized biomolecules.
Molecular dynamics simulations of uniaxial deformation of thermoplastic polyimides.
Nazarychev, V M; Lyulin, A V; Larin, S V; Gurtovenko, A A; Kenny, J M; Lyulin, S V
2016-05-01
The results of atomistic molecular-dynamics simulations of mechanical properties of heterocyclic polymer subjected to uniaxial deformation are reported. A new amorphous thermoplastic polyimide R-BAPO with a repeat unit consisting of dianhydride 1,3-bis-(3',4,-dicarboxyphenoxy)diphenyl (dianhydride R) and diamine 4,4'-bis-(4''-aminophenoxy)diphenyloxide (diamine BAPO) was chosen for the simulations. Our primary goal was to establish the impact of various factors (sample preparation method, molecular mass, and cooling and deformation rates) on the elasticity modulus. In particular, we found that the elasticity modulus was only slightly affected by the degree of equilibration, the molecular mass and the size of the simulation box. This is most likely due to the fact that the main contribution to the elasticity modulus is from processes on scales smaller than the entanglement length. Essentially, our simulations reproduce the logarithmic dependence of the elasticity modulus on cooling and deformation rates, which is normally observed in experiments. With the use of the temperature dependence analysis of the elasticity modulus we determined the flow temperature of R-BAPO to be 580 K in line with the experimental data available. Furthermore, we found that the application of high external pressure to the polymer sample during uniaxial deformation can improve the mechanical properties of the polyimide. Overall, the results of our simulations clearly demonstrate that atomistic molecular-dynamics simulations represent a powerful and accurate tool for studying the mechanical properties of heterocyclic polymers and can therefore be useful for the virtual design of new materials, thereby supporting cost-effective synthesis and experimental research. PMID:27033967
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
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.
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.
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.
Accelerating ab initio molecular dynamics simulations by linear prediction methods
NASA Astrophysics Data System (ADS)
Herr, Jonathan D.; Steele, Ryan P.
2016-09-01
Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.
Molecular Dynamics Simulation of Telomere and TRF1
NASA Astrophysics Data System (ADS)
Kaburagi, Masaaki; Fukuda, Masaki; Yamada, Hironao; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako; Kato, Takamitsu A.; Uesaka, Mitsuru
Telomeres play a central role in determining longevity of a cell. Our study focuses on the interaction between telomeric guanines and TRF1 as a means to observe the telomeric based mechanism of the genome protection. In this research, we performed molecular dynamics simulations of a telomeric DNA and TRF1. Our results show a stable structure with a high affinity for the specific protein. Additionally, we calculated the distance between guanines and the protein in their complex state. From this comparison, we found the calculated values of distance to be very similar, and the angle of guanines in their complex states was larger than that in their single state.
Moderate pressure phase diagram of methane by Molecular Dynamics simulations
NASA Astrophysics Data System (ADS)
Spanu, L.; Donadio, D.; Galli, G.
2008-12-01
By using classical and ab initio Molecular Dynamics simulations we have investigated the phase diagram of methane up to ~ 25 Gpa. The melting line of phase I (fcc) was computed in a range of pressure corresponding to the Earth's crust conditions by using classical potentials and three different approaches -free energy calculations, phase coexistence method and integration over the coexistence line. The three techniques consistently give a phase boundary in good agreement with known experimental values. The solid phases in a range of temperature between 100K and 300K were investigated using a metadynamics technique, our results providing a possible assignments of structure and explanation of existing, controversial experiments.
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.
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.
Melting of icosahedral gold nanoclusters from molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Wang, Yanting; Teitel, S.; Dellago, Christoph
2005-06-01
Molecular dynamics simulations show that gold clusters with about 600-3000 atoms crystallize into a Mackay icosahedron upon cooling from the liquid. A detailed surface analysis shows that the facets on the surface of the Mackay icosahedral gold clusters soften but do not premelt below the bulk melting temperature. This softening is found to be due to the increasing mobility of vertex and edge atoms with temperature, which leads to inter-layer and intra-layer diffusion, and a shrinkage of the average facet size, so that the average shape of the cluster is nearly spherical at melting.
Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization.
Kohagen, Miriam; Lepšík, Martin; Jungwirth, Pavel
2014-11-20
Calcium represents a key biological signaling ion with the EF-hand loops being its most prevalent binding motif in proteins. We show using molecular dynamics simulations with umbrella sampling that including electronic polarization effects via ionic charge rescaling dramatically improves agreements with experiment in terms of the strength of calcium binding and structures of the calmodulin binding sites. The present study thus opens way to accurate calculations of interactions of calcium and other computationally difficult high-charge-density ions in biological contexts.
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.
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.
Molecular dynamics simulations of calcium binding in gramicidin A
NASA Astrophysics Data System (ADS)
Baştuğ, Turgut; Kuyucak, Serdar
2006-06-01
An important issue in molecular dynamics (MD) simulations of biomolecules is whether membrane proteins can be described using nonpolarizable force fields. To shed further light into this question, we study calcium ion binding and blocking of the gramicidin A channel which has not been investigated in MD simulations before. Potential of mean force calculations for calcium and potassium ions using a nonpolarizable force field reveal that calcium binding to the channel is much weaker compared to potassium, and hence calcium block of potassium current cannot be described. Inclusion of polarization interaction in force fields may help to rectify this problem.
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.
Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations
Schreiner, Wolfgang; Karch, Rudolf; Knapp, Bernhard; Ilieva, Nevena
2012-01-01
Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged. PMID:23019425
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 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.
Large-scale molecular dynamics simulations of fracture and deformation
NASA Astrophysics Data System (ADS)
Zhou, S. J.; Beazley, D. M.; Lomdahl, P. S.; Holian, B. L.
1996-08-01
We have discussed the prospects of applying massively parallel molecular dynamics simulation to investigate brittle versus ductile fracture behaviors and dislocation intersection. This idea is illustrated by simulating dislocation emission from a three-dimensional crack. Unprecedentedly, the dislocation loops emitted from the crack fronts have been observed. It is found that dislocation-emission modes, jogging or blunting, are very sensitive to boundary conditions and interatomic potentials. These 3D phenomena can be effectively visualized and analyzed by a new technique, namely, plotting only those atoms within the certain ranges of local potential energies.
Parallel-in-time molecular-dynamics simulations.
Baffico, L; Bernard, S; Maday, Y; Turinici, G; Zérah, G
2002-11-01
While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations. PMID:12513644
Parallel-in-time molecular-dynamics simulations
NASA Astrophysics Data System (ADS)
Baffico, L.; Bernard, S.; Maday, Y.; Turinici, G.; Zérah, G.
2002-11-01
While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations.
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
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.
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.
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.
Mugnai, Mauro L; Elber, Ron
2015-01-01
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system-the diffusion along the backbone torsions of a solvated alanine dipeptide.
Molecular Dynamics Models of Shaped Particles Using Filling Solutions
NASA Astrophysics Data System (ADS)
Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.
Algorithms such as molecular dynamics are useful computational methods for generating trajectories for studying kinetics and nonequilibrium, as well as equilibrium, problems involving ensembles of nano- and colloidal particles. Highly coarse-grained representations of complex particles can be created by rigidly connecting beads into a compos- ite particle. Here we show that by permitting the beads to vary in radii and to overlap, particles can be modeled with more complicated shapes, approaching perfect polygons and polyhedra in two and three dimensions, respectively. The positions and radii of the beads correspond to afilling solution of the very short-range repulsive shape of the modeled nanoparticle.
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.
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
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.
Molecular dynamics simulations of a lithium/sodium carbonate mixture.
Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo
2016-03-01
The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates. PMID:26897519
Molecular dynamics simulations of detonation on the roadrunner supercomputer
NASA Astrophysics Data System (ADS)
Mniszewski, Susan; Cawkwell, Marc; Germann, Timothy C.
2012-03-01
The temporal and spatial scales intrinsic to a real detonating explosive are extremely difficult to capture using molecular dynamics (MD) simulations. Nevertheless, MD remains very attractive since it allows for the resolution of dynamic phenomena at the atomic scale. Large-scale reactive MD simulations in three dimensions require immense computational resources even when simple reactive force fields are employed. We focus on the REBO force field for 'AB' since it has been shown to support a detonation while being simple, analytic, and short-ranged. The transition from two-to three- dimensional simulations is being facilitated by the port of the REBO force field in the parallel MD code SPaSM to LANL's petaflop supercomputer 'Roadrunner'. We provide a detailed discussion of the challenges associated with computing interatomic forces on a hybrid Opteron/Cell BE computational architecture.
Clustering effects in ionic polymers: Molecular dynamics simulations
Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.
2015-08-18
Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing themore » electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.« less
Clustering effects in ionic polymers: Molecular dynamics simulations
Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.
2015-08-18
Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.
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 github.com/CTCNano/proto_md.
Roj, Jerzy
2016-01-01
The paper presents two methods of dynamic error correction applied to transducers used for the measurement of gas concentration. One of them is based on a parametric model of the transducer dynamics, and the second one uses the artificial neural network (ANN) technique. This article describes research of the dynamic properties of the gas concentration measuring transducer with a typical sensor based on tin dioxide. Its response time is about 8 min, which may be not acceptable in many applications. On the basis of these studies, a parametric model of the transducer dynamics and an adequate correction algorithm has been developed. The results obtained in the research of the transducer were also used for learning and testing ANN, which were implemented in the dynamic correction task. Despite the simplicity of the used models, both methods allowed a significant reduction of the transducer’s response time. For the algorithm based on the parametric model the response time was shorter by approximately eight-fold (reduced up to 40–80 s, i.e., about 2–4 sample periods), whereas with the use of an ANN the output signal was practically fixed after a time equal to one sampling period, i.e., 20 s. In addition, the use of ANN has allowed reducing the impact of the transducer dynamic non-linearity on the correction effectiveness. PMID:27517933
Compartment modeling of dynamic brain PET—The impact of scatter corrections on parameter errors
Häggström, Ida Karlsson, Mikael; Larsson, Anne; Schmidtlein, C. Ross
2014-11-01
Purpose: The aim of this study was to investigate the effect of scatter and its correction on kinetic parameters in dynamic brain positron emission tomography (PET) tumor imaging. The 2-tissue compartment model was used, and two different reconstruction methods and two scatter correction (SC) schemes were investigated. Methods: The GATE Monte Carlo (MC) software was used to perform 2 × 15 full PET scan simulations of a voxelized head phantom with inserted tumor regions. The two sets of kinetic parameters of all tissues were chosen to represent the 2-tissue compartment model for the tracer 3′-deoxy-3′-({sup 18}F)fluorothymidine (FLT), and were denoted FLT{sub 1} and FLT{sub 2}. PET data were reconstructed with both 3D filtered back-projection with reprojection (3DRP) and 3D ordered-subset expectation maximization (OSEM). Images including true coincidences with attenuation correction (AC) and true+scattered coincidences with AC and with and without one of two applied SC schemes were reconstructed. Kinetic parameters were estimated by weighted nonlinear least squares fitting of image derived time–activity curves. Calculated parameters were compared to the true input to the MC simulations. Results: The relative parameter biases for scatter-eliminated data were 15%, 16%, 4%, 30%, 9%, and 7% (FLT{sub 1}) and 13%, 6%, 1%, 46%, 12%, and 8% (FLT{sub 2}) for K{sub 1}, k{sub 2}, k{sub 3}, k{sub 4}, V{sub a}, and K{sub i}, respectively. As expected, SC was essential for most parameters since omitting it increased biases by 10 percentage points on average. SC was not found necessary for the estimation of K{sub i} and k{sub 3}, however. There was no significant difference in parameter biases between the two investigated SC schemes or from parameter biases from scatter-eliminated PET data. Furthermore, neither 3DRP nor OSEM yielded the smallest parameter biases consistently although there was a slight favor for 3DRP which produced less biased k{sub 3} and K{sub i
Advanced techniques for constrained internal coordinate molecular dynamics.
Wagner, Jeffrey R; Balaraman, Gouthaman S; Niesen, Michiel J M; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan
2013-04-30
Internal coordinate molecular dynamics (ICMD) methods provide a more natural description of a protein by using bond, angle, and torsional coordinates instead of a Cartesian coordinate representation. Freezing high-frequency bonds and angles in the ICMD model gives rise to constrained ICMD (CICMD) models. There are several theoretical aspects that need to be developed to make the CICMD method robust and widely usable. In this article, we have designed a new framework for (1) initializing velocities for nonindependent CICMD coordinates, (2) efficient computation of center of mass velocity during CICMD simulations, (3) using advanced integrators such as Runge-Kutta, Lobatto, and adaptive CVODE for CICMD simulations, and (4) cancelling out the "flying ice cube effect" that sometimes arises in Nosé-Hoover dynamics. The Generalized Newton-Euler Inverse Mass Operator (GNEIMO) method is an implementation of a CICMD method that we have developed to study protein dynamics. GNEIMO allows for a hierarchy of coarse-grained simulation models based on the ability to rigidly constrain any group of atoms. In this article, we perform tests on the Lobatto and Runge-Kutta integrators to determine optimal simulation parameters. We also implement an adaptive coarse-graining tool using the GNEIMO Python interface. This tool enables the secondary structure-guided "freezing and thawing" of degrees of freedom in the molecule on the fly during molecular dynamics simulations and is shown to fold four proteins to their native topologies. With these advancements, we envision the use of the GNEIMO method in protein structure prediction, structure refinement, and in studying domain motion.
Molecular dynamics simulations of heme reorientational motions in myoglobin.
Henry, E R
1993-01-01
Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes
NASA Astrophysics Data System (ADS)
Komath, Sneha Sudha; Bagchi, Biman
1993-06-01
Several recent theoretical and computer simulation studies have considered solvation dynamics in a Brownian dipolar lattice which provides a simple model solvent for which detailed calculations can be carried out. In this article a fully microscopic calculation of the solvation dynamics of an ion in a Brownian dipolar lattice is presented. The calculation is based on the non-Markovian molecular hydrodynamic theory developed recently. The main assumption of the present calculation is that the two-particle orientational correlation functions of the solid can be replaced by those of the liquid state. It is shown that such a calculation provides an excellent agreement with the computer simulation results. More importantly, the present calculations clearly demonstrate that the frequency-dependent dielectric friction plays an important role in the long time decay of the solvation time correlation function. We also find that the present calculation provides somewhat better agreement than either the dynamic mean spherical approximation (DMSA) or the Fried-Mukamel theory which use the simulated frequency-dependent dielectric function. It is found that the dissipative kernels used in the molecular hydrodynamic approach and in the Fried-Mukamel theory are vastly different, especially at short times. However, in spite of this disagreement, the two theories still lead to comparable results in good agreement with computer simulation, which suggests that even a semiquantitatively accurate dissipative kernel may be sufficient to obtain a reliable solvation time correlation function. A new wave vector and frequency-dependent dissipative kernel (or memory function) is proposed which correctly goes over to the appropriate expressions in both the single particle and the collective limits. This form is expected to lead to better results than all the existing descriptions.
Al-Jabour, Salih; Leibscher, Monika
2015-01-15
Nonadiabatic coupling terms (NACTs) between different electronic states lead to fast radiationless decay in photoexcited molecules. Using molecular symmetry, i.e., symmetry with respect to permutation of identical nuclei and inversion of the molecule in space, the irreducible representations of the NACTs can be determined with a combination of molecular symmetry arguments and quantization rules. Here, we extend these symmetry rules for electronic states and coupling elements and demonstrate the importance of molecular symmetry for nonadiabatic nuclear dynamics. As an example, we consider the NACTs related to the torsion around the CN bond in C5H4NH. We present the results of quantum dynamical simulations of the photoinduced large amplitude torsion on three coupled electronic states and show how the interference between wavepackets leads to radiationless decay, which depends on the symmetry of the NACTs. Moreover, we show that the nuclear spin of the system determines the symmetry of the initial nuclear wave function and thus influences the torsional dynamics. This may open new possibilities for nuclear spin selective laser control of nuclear dynamics.
An Inside Look at Traube's Rule: A Molecular Dynamics Study
NASA Astrophysics Data System (ADS)
Dickey, Allison; Faller, Roland
2006-03-01
According to Traube's Rule [1], the alcohol concentration required to maintain the interfacial tension (γ) of a bilayer is reduced by a factor of three for each additional CH2 group that is added to the alkyl chain of the alcohol. Recent experimental work confirmed that Traube’s Rule applies to 1-stearoyl, 2-oleoyl phosphatidylcholine (SOPC) lipid bilayers that are exposed to alcohol solutions of methanol, ethanol, propanol, and butanol [2]. To examine the molecular mechanisms leading to Traube’s Rule, we use molecular dynamics simulations to study the interactions between a dipalmitoylphsphatidylcholine (DPPC) bilayer and ethanol, propanol, and butanol solutions. We first examine how the bilayer structure variation depends on alcohol chain length via the area per lipid headgroup, lipid chain disorder, and electron distribution functions. We also study the alcohol dynamics within the bilayer by monitoring the time length, number, and location of hydrogen bonds. Lipid mean squared displacements are also calculated to determine the extent to which lipid mobility is affected by alcohols. [1] I. Traube Liebigs Annalen (1891)[2] H. Ly, M. Longo Biophys J (2004)
Ion motions in molecular dynamics simulations on DNA
NASA Astrophysics Data System (ADS)
Ponomarev, Sergei Y.; Thayer, Kelly M.; Beveridge, David L.
2004-10-01
Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for convergence of each of the properties of interest. To address this issue, MD on a d(CGCGAATTCGCG) duplex in a dilute aqueous solution of water and 22 Na+ counterions was performed until convergence was achieved. The calculated first shell ion occupancies and DNA-Na+ radial distribution functions were computed as a function of time to assess convergence, and compared with relaxation times of the DNA internal parameters shift, slide, rise, tilt, roll, and twist. The sequence dependence of fractional occupancies of ions in the major and minor grooves of the DNA is examined, and the possibility of correlation between ion proximity and DNA minor groove widths is investigated.
Sex speeds adaptation by altering the dynamics of molecular evolution.
McDonald, Michael J; Rice, Daniel P; Desai, Michael M
2016-03-10
Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.
Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Laghaei, Rozita; Mousseau, Normand
2010-04-01
Expansion of polyglutamine (polyQ) beyond the pathogenic threshold (35-40 Gln) is associated with several neurodegenerative diseases including Huntington's disease, several forms of spinocerebellar ataxias and spinobulbar muscular atrophy. To determine the structure of polyglutamine aggregates we perform replica-exchange molecular dynamics simulations coupled with the optimized potential for effective peptide forcefield. Using a range of temperatures from 250 to 700 K, we study the aggregation kinetics of the polyglutamine monomer and dimer with chain lengths from 30 to 50 residues. All monomers show a similar structural change at the same temperature from α-helical structure to random coil, without indication of any significant β-strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel β-sheets and triangular and circular β-helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 μs). This ˜32 Å diameter structure reorganizes further into a tight antiparallel double-stranded ˜22 Å nanotube with 22 residues per turn close to Perutz' model for amyloid fibers as water-filled nanotubes. This diversity of structures suggests the existence of polymorphism for polyglutamine with possibly different pathways leading to the formation of toxic oligomers and to fibrils.
Molecular-Dynamics Study Melting Aluminum at High Pressures
NASA Astrophysics Data System (ADS)
Gubin, S. A.; Maklashova, I. V.; Selezenev, A. A.; Kozlova, S. A.
The dependence of the melting temperature versus the pressure under static conditions and under shock-wave compression of aluminum was calculated by molecular-dynamic modeling technique. The Morse potential and EAM potential (embedded atom method) was used for the interatomic interaction for the solid and liquid phases of aluminum. The calculations show a change of crystal structure of aluminum close to the melting range static compression and compression in the shock wave. Melting point was determined by analysis of the radial distribution function and the standard deviation of the atoms with the visualization of crystal structure. The results of molecular dynamics calculations are consistent with experimental data on the compressibility of the shock wave up to 200 GPa. Static melting results are consistent across the field of experimental data up to 30 GPa. A short-term compression in the shock wave, accompanied by the increase of entropy can be leads to overheating nonequilibrium substances. Under these conditions, the melting temperature under static and shock compression may be different from each other. However, the calculations showed on pressure in the shock wave 122 GPa aluminum melting occurs at temperatures close to the melting temperature in static conditions.
Sex speeds adaptation by altering the dynamics of molecular evolution.
McDonald, Michael J; Rice, Daniel P; Desai, Michael M
2016-03-10
Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations. PMID:26909573
Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution
McDonald, Michael J.; Rice, Daniel P.; Desai, Michael M.
2016-01-01
Sex and recombination are pervasive throughout nature despite their substantial costs1. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology2,3. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation4. Theory has proposed a number of distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect)5,6 or by separating them from deleterious load (the ruby in the rubbish effect)7,8. Previous experiments confirm that sex can increase the rate of adaptation9–17, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here, we present the first comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations. PMID:26909573
Rigid-body molecular dynamics of DNA inside a nucleosome.
Fathizadeh, Arman; Berdy Besya, Azim; Reza Ejtehadi, Mohammad; Schiessel, Helmut
2013-03-01
The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use Kramers theory to calculate nucleosome sliding caused by such defects. It is shown that the twist defect scenario together with the sequence-dependent elasticity of DNA can explain the slow time scales observed for nucleosome mobility along DNA. With this method we also show how the twist defect mechanism leads to a higher mobility of DNA in the presence of sin mutations near the dyad axis. Finally, by performing simulations on 5s rDNA, 601, and telomeric base pair sequences, it is demonstrated that the current model is a powerful tool to predict nucleosome positioning. PMID:23475204
Molecular Dynamics Study of Polyethylene under Extreme Confinement
NASA Astrophysics Data System (ADS)
Kritikos, G.; Sgouros, A.; Vogiatzis, G. G.; Theodorou, D. N.
2016-08-01
We present results concerning the dynamics and the structure of adsorbed layers of molten polyethylene (PE) between two graphite surfaces. The molecular weight of the monodisperse PE chains reaches the entanglement regime. We study three cases of interwall distances, equal to two, three and four times the unperturbed radius of gyration (Rg ) of PE chains. The confined system is equilibrated by use of efficient Monte Carlo (MC) algorithms. Conducting molecular dynamics (MD) simulations, we reveal the distribution of relaxation times as a function of distance from the graphite walls at the temperature of 450 K. From the atomic-level stresses we calculate a realistic estimate of the adhesion tension, which is not affected significantly by the width of the pore. Although the distance between the two walls is comparable to the width of the adsorbed layer, we do not record the formation of ‘glassy bridges’ under the studied conditions. The diffusion of polymer chains in the middle layer is not inhibited by the existence of the two adsorbed layers. Extreme confinement conditions imposed by the long range wall potentials bring about an increase in both the adsorption and desorption rates of chains. The presented results seem to cohere with a reduction in the calorimetric (heat capacity step) glass transition temperature (Tg ).
Molecular dynamics modeling of ultrathin amorphous carbon films
Glosli, J.N.; Belak, J.; Philpott, M.R.
1995-05-01
Amorphous carbon films about 20 mn thick are used by the computer industry as protective coatings on magnetic disks. The structure and function of this family of materials at the atomic level is poorly understood. The growth and properties of a:C and a:CH films 1 to 5 nm thick has been simulated using classical molecular dynamics and a bond-order potential with torsional terms. Studies of quenched melts that verify the ability of this potential to reproduce known features of extended structures of carbon in two and three dimensions are briefly described. In molecular dynamics calculations the incident species were neutral atoms C, or C and H with energies up to 100 eV. The stoichiometry, chemical bonding and distribution functions within the films were analyzed using IBM`s Power Visualization System for different incident gas energies. Microscopic features such as multiple ring structures, including planar graphitic structures, were easily identified. Some preliminary studies of the nanotribology of the a:C films are described, including nano-indentation and sliding in contact with a rigid probe.
Diffusion in liquid Germanium using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.
1996-03-01
We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.
Entropy of Liquid Water from Ab Initio Molecular Dynamics
NASA Astrophysics Data System (ADS)
Spanu, Leonardo; Zhang, Cui; Galli, Giulia
2012-02-01
The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)
TIREX: Replica-exchange molecular dynamics using TINKER
NASA Astrophysics Data System (ADS)
Penev, Evgeni S.; Lampoudi, Sotiria; Shea, Joan-Emma
2009-10-01
We present a driver program for performing replica-exchange molecular dynamics simulations with the TINKER package. Parallelization is based on the Message Passing Interface, with every replica assigned to a separate process. The algorithm is not communication intensive, which makes the program suitable for running even on loosely coupled cluster systems. Particular attention is paid to the practical aspects of analyzing the program output. Program summaryProgram title: TiReX Catalogue identifier: AEEK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 43 385 No. of bytes in distributed program, including test data, etc.: 502 262 Distribution format: tar.gz Programming language: Fortran 90/95 Computer: Most UNIX machines Operating system: Linux Has the code been vectorized or parallelized?: parallelized with MPI Classification: 16.13 External routines: TINKER version 4.2 or 5.0, built as a library Nature of problem: Replica-exchange molecular dynamics. Solution method: Each replica is assigned to a separate process; temperatures are swapped between replicas at regular time intervals. Running time: The sample run may take up to a few minutes.
Molecular dynamics simulations through GPU video games technologies
Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia
2016-01-01
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251
Kinetic distance and kinetic maps from molecular dynamics simulation.
Noé, Frank; Clementi, Cecilia
2015-10-13
Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly interconverting states. Here, we build upon diffusion map theory and define a kinetic distance metric for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here, we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets.