On the parallelization of molecular dynamics codes
NASA Astrophysics Data System (ADS)
Trabado, G. P.; Plata, O.; Zapata, E. L.
2002-08-01
Molecular dynamics (MD) codes present a high degree of spatial data locality and a significant amount of independent computations. However, most of the parallelization strategies are usually based on the manual transformation of sequential programs either by completely rewriting the code with message passing routines or using specific libraries intended for writing new MD programs. In this paper we propose a new library-based approach (DDLY) which supports parallelization of existing short-range MD sequential codes. The novelty of this approach is that it can directly handle the distribution of common data structures used in MD codes to represent data (arrays, Verlet lists, link cells), using domain decomposition. Thus, the insertion of run-time support for distribution and communication in a MD program does not imply significant changes to its structure. The method is simple, efficient and portable. It may be also used to extend existing parallel programming languages, such as HPF.
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)
Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida
2009-06-01
A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.
Parallelization of a Tight-Binding Molecular Dynamics Code by Using the Hpf Environment
NASA Astrophysics Data System (ADS)
Celino, M.; Rosato, V.; di Martino, B.
Molecular Dynamics simulations in the Tight-Binding approach allow the study of the ionic and electronic structures of semiconductors. The Tight-Binding codes are characterized by inhomogeneous data distribution and require the repeated diagonalization of a large sparse matrix to compute the whole body of its eigenvalues and eigenvectors. The code parallelization, by using the High Performance Fortran (HPF) environment, and the integration of optimized parallel mathematical routines is described.
SPILADY: A parallel CPU and GPU code for spin-lattice magnetic molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ma, Pui-Wai; Dudarev, S. L.; Woo, C. H.
2016-10-01
Spin-lattice dynamics generalizes molecular dynamics to magnetic materials, where dynamic variables describing an evolving atomic system include not only coordinates and velocities of atoms but also directions and magnitudes of atomic magnetic moments (spins). Spin-lattice dynamics simulates the collective time evolution of spins and atoms, taking into account the effect of non-collinear magnetism on interatomic forces. Applications of the method include atomistic models for defects, dislocations and surfaces in magnetic materials, thermally activated diffusion of defects, magnetic phase transitions, and various magnetic and lattice relaxation phenomena. Spin-lattice dynamics retains all the capabilities of molecular dynamics, adding to them the treatment of non-collinear magnetic degrees of freedom. The spin-lattice dynamics time integration algorithm uses symplectic Suzuki-Trotter decomposition of atomic coordinate, velocity and spin evolution operators, and delivers highly accurate numerical solutions of dynamic evolution equations over extended intervals of time. The code is parallelized in coordinate and spin spaces, and is written in OpenMP C/C++ for CPU and in CUDA C/C++ for Nvidia GPU implementations. Temperatures of atoms and spins are controlled by Langevin thermostats. Conduction electrons are treated by coupling the discrete spin-lattice dynamics equations for atoms and spins to the heat transfer equation for the electrons. Worked examples include simulations of thermalization of ferromagnetic bcc iron, the dynamics of laser pulse demagnetization, and collision cascades.
COOL: A code for Dynamic Monte Carlo Simulation of molecular dynamics
NASA Astrophysics Data System (ADS)
Barletta, Paolo
2012-02-01
Cool is a program to simulate evaporative and sympathetic cooling for a mixture of two gases co-trapped in an harmonic potential. The collisions involved are assumed to be exclusively elastic, and losses are due to evaporation from the trap. Each particle is followed individually in its trajectory, consequently properties such as spatial densities or energy distributions can be readily evaluated. The code can be used sequentially, by employing one output as input for another run. The code can be easily generalised to describe more complicated processes, such as the inclusion of inelastic collisions, or the possible presence of more than two species in the trap. New version program summaryProgram title: COOL Catalogue identifier: AEHJ_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHJ_v2_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.: 1 097 733 No. of bytes in distributed program, including test data, etc.: 18 425 722 Distribution format: tar.gz Programming language: C++ Computer: Desktop Operating system: Linux RAM: 500 Mbytes Classification: 16.7, 23 Catalogue identifier of previous version: AEHJ_v1_0 Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 388 Does the new version supersede the previous version?: Yes Nature of problem: Simulation of the sympathetic process occurring for two molecular gases co-trapped in a deep optical trap. Solution method: The Direct Simulation Monte Carlo method exploits the decoupling, over a short time period, of the inter-particle interaction from the trapping potential. The particle dynamics is thus exclusively driven by the external optical field. The rare inter-particle collisions are considered with an acceptance/rejection mechanism, that is, by comparing a random number to the collisional probability
COOL: A code for dynamic Monte Carlo simulation of molecular dynamics
NASA Astrophysics Data System (ADS)
Barletta, Paolo
2011-02-01
COOL is a program to simulate evaporative and sympathetic cooling for a mixture of two gases co-trapped in a harmonic potential. The collisions involved are assumed to be exclusively elastic, and losses are due to evaporation from the trap. Each particle is followed individually in its trajectory, consequently properties such as spatial densities or energy distributions can be readily evaluated. The code can be used sequentially, by employing one output as input for another run. The code can be easily generalised to describe more complicated processes, such as the inclusion of inelastic collisions, or the possible presence of more than two species in the trap. Program summaryProgram title: COOL Catalogue identifier: AEHJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHJ_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.: 1 111 674 No. of bytes in distributed program, including test data, etc.: 18 618 045 Distribution format: tar.gz Programming language: C++ Computer: Desktop Operating system: Linux RAM: 500 Mbytes Classification: 16.7, 23 Nature of problem: Simulation of the sympathetic process occurring for two molecular gases co-trapped in a deep optical trap. Solution method: The Direct Simulation Monte Carlo method exploits the decoupling, over a short time period, of the inter-particle interaction from the trapping potential. The particle dynamics is thus exclusively driven by the external optical field. The rare interparticle collisions are considered with an acceptance/rejection mechanism, that is by comparing a random number to the collisional probability defined in terms of the inter-particle cross section and centre-of-mass energy. All particles in the trap are individually simulated so that at each time step a number of useful quantities, such as
NASA Astrophysics Data System (ADS)
Otsuka, Takao; Taiji, Makoto; Bowler, David R.; Miyazaki, Tsuyoshi
2016-11-01
The recent progress of linear-scaling or O(N) methods in density functional theory (DFT) is remarkable. In this paper, we show that all-atom molecular dynamics simulations of complex biological systems based on DFT are now possible using our linear-scaling DFT code Conquest. We first overview the calculation methods used in Conquest and explain the method introduced recently to realise efficient and robust first-principles molecular dynamics (FPMD) with O(N) DFT. Then, we show that we can perform reliable all-atom FPMD simulations of a hydrated DNA model containing about 3400 atoms. We also report that the velocity scaling method is both reliable and useful for controlling the temperature of the FPMD simulation of this system. From these results, we conclude that reliable FPMD simulations of complex biological systems are now possible with Conquest.
A highly vectorised "link-cell" FORTRAN code for the DL_POLY molecular dynamics simulation package
NASA Astrophysics Data System (ADS)
Kholmurodov, Kholmirzo; Smith, William; Yasuoka, Kenji; Ebisuzaki, Toshikazu
2000-03-01
Highly vectorised FORTRAN subroutines, based on the link-cell algorithm for DL_POLY molecular dynamics simulation package, are developed. For several specific benchmark systems the efficiency of the proposed codes on a Fujitsu VPP700/128E vector computer has been tested. It is shown that in constructing the neighbor list and in calculating atomic forces our link-cell method is significantly faster than the original code.
DL_POLY_3: the CCP5 national UK code for molecular-dynamics simulations.
Todorov, I T; Smith, W
2004-09-15
DL_POLY_3 is a general-purpose molecular-dynamics simulation package embedding a highly efficient domain decomposition (DD) parallelization strategy. It was developed at Daresbury Laboratory under the auspices of the Engineering and Physical Sciences Research Council. Written to support academic research, it has a wide range of applications and will run on a wide range of computers; from single-processor workstations to multi-processor computers, with accent on the efficient use of multi-processor power. A new DD adaptation of the smoothed particle mesh Ewald method for calculating long-range forces in molecular simulations, incorporating a novel three-dimensional fast Fourier transform (the Daresbury Advanced Fourier Transform), makes it possible to simulate systems of the order of one million particles and beyond. DL_POLY_3 structure, functionality, performance and availability are described in this feature paper.
DNA: Polymer and molecular code
NASA Astrophysics Data System (ADS)
Shivashankar, G. V.
1999-10-01
The thesis work focusses upon two aspects of DNA, the polymer and the molecular code. Our approach was to bring single molecule micromanipulation methods to the study of DNA. It included a home built optical microscope combined with an atomic force microscope and an optical tweezer. This combined approach led to a novel method to graft a single DNA molecule onto a force cantilever using the optical tweezer and local heating. With this method, a force versus extension assay of double stranded DNA was realized. The resolution was about 10 picoN. To improve on this force measurement resolution, a simple light backscattering technique was developed and used to probe the DNA polymer flexibility and its fluctuations. It combined the optical tweezer to trap a DNA tethered bead and the laser backscattering to detect the beads Brownian fluctuations. With this technique the resolution was about 0.1 picoN with a millisecond access time, and the whole entropic part of the DNA force-extension was measured. With this experimental strategy, we measured the polymerization of the protein RecA on an isolated double stranded DNA. We observed the progressive decoration of RecA on the l DNA molecule, which results in the extension of l , due to unwinding of the double helix. The dynamics of polymerization, the resulting change in the DNA entropic elasticity and the role of ATP hydrolysis were the main parts of the study. A simple model for RecA assembly on DNA was proposed. This work presents a first step in the study of genetic recombination. Recently we have started a study of equilibrium binding which utilizes fluorescence polarization methods to probe the polymerization of RecA on single stranded DNA. In addition to the study of material properties of DNA and DNA-RecA, we have developed experiments for which the code of the DNA is central. We studied one aspect of DNA as a molecular code, using different techniques. In particular the programmatic use of template specificity makes
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.
Video coding with dynamic background
NASA Astrophysics Data System (ADS)
Paul, Manoranjan; Lin, Weisi; Lau, Chiew Tong; Lee, Bu-Sung
2013-12-01
Motion estimation (ME) and motion compensation (MC) using variable block size, sub-pixel search, and multiple reference frames (MRFs) are the major reasons for improved coding performance of the H.264 video coding standard over other contemporary coding standards. The concept of MRFs is suitable for repetitive motion, uncovered background, non-integer pixel displacement, lighting change, etc. The requirement of index codes of the reference frames, computational time in ME & MC, and memory buffer for coded frames limits the number of reference frames used in practical applications. In typical video sequences, the previous frame is used as a reference frame with 68-92% of cases. In this article, we propose a new video coding method using a reference frame [i.e., the most common frame in scene (McFIS)] generated by dynamic background modeling. McFIS is more effective in terms of rate-distortion and computational time performance compared to the MRFs techniques. It has also inherent capability of scene change detection (SCD) for adaptive group of picture (GOP) size determination. As a result, we integrate SCD (for GOP determination) with reference frame generation. The experimental results show that the proposed coding scheme outperforms the H.264 video coding with five reference frames and the two relevant state-of-the-art algorithms by 0.5-2.0 dB with less computational time.
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.
Modeling Nanocomposites for Molecular Dynamics (MD) Simulations
2015-01-01
Maximum 200 Words) The minimum energy configuration for Molecular Dynamics (MD) simulations is found for a carbon nanotube (CNT)/polymer... Carbon Nanotubes (CNTs), Molecular Dynamics Simulations 15. NUMBER OF PAGES 18 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT... Carbon Nanotubes ,” Macromolecules, Volume 39, Number 16, pp. 5194-5205, July 2006. 6. “VMD-Visual Molecular Dynamics ,” March 2014, http
VMD: visual molecular dynamics.
Humphrey, W; Dalke, A; Schulten, K
1996-02-01
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
de Lima Neto, Quirino Alves; Duarte Junior, Francisco Ferreira; Bueno, Paulo Sérgio Alves; Seixas, Flavio Augusto Vicente; Kowalski, Madzia Pauline; Kheir, Eyemen; Krude, Torsten; Fernandez, Maria Aparecida
2016-01-05
The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is available about Y RNAs in Chinese hamster cells, which have already been used to detect replication origins and alternative DNA structures around these sites. Here, we report the gene sequences and predicted structural characteristics of the Chinese hamster Y RNAs, and analyze their ability to support the initiation of chromosomal DNA replication in vitro. We identified DNA sequences in the Chinese hamster genome of four Y RNAs (chY1, chY3, chY4 and chY5) with upstream promoter sequences, which are homologous to the four main types of vertebrate Y RNAs. The chY1, chY3 and chY5 genes were highly conserved with their vertebrate counterparts, whilst the chY4 gene showed a relatively high degree of diversification from the other vertebrate Y4 genes. Molecular dynamics simulations suggest that chY4 RNA is structurally stable despite its evolutionarily divergent predicted stem structure. Of the four Y RNA genes present in the hamster genome, we found that only the chY1 and chY3 RNA were strongly expressed in the Chinese hamster GMA32 cell line, while expression of the chY4 and chY5 RNA genes was five orders of magnitude lower, suggesting that they may in fact not be expressed. We synthesized all four chY RNAs and showed that any of these four could support the initiation of DNA replication in an established human cell-free system. These data therefore establish that non-coding chY RNAs are stable structures and can substitute for human Y RNAs in a reconstituted cell-free DNA replication initiation system. The pattern of Y RNA expression and functionality is consistent with Y RNAs of other rodents, including mouse and rat.
TRACK : the new beam dynamics code.
Aseev, V. N.; Ostroumov, P. N.; Lessner, E. S.; Mustapha, B.; Physics
2005-01-01
The new ray-tracing code TRACK originally developed to fulfill the special requirements of the RIA accelerator systems is a general beam dynamics code. It is currently being used for the design and simulation of future proton and heavy-ion linacs at several Labs. This paper presents a general description of the code TRACK emphasizing its main new features and recent updates.
Nonequilibrium molecular dynamics
Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
Incorporating DNA Methylation Dynamics Into Epigenetic Codes
Szulwach, Keith E.; Jin, Peng
2014-01-01
Summary Genomic function is dictated by a combination of DNA sequence and the molecular mechanisms controlling access to genetic information. Access to DNA can be determined by the interpretation of covalent modifications that influence the packaging of DNA into chromatin, including DNA methylation and histone modifications. These modifications are believed to be forms of “epigenetic codes” that exist in discernable combinations that reflect cellular phenotype. Although DNA methylation is known to play important roles in gene regulation and genomic function, its contribution to the encoding of epigenetic information is just beginning to emerge. Here we discuss paradigms associated with the various components of DNA methylation/demethylation and recent advances in the understanding of its dynamic regulation in the genome, integrating these mechanisms into a framework to explain how DNA methylation could contribute to epigenetic codes. PMID:24242211
TRACKING CODE DEVELOPMENT FOR BEAM DYNAMICS OPTIMIZATION
Yang, L.
2011-03-28
Dynamic aperture (DA) optimization with direct particle tracking is a straight forward approach when the computing power is permitted. It can have various realistic errors included and is more close than theoretical estimations. In this approach, a fast and parallel tracking code could be very helpful. In this presentation, we describe an implementation of storage ring particle tracking code TESLA for beam dynamics optimization. It supports MPI based parallel computing and is robust as DA calculation engine. This code has been used in the NSLS-II dynamics optimizations and obtained promising performance.
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
Scalable molecular dynamics with NAMD.
Phillips, James C; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D; Kalé, Laxmikant; Schulten, Klaus
2005-12-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. (c) 2005 Wiley Periodicals, Inc.
Dynamic code block size for JPEG 2000
NASA Astrophysics Data System (ADS)
Tsai, Ping-Sing; LeCornec, Yann
2008-02-01
Since the standardization of the JPEG 2000, it has found its way into many different applications such as DICOM (digital imaging and communication in medicine), satellite photography, military surveillance, digital cinema initiative, professional video cameras, and so on. The unified framework of the JPEG 2000 architecture makes practical high quality real-time compression possible even in video mode, i.e. motion JPEG 2000. In this paper, we present a study of the compression impact using dynamic code block size instead of fixed code block size as specified in the JPEG 2000 standard. The simulation results show that there is no significant impact on compression if dynamic code block sizes are used. In this study, we also unveil the advantages of using dynamic code block sizes.
Coding and Dynamics of Memory. Final Report.
ERIC Educational Resources Information Center
Wickelgren, Wayne
This report provides a nontechnical summary of a series of studies from a research project with three major foci: memory storage dynamics, memory retrieval dynamics, and coding in semantic memory. A theory of forgetting was developed, involving time and interference factors. Memory traces have two properties: strength and fragility. Consolidation…
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.
Multiscale reactive molecular dynamics
NASA Astrophysics Data System (ADS)
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-12-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
Minimal Increase Network Coding for Dynamic Networks
Wu, Yanxia
2016-01-01
Because of the mobility, computing power and changeable topology of dynamic networks, it is difficult for random linear network coding (RLNC) in static networks to satisfy the requirements of dynamic networks. To alleviate this problem, a minimal increase network coding (MINC) algorithm is proposed. By identifying the nonzero elements of an encoding vector, it selects blocks to be encoded on the basis of relationship between the nonzero elements that the controls changes in the degrees of the blocks; then, the encoding time is shortened in a dynamic network. The results of simulations show that, compared with existing encoding algorithms, the MINC algorithm provides reduced computational complexity of encoding and an increased probability of delivery. PMID:26867211
Minimal Increase Network Coding for Dynamic Networks.
Zhang, Guoyin; Fan, Xu; Wu, Yanxia
2016-01-01
Because of the mobility, computing power and changeable topology of dynamic networks, it is difficult for random linear network coding (RLNC) in static networks to satisfy the requirements of dynamic networks. To alleviate this problem, a minimal increase network coding (MINC) algorithm is proposed. By identifying the nonzero elements of an encoding vector, it selects blocks to be encoded on the basis of relationship between the nonzero elements that the controls changes in the degrees of the blocks; then, the encoding time is shortened in a dynamic network. The results of simulations show that, compared with existing encoding algorithms, the MINC algorithm provides reduced computational complexity of encoding and an increased probability of delivery.
Introduction to Accelerated Molecular Dynamics
Perez, Danny
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
Molecular Dynamics Calculations
NASA Technical Reports Server (NTRS)
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
The Proteomic Code: a molecular recognition code for proteins
Biro, Jan C
2007-01-01
Background The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code. Review The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding. Methods and conclusions A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides. PMID:17999762
Adaptive Dynamic Event Tree in RAVEN code
Alfonsi, Andrea; Rabiti, Cristian; Mandelli, Diego; Cogliati, Joshua Joseph; Kinoshita, Robert Arthur
2014-11-01
RAVEN is a software tool that is focused on performing statistical analysis of stochastic dynamic systems. RAVEN has been designed in a high modular and pluggable way in order to enable easy integration of different programming languages (i.e., C++, Python) and coupling with other applications (system codes). Among the several capabilities currently present in RAVEN, there are five different sampling strategies: Monte Carlo, Latin Hyper Cube, Grid, Adaptive and Dynamic Event Tree (DET) sampling methodologies. The scope of this paper is to present a new sampling approach, currently under definition and implementation: an evolution of the DET me
NASA Astrophysics Data System (ADS)
Martin, Fernando
2015-05-01
The development of attosecond laser pulses allows one to probe the inner working of atoms, molecules and surfaces on the timescale of the electronic response. In molecules, attosecond pump-probe spectroscopy enables investigations of the prompt charge redistribution and localization that accompany photo-excitation processes, where a molecule is lifted from the ground Born-Oppenheimer potential energy surface to one or more excited surfaces, and where subsequent photochemistry evolves on femto- and attosecond timescales. In this talk I will present a few theoretical examples of realistic molecular attosecond pump-probe experiments in which simple molecules are ionized with a single attosecond pulse (or a train of attosecond pulses) and are subsequently probed by one or several infrared or xuv few-cycle pulses. The evolution of the electronic and nuclear densities in the photo-excited molecule or remaining molecular ions is calculated with attosecond time-resolution and is visualized by varying the delay between the pump and probe pulses. The results of these calculations allow us to explain several experimental observations as well as to guide future experimental efforts to uncover ultrafast electron and nuclear dynamics in molecules.
Beyond Molecular Codes: Simple Rules to Wire Complex Brains
Hassan, Bassem A.; Hiesinger, P. Robin
2015-01-01
Summary Molecular codes, like postal zip codes, are generally considered a robust way to ensure the specificity of neuronal target selection. However, a code capable of unambiguously generating complex neural circuits is difficult to conceive. Here, we re-examine the notion of molecular codes in the light of developmental algorithms. We explore how molecules and mechanisms that have been considered part of a code may alternatively implement simple pattern formation rules sufficient to ensure wiring specificity in neural circuits. This analysis delineates a pattern-based framework for circuit construction that may contribute to our understanding of brain wiring. PMID:26451480
Floating orbital molecular dynamics simulations.
Perlt, Eva; Brüssel, Marc; Kirchner, Barbara
2014-04-21
We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated.
MDplot: Visualise Molecular Dynamics.
Margreitter, Christian; Oostenbrink, Chris
2017-05-10
The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.
Molecular dynamics with quantum fluctuations
Georgescu, Ionut; Mandelshtam, Vladimir A.
2010-09-01
A quantum dynamics approach, called Gaussian molecular dynamics, is introduced. As in the centroid molecular dynamics, the N-body quantum system is mapped to an N-body classical system with an effective Hamiltonian arising within the variational Gaussian wave-packet approximation. The approach is exact for the harmonic oscillator and for the high-temperature limit, accurate in the short-time limit and is computationally very efficient.
Dynamic Alignment Models for Neural Coding
Kollmorgen, Sepp; Hahnloser, Richard H. R.
2014-01-01
Recently, there have been remarkable advances in modeling the relationships between the sensory environment, neuronal responses, and behavior. However, most models cannot encompass variable stimulus-response relationships such as varying response latencies and state or context dependence of the neural code. Here, we consider response modeling as a dynamic alignment problem and model stimulus and response jointly by a mixed pair hidden Markov model (MPH). In MPHs, multiple stimulus-response relationships (e.g., receptive fields) are represented by different states or groups of states in a Markov chain. Each stimulus-response relationship features temporal flexibility, allowing modeling of variable response latencies, including noisy ones. We derive algorithms for learning of MPH parameters and for inference of spike response probabilities. We show that some linear-nonlinear Poisson cascade (LNP) models are a special case of MPHs. We demonstrate the efficiency and usefulness of MPHs in simulations of both jittered and switching spike responses to white noise and natural stimuli. Furthermore, we apply MPHs to extracellular single and multi-unit data recorded in cortical brain areas of singing birds to showcase a novel method for estimating response lag distributions. MPHs allow simultaneous estimation of receptive fields, latency statistics, and hidden state dynamics and so can help to uncover complex stimulus response relationships that are subject to variable timing and involve diverse neural codes. PMID:24625448
Suarez, J.; Stamatiadis, S.; Farantos, S. C.; Lathouwers, L.
2009-08-13
Reproducing molecular dynamics is at the root of the basic principles of chemical change and physical properties of the matter. New insight on molecular encounters can be gained by solving the Schroedinger equation in cartesian coordinates, provided one can overcome the massive calculations that it implies. We have developed a parallel code for solving the molecular Time Dependent Schroedinger Equation (TDSE) in cartesian coordinates. Variable order Finite Difference methods result in sparse Hamiltonian matrices which can make the large scale problem solving feasible.
Molecular dynamics of silicon indentation
NASA Astrophysics Data System (ADS)
Kallman, J. S.; Hoover, W. G.; Hoover, C. G.; de Groot, A. J.; Lee, S. M.; Wooten, F.
1993-04-01
We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.
Molecular modelling and molecular dynamics of CFTR.
Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul
2017-01-01
The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.
Efficient Quantum Private Communication Based on Dynamic Control Code Sequence
NASA Astrophysics Data System (ADS)
Cao, Zheng-Wen; Feng, Xiao-Yi; Peng, Jin-Ye; Zeng, Gui-Hua; Qi, Jin
2017-04-01
Based on chaos and quantum properties, we propose a quantum private communication scheme with dynamic control code sequence. The initial sequence is obtained via chaotic systems, and the control code sequence is derived by grouping, XOR and extracting. A shift cycle algorithm is designed to enable the dynamic change of control code sequence. Analysis shows that transmission efficiency could reach 100 % with high dynamics and security.
Efficient Quantum Private Communication Based on Dynamic Control Code Sequence
NASA Astrophysics Data System (ADS)
Cao, Zheng-Wen; Feng, Xiao-Yi; Peng, Jin-Ye; Zeng, Gui-Hua; Qi, Jin
2016-12-01
Based on chaos and quantum properties, we propose a quantum private communication scheme with dynamic control code sequence. The initial sequence is obtained via chaotic systems, and the control code sequence is derived by grouping, XOR and extracting. A shift cycle algorithm is designed to enable the dynamic change of control code sequence. Analysis shows that transmission efficiency could reach 100 % with high dynamics and security.
Dynamic switching of neural codes in networks with gap junctions.
Katori, Yuichi; Masuda, Naoki; Aihara, Kazuyuki
2006-12-01
Population rate coding and temporal coding are common neural codes. Recent studies suggest that these two codes may be alternatively used in one neural system. Based on the fact that there are massive gap junctions in the brain, we explore how this switching behavior may be related to neural codes in networks of neurons connected by gap junctions. First, we show that under time-varying inputs, such neural networks show switching between synchronous and asynchronous states. Then, we quantify network dynamics by three mutual information measures to show that population rate coding carries more information in asynchronous states and temporal coding does so in synchronous states.
Modeling Molecular Dynamics from Simulations
Hinrichs, Nina Singhal
2009-01-28
Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.
Molecular dynamics at constant Cauchy stress.
Miller, Ronald E; Tadmor, Ellad B; Gibson, Joshua S; Bernstein, Noam; Pavia, Fabio
2016-05-14
The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.
Dynamic Forces in Spur Gears - Measurement, Prediction, and Code Validation
NASA Technical Reports Server (NTRS)
Oswald, Fred B.; Townsend, Dennis P.; Rebbechi, Brian; Lin, Hsiang Hsi
1996-01-01
Measured and computed values for dynamic loads in spur gears were compared to validate a new version of the NASA gear dynamics code DANST-PC. Strain gage data from six gear sets with different tooth profiles were processed to determine the dynamic forces acting between the gear teeth. Results demonstrate that the analysis code successfully simulates the dynamic behavior of the gears. Differences between analysis and experiment were less than 10 percent under most conditions.
Molecular dynamics simulation of pyridine
NASA Astrophysics Data System (ADS)
Trumpakaj, Zygmunt; Linde, Bogumił
2015-04-01
Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.
Integration methods for molecular dynamics
Leimkuhler, B.J.; Reich, S.; Skeel, R.D.
1996-12-31
Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplecticness, can be imposed on the discretization which tend to imply good long term behavior. The presence of a variety of types and strengths of interatom potentials in standard molecular models places severe restrictions on the timestep for numerical integration used in explicit integration schemes, so much recent research has concentrated on the search for alternatives that possess (1) proper dynamical properties, and (2) a relative insensitivity to the fastest components of the dynamics. We survey several recent approaches. 48 refs., 2 figs.
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A
2012-12-11
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.
2012-01-01
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924
SEARS,T.J.; HALL,G.E.; PRESES,J.M.; WESTON,R.E.,JR.
1999-06-09
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution, high-sensitivity, laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule. The work of group members Fockenberg and Muckerman is described in separate abstracts of this volume.
Dynamic molecular graphs: "hopping" structures.
Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María
2014-05-05
This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions.
Trillion-atom molecular dynamics becomes a reality
Kadau, Kai; Germann, Timothy C
2008-01-01
By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD{_}render.
Oleuropein: Molecular Dynamics and Computation.
Gentile, Luigi; Uccella, Nicola A; Sivakumar, Ganapathy
2017-09-11
Olive oil and table olive biophenols have been shown to significantly enrich the hedonic-sensory and nutritional quality of the Mediterranean diet. Oleuropein is one of the predominate biophenols in green olives and leaves, which not only has noteworthy free-radical quenching activity but also putatively reduces the incidence of various cancers. Clinical trials suggest that the consumption of extra virgin olive oil reduces the risk of several degenerative diseases. The oleuropein-based bioactives in olive oil could reduce tumor necrosis factor α, interleukin-1β and nitric oxide. Therefore, olive bioactives quality should be preserved and even improved due to their disease-fighting properties. Understanding the molecular dynamics of oleuropein is crucial to increase olive oil and table olive quality. The objective of this review is to provide the molecular dynamics and computational mapping of oleuropein. It is a biophenol-secoiridoid expressing different functionalities such as two π-bonds, two esters, two acetals, one catechol, and four hexose hydroxyls within 540 mw. The molecular bond sequential breaking mechanisms were analyzed through unimolecular reactions under electron spray ionization, collision activated dissociations, and fast atom bombardment mass spectrometry. The oleuropein solvent-free reactivity is leading to glucose loss and bioactive aglycone-dialdehydes via secoiridoid ring opening. Oleuropein electron distribution revealed that the free-radical non-polar processes occur from its highest occupied molecular orbital, while the lowest unoccupied molecular orbital is clearly devoted to nucleophilic and base site reactivity. This molecular dynamics and computational mapping of oleuropein could contribute to the engineering of olive-based biomedicine and/or functional food. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon
D`Azevedo, E.F.; Romine, C.H.
1994-12-01
This report describes the use of shared memory emulation with DOLIB (Distributed Object Library) to simplify parallel programming on the Intel Paragon. A molecular dynamics application is used as an example to illustrate the use of the DOLIB shared memory library. SOTON-PAR, a parallel molecular dynamics code with explicit message-passing using a Lennard-Jones 6-12 potential, is rewritten using DOLIB primitives. The resulting code has no explicit message primitives and resembles a serial code. The new code can perform dynamic load balancing and achieves better performance than the original parallel code with explicit message-passing.
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
Novel methods for molecular dynamics simulations.
Elber, R
1996-04-01
In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced.
Automatic code generation from the OMT-based dynamic model
Ali, J.; Tanaka, J.
1996-12-31
The OMT object-oriented software development methodology suggests creating three models of the system, i.e., object model, dynamic model and functional model. We have developed a system that automatically generates implementation code from the dynamic model. The system first represents the dynamic model as a table and then generates executable Java language code from it. We used inheritance for super-substate relationships. We considered that transitions relate to states in a state diagram exactly as operations relate to classes in an object diagram. In the generated code, each state in the state diagram becomes a class and each event on a state becomes an operation on the corresponding class. The system is implemented and can generate executable code for any state diagram. This makes the role of the dynamic model more significant and the job of designers even simpler.
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.
ParaDiS-FEM dislocation dynamics simulation code primer
Tang, M; Hommes, G; Aubry, S; Arsenlis, A
2011-09-27
The ParaDiS code is developed to study bulk systems with periodic boundary conditions. When we try to perform discrete dislocation dynamics simulations for finite systems such as thin films or cylinders, the ParaDiS code must be extended. First, dislocations need to be contained inside the finite simulation box; Second, dislocations inside the finite box experience image stresses due to the free surfaces. We have developed in-house FEM subroutines to couple with the ParaDiS code to deal with free surface related issues in the dislocation dynamics simulations. This primer explains how the coupled code was developed, the main changes from the ParaDiS code, and the functions of the new FEM subroutines.
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.
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.
The Digital Material: Molecular Dynamics
NASA Astrophysics Data System (ADS)
Bailey, Nicholas P.; Cretegny, Thierry; Dolgert, Andrew J.; Myers, Christopher R.; Schiøtz, Jakob; Sethna, James P.
2001-03-01
We announce the release of the molecular dynamics component of the Digital Material. The Digital Material is our multiscale modeling software infrastructure, designed for flexibility, extensibility, and for compatibility between simulations on disparate length scales. We illustrate how we use the high-level scripting language Python to control our low-level numerical kernals, and to interface them with standard visualization and data repository tools. Our use of design-patterns methodology leads us to decompose the MD simulation into a few weakly-coupled classes, such as AtomsMover, NeighborLocator, Potential, Constraint, and BoundaryConditions.
Non-Equilibrium Molecular Dynamics
NASA Astrophysics Data System (ADS)
Ciccotti, Giovanni; Kapral, Raymond; Sergi, Alessandro
Statistical mechanics provides a well-established link between microscopic equilibrium states and thermodynamics. If one considers systems out of equilibrium, the link between microscopic dynamical properties and non-equilibrium macroscopic states is more difficult to establish [1,2]. For systems lying near equilibrium, linear response theory provides a route to derive linear macroscopic laws and the microscopic expressions for the transport properties that enter the constitutive relations. If the system is displaced far from equilibrium, no fully general theory exists to treat such systems. By restricting consideration to a class of non-equilibrium states which arise from perturbations (linear or non-linear) of an equilibrium state, methods can be developed to treat non-equilibrium states. Furthermore, non-equilibrium molecular dynamics (NEMD) simulation methods can be devised to provide estimates for the transport properties of these systems.
Spatiotopic coding during dynamic head tilt
Turi, Marco; Burr, David C.
2016-01-01
Humans maintain a stable representation of the visual world effortlessly, despite constant movements of the eyes, head, and body, across multiple planes. Whereas visual stability in the face of saccadic eye movements has been intensely researched, fewer studies have investigated retinal image transformations induced by head movements, especially in the frontal plane. Unlike head rotations in the horizontal and sagittal planes, tilting the head in the frontal plane is only partially counteracted by torsional eye movements and consequently induces a distortion of the retinal image to which we seem to be completely oblivious. One possible mechanism aiding perceptual stability is an active reconstruction of a spatiotopic map of the visual world, anchored in allocentric coordinates. To explore this possibility, we measured the positional motion aftereffect (PMAE; the apparent change in position after adaptation to motion) with head tilts of ∼42° between adaptation and test (to dissociate retinal from allocentric coordinates). The aftereffect was shown to have both a retinotopic and spatiotopic component. When tested with unpatterned Gaussian blobs rather than sinusoidal grating stimuli, the retinotopic component was greatly reduced, whereas the spatiotopic component remained. The results suggest that perceptual stability may be maintained at least partially through mechanisms involving spatiotopic coding. NEW & NOTEWORTHY Given that spatiotopic coding could play a key role in maintaining visual stability, we look for evidence of spatiotopic coding after retinal image transformations caused by head tilt. To this end, we measure the strength of the positional motion aftereffect (PMAE; previously shown to be largely spatiotopic after saccades) after large head tilts. We find that, as with eye movements, the spatial selectivity of the PMAE has a large spatiotopic component after head rotation. PMID:27903636
General Dynamics' perspective on CFD code calibration/validation
NASA Technical Reports Server (NTRS)
Bhateley, I. C.; Hull, Gene H.
1987-01-01
Information is given in viewgraph form on General Dynamics' perspective on computational fluid dynamics (CFD) code calibration and validation. Topics covered include a hypersonic blunted cone, a hypersonic wedge/cylinder, a wing vortex defined by Mach contours, pressure distributions, and 3D turbulent flow behind a 2D flat plate as measured in a water tunnel with a laser Doppler velocimeter.
GPU Optimizations for a Production Molecular Docking Code.
Landaverde, Raphael; Herbordt, Martin C
2014-09-01
Modeling molecular docking is critical to both understanding life processes and designing new drugs. In previous work we created the first published GPU-accelerated docking code (PIPER) which achieved a roughly 5× speed-up over a contemporaneous 4 core CPU. Advances in GPU architecture and in the CPU code, however, have since reduced this relalative performance by a factor of 10. In this paper we describe the upgrade of GPU PIPER. This required an entire rewrite, including algorithm changes and moving most remaining non-accelerated CPU code onto the GPU. The result is a 7× improvement in GPU performance and a 3.3× speedup over the CPU-only code. We find that this difference in time is almost entirely due to the difference in run times of the 3D FFT library functions on CPU (MKL) and GPU (cuFFT), respectively. The GPU code has been integrated into the ClusPro docking server which has over 4000 active users.
GPU Optimizations for a Production Molecular Docking Code*
Landaverde, Raphael; Herbordt, Martin C.
2015-01-01
Modeling molecular docking is critical to both understanding life processes and designing new drugs. In previous work we created the first published GPU-accelerated docking code (PIPER) which achieved a roughly 5× speed-up over a contemporaneous 4 core CPU. Advances in GPU architecture and in the CPU code, however, have since reduced this relalative performance by a factor of 10. In this paper we describe the upgrade of GPU PIPER. This required an entire rewrite, including algorithm changes and moving most remaining non-accelerated CPU code onto the GPU. The result is a 7× improvement in GPU performance and a 3.3× speedup over the CPU-only code. We find that this difference in time is almost entirely due to the difference in run times of the 3D FFT library functions on CPU (MKL) and GPU (cuFFT), respectively. The GPU code has been integrated into the ClusPro docking server which has over 4000 active users. PMID:26594667
NASA Astrophysics Data System (ADS)
Benecke, A.
2006-03-01
Chromatin is a, if not the, hallmark of eukaryotic life. Any molecular process entailing genomic DNA or the nucleus by default provokes or depends on chromatin structural dynamics on various space and time scales. Chromatin dynamics are result of changes in the physico-chemical properties of the chromatin constituents themselves or the nuclear environment. Chromatin has been found in the former case to undergo many different covalent enzyme-mediated chemical modifications. Their identification sheds light on the molecular mechanisms and the physico-chemical properties underlying chromatin dynamics, and allows the development of quantitative models for the chromatin fiber. The abundance of the different modifications, their dynamics, and short- as well as long-range correlation phenomena between different modifications also point to a second layer of genomic coding implemented at the level of chromatin. Especially, gene regulatory coding seems to depend on such a second-level code. The information-theoretical properties of chromatin in the context of gene regulatory coding are discussed. A model for the emergence of cellular differentiation from the intricate interplay between genomic and chromatin code is presented and discussed in light of recent experimental insights.
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.
Molecular dynamics of interface rupture
NASA Astrophysics Data System (ADS)
Koplik, Joel; Banavar, Jayanth R.
1993-03-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Molecular dynamics of interface rupture
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.
The "Collisions Cube" Molecular Dynamics Simulator.
ERIC Educational Resources Information Center
Nash, John J.; Smith, Paul E.
1995-01-01
Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)
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.
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; ...
2015-05-14
The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less
Optimizing legacy molecular dynamics software with directive-based offload
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.
Population Code Dynamics in Categorical Perception
Tajima, Chihiro I.; Tajima, Satohiro; Koida, Kowa; Komatsu, Hidehiko; Aihara, Kazuyuki; Suzuki, Hideyuki
2016-01-01
Categorical perception is a ubiquitous function in sensory information processing, and is reported to have important influences on the recognition of presented and/or memorized stimuli. However, such complex interactions among categorical perception and other aspects of sensory processing have not been explained well in a unified manner. Here, we propose a recurrent neural network model to process categorical information of stimuli, which approximately realizes a hierarchical Bayesian estimation on stimuli. The model accounts for a wide variety of neurophysiological and cognitive phenomena in a consistent framework. In particular, the reported complexity of categorical effects, including (i) task-dependent modulation of neural response, (ii) clustering of neural population representation, (iii) temporal evolution of perceptual color memory, and (iv) a non-uniform discrimination threshold, are explained as different aspects of a single model. Moreover, we directly examine key model behaviors in the monkey visual cortex by analyzing neural population dynamics during categorization and discrimination of color stimuli. We find that the categorical task causes temporally-evolving biases in the neuronal population representations toward the focal colors, which supports the proposed model. These results suggest that categorical perception can be achieved by recurrent neural dynamics that approximates optimal probabilistic inference in the changing environment. PMID:26935275
Multitasking the code ARC3D. [for computational fluid dynamics
NASA Technical Reports Server (NTRS)
Barton, John T.; Hsiung, Christopher C.
1986-01-01
The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.
Nonadiabatic Molecular Dynamics with Trajectories
NASA Astrophysics Data System (ADS)
Tavernelli, Ivano
2012-02-01
In the mixed quantum-classical description of molecular systems, only the quantum character of the electronic degrees of freedom is considered while the nuclear motion is treated at a classical level. In the adiabatic case, this picture corresponds to the Born-Oppenheimer limit where the nuclei move as point charges on the potential energy surface (PES) associated with a given electronic state. Despite the success of this approximation, many physical and chemical processes do not fall in the regime where nuclei and electrons can be considered decoupled. In particular, most photoreactions pass through regions of the PES in which electron-nuclear quantum interference effects are sizeable and often crucial for a correct description of the phenomena. Recently, we have developed a trajectory-based nonadiabatic molecular dynamics scheme that describes the nuclear wavepacket as an ensemble of particles following classical trajectories on PESs derived from time-dependent density functional theory (TDDFT) [1]. The method is based on Tully's fewest switches trajectories surface hopping (TSH) where the nonadiabatic coupling elements between the different potential energy surfaces are computed on-the-fly as functionals of the ground state electron density or, equivalently, of the corresponding Kohn-Sham orbitals [2]. Here, we present the theoretical fundamentals of our approach together with an extension that allows for the direct coupling of the dynamics to an external electromagnetic field [3] as well as to the external potential generated by the environment (solvent effects) [4]. The method is applied to the study of the photodissociation dynamics of simple molecules in gas phase and to the description of the fast excited state dynamics of molecules in solution (in particular Ruthenium (II) tris(bipyridine) in water). [4pt] [1] E. Tapavicza, I. Tavernelli, U. Rothlisberger, Phys. Rev. Lett., 98, (2007) 023001. [0pt] [2] Tavernelli I.; Tapavicza E.; Rothlisberger U., J. Chem
Molecular dynamics simulation of benzene
NASA Astrophysics Data System (ADS)
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Code Pulse: Software Assurance (SWA) Visual Analytics for Dynamic Analysis of Code
2014-09-01
the data flow, leading to definite performance issues. Fortunately, it is viable to overhaul the tracing pipeline to focus on the specific needs of...major area of potential future work lies in the improvement of the dynamic tracing pipeline . The current implementation is extremely powerful, and...weakness-correlation necessary data, and the Code Dx data processing pipeline was upgraded to accept dynamic traces and cor- relate them with static
Uncertainty quantification in molecular dynamics
NASA Astrophysics Data System (ADS)
Rizzi, Francesco
This dissertation focuses on uncertainty quantification (UQ) in molecular dynamics (MD) simulations. The application of UQ to molecular dynamics is motivated by the broad uncertainty characterizing MD potential functions and by the complexity of the MD setting, where even small uncertainties can be amplified to yield large uncertainties in the model predictions. Two fundamental, distinct sources of uncertainty are investigated in this work, namely parametric uncertainty and intrinsic noise. Intrinsic noise is inherently present in the MD setting, due to fluctuations originating from thermal effects. Averaging methods can be exploited to reduce the fluctuations, but due to finite sampling, this effect cannot be completely filtered, thus yielding a residual uncertainty in the MD predictions. Parametric uncertainty, on the contrary, is introduced in the form of uncertain potential parameters, geometry, and/or boundary conditions. We address the UQ problem in both its main components, namely the forward propagation, which aims at characterizing how uncertainty in model parameters affects selected observables, and the inverse problem, which involves the estimation of target model parameters based on a set of observations. The dissertation highlights the challenges arising when parametric uncertainty and intrinsic noise combine to yield non-deterministic, noisy MD predictions of target macroscale observables. Two key probabilistic UQ methods, namely Polynomial Chaos (PC) expansions and Bayesian inference, are exploited to develop a framework that enables one to isolate the impact of parametric uncertainty on the MD predictions and, at the same time, properly quantify the effect of the intrinsic noise. Systematic applications to a suite of problems of increasing complexity lead to the observation that an uncertain PC representation built via Bayesian regression is the most suitable model for the representation of uncertain MD predictions of target observables in the
Experimental methodology for computational fluid dynamics code validation
Aeschliman, D.P.; Oberkampf, W.L.
1997-09-01
Validation of Computational Fluid Dynamics (CFD) codes is an essential element of the code development process. Typically, CFD code validation is accomplished through comparison of computed results to previously published experimental data that were obtained for some other purpose, unrelated to code validation. As a result, it is a near certainty that not all of the information required by the code, particularly the boundary conditions, will be available. The common approach is therefore unsatisfactory, and a different method is required. This paper describes a methodology developed specifically for experimental validation of CFD codes. The methodology requires teamwork and cooperation between code developers and experimentalists throughout the validation process, and takes advantage of certain synergisms between CFD and experiment. The methodology employs a novel uncertainty analysis technique which helps to define the experimental plan for code validation wind tunnel experiments, and to distinguish between and quantify various types of experimental error. The methodology is demonstrated with an example of surface pressure measurements over a model of varying geometrical complexity in laminar, hypersonic, near perfect gas, 3-dimensional flow.
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.
Wang, Z.; Lupo, J.; Patnaik, S.S.; McKenney, A.; Pachter, R.
1999-07-01
The Fast Multipole Method (FMM) offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling more realistic molecular dynamics simulations of large molecular systems. The performance of the fast molecular dynamics (FMD) code, a parallel MD code being developed in the group, using the three-dimensional fast multipole method, shows a good speedup. The application to the full atomic-scale molecular dynamics simulation of a liquid crystalline droplet of 4-n-pentyl-4{prime}-cyanobiphenyl (5CB) molecules, of size 35,872 atoms, shows strong surface effects on various orientational order parameters.
The SCEC/USGS dynamic earthquake rupture code verification exercise
Harris, R.A.; Barall, M.; Archuleta, R.; Dunham, E.; Aagaard, B.; Ampuero, J.-P.; Bhat, H.; Cruz-Atienza, Victor M.; Dalguer, L.; Dawson, P.; Day, S.; Duan, B.; Ely, G.; Kaneko, Y.; Kase, Y.; Lapusta, N.; Liu, Yajing; Ma, S.; Oglesby, D.; Olsen, K.; Pitarka, A.; Song, S.; Templeton, E.
2009-01-01
Numerical simulations of earthquake rupture dynamics are now common, yet it has been difficult to test the validity of these simulations because there have been few field observations and no analytic solutions with which to compare the results. This paper describes the Southern California Earthquake Center/U.S. Geological Survey (SCEC/USGS) Dynamic Earthquake Rupture Code Verification Exercise, where codes that simulate spontaneous rupture dynamics in three dimensions are evaluated and the results produced by these codes are compared using Web-based tools. This is the first time that a broad and rigorous examination of numerous spontaneous rupture codes has been performed—a significant advance in this science. The automated process developed to attain this achievement provides for a future where testing of codes is easily accomplished.Scientists who use computer simulations to understand earthquakes utilize a range of techniques. Most of these assume that earthquakes are caused by slip at depth on faults in the Earth, but hereafter the strategies vary. Among the methods used in earthquake mechanics studies are kinematic approaches and dynamic approaches.The kinematic approach uses a computer code that prescribes the spatial and temporal evolution of slip on the causative fault (or faults). These types of simulations are very helpful, especially since they can be used in seismic data inversions to relate the ground motions recorded in the field to slip on the fault(s) at depth. However, these kinematic solutions generally provide no insight into the physics driving the fault slip or information about why the involved fault(s) slipped that much (or that little). In other words, these kinematic solutions may lack information about the physical dynamics of earthquake rupture that will be most helpful in forecasting future events.To help address this issue, some researchers use computer codes to numerically simulate earthquakes and construct dynamic, spontaneous
Molecular codes in biological and chemical reaction networks.
Görlich, Dennis; Dittrich, Peter
2013-01-01
Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries), biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades), an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.
Molecular Code Division Multiple Access: Gaussian Mixture Modeling
NASA Astrophysics Data System (ADS)
Zamiri-Jafarian, Yeganeh
Communications between nano-devices is an emerging research field in nanotechnology. Molecular Communication (MC), which is a bio-inspired paradigm, is a promising technique for communication in nano-network. In MC, molecules are administered to exchange information among nano-devices. Due to the nature of molecular signals, traditional communication methods can't be directly applied to the MC framework. The objective of this thesis is to present novel diffusion-based MC methods when multi nano-devices communicate with each other in the same environment. A new channel model and detection technique, along with a molecular-based access method, are proposed in here for communication between asynchronous users. In this work, the received molecular signal is modeled as a Gaussian mixture distribution when the MC system undergoes Brownian noise and inter-symbol interference (ISI). This novel approach demonstrates a suitable modeling for diffusion-based MC system. Using the proposed Gaussian mixture model, a simple receiver is designed by minimizing the error probability. To determine an optimum detection threshold, an iterative algorithm is derived which minimizes a linear approximation of the error probability function. Also, a memory-based receiver is proposed to improve the performance of the MC system by considering previously detected symbols in obtaining the threshold value. Numerical evaluations reveal that theoretical analysis of the bit error rate (BER) performance based on the Gaussian mixture model match simulation results very closely. Furthermore, in this thesis, molecular code division multiple access (MCDMA) is proposed to overcome the inter-user interference (IUI) caused by asynchronous users communicating in a shared propagation environment. Based on the selected molecular codes, a chip detection scheme with an adaptable threshold value is developed for the MCDMA system when the proposed Gaussian mixture model is considered. Results indicate that the
On the performance of molecular dynamics applications on current high-end systems.
Hein, Joachim; Reid, Fiona; Smith, Lorna; Bush, Ian; Guest, Martyn; Sherwood, Paul
2005-08-15
The effective exploitation of current high performance computing (HPC) platforms in molecular simulation relies on the ability of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components, including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics codes on the UK's national HPC resources, an IBM p690+ cluster and an SGI Altix 3700. Focusing primarily on the AMBER, DL_POLY and NAMD simulation codes, we demonstrate the major performance and scalability advantages that arise through a distributed, rather than a replicated data approach.
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
Molecular dynamics simulation of ion flows around microparticles
NASA Astrophysics Data System (ADS)
Piel, Alexander
2017-03-01
The interaction of an ion flow with charged microparticles is studied by simulations with the molecular asymmetric dynamics (MAD) code. This code treats positive ions as "Yukawa particles" that are shielded by thermal electrons while the microparticle is assumed unshielded. The code is described and critically compared with results from published particle-in-cell simulations of other authors. As an application, the MAD code is used for a systematic study of the repulsive and ion-wake induced attractive forces in a particle pair. It is shown that the combined wake charges of a vertically, flow-aligned particle pair do not lead to a net attractive force. When the lower particle is shifted sidewards, a horizontal restoring force is found, which gives harmonic confinement for small displacements and a decreasing attraction force for a large distance.
Molecular Dynamics Simulation of Supercritical Spray Phenomena
2008-09-26
Dynamics of the Rheological and Structural Properties of Linear and Branched Molecules. Simple Shear and Poiseuille Flows ; Instabilities and Slip...Michael Barrucco Publications: "Comparison of Wall Models for the Molecular Dynamics Simulation of Micro flows ," R. D. Branam and M. M...Performance 3. DATES COVERED (From - To) 1 Dec. 2003 - 31 May 2008 4. TITLE AND SUBTITLE Molecular Dynamics Simulation of Supercritical
A new tree code method for simulation of planetesimal dynamics
NASA Astrophysics Data System (ADS)
Richardson, D. C.
1993-03-01
A new tree code method for simulation of planetesimal dynamics is presented. A self-similarity argument is used to restrict the problem to a small patch of a ring of planetesimals at 1 AU from the sun. The code incorporates a sliding box model with periodic boundary conditions and surrounding ghost particles. The tree is self-repairing and exploits the flattened nature of Keplerian disks to maximize efficiency. The code uses a fourth-order force polynomial integration algorithm with individual particle time-steps. Collisions and mergers, which play an important role in planetesimal evolution, are treated in a comprehensive manner. In typical runs with a few hundred central particles, the tree code is approximately 2-3 times faster than a recent direct summation method and requires about 1 CPU day on a Sparc IPX workstation to simulate 100 yr of evolution. The average relative force error incurred in such runs is less than 0.2 per cent in magnitude. In general, the CPU time as a function of particle number varies in a way consistent with an O(N log N) algorithm. In order to take advantage of facilities available, the code was written in C in a Unix workstation environment. The unique aspects of the code are discussed in detail and the results of a number of performance tests - including a comparison with previous work - are presented.
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.
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.
Simulation of dynamic material response with the PAGOSA code
Holian, K.S.; Adams, T.F.
1993-08-01
The 3D Eulerian PAGOSA hydrocode is being run on the massively parallel Connection Machine (CM) to simulate the response of materials to dynamic loading, such as by high explosives or high velocity impact. The code has a variety of equation of state forms, plastic yield models, and fracture and fragmentation models. The numerical algorithms in PAGOSA and the implementation of material models are discussed briefly.
Methodology for computational fluid dynamics code verification/validation
Oberkampf, W.L.; Blottner, F.G.; Aeschliman, D.P.
1995-07-01
The issues of verification, calibration, and validation of computational fluid dynamics (CFD) codes has been receiving increasing levels of attention in the research literature and in engineering technology. Both CFD researchers and users of CFD codes are asking more critical and detailed questions concerning the accuracy, range of applicability, reliability and robustness of CFD codes and their predictions. This is a welcomed trend because it demonstrates that CFD is maturing from a research tool to the world of impacting engineering hardware and system design. In this environment, the broad issue of code quality assurance becomes paramount. However, the philosophy and methodology of building confidence in CFD code predictions has proven to be more difficult than many expected. A wide variety of physical modeling errors and discretization errors are discussed. Here, discretization errors refer to all errors caused by conversion of the original partial differential equations to algebraic equations, and their solution. Boundary conditions for both the partial differential equations and the discretized equations will be discussed. Contrasts are drawn between the assumptions and actual use of numerical method consistency and stability. Comments are also made concerning the existence and uniqueness of solutions for both the partial differential equations and the discrete equations. Various techniques are suggested for the detection and estimation of errors caused by physical modeling and discretization of the partial differential equations.
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.
Molecular rheology of perfluoropolyether lubricant via nonequilibrium molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Guo, Qian; Chung, Pil Seung; Chen, Haigang; Jhon, Myung S.
2006-04-01
Molecular rheology of perfluoropolyether (PFPE) systems is particularly important in designing effective lubricants that control the friction and wear in tribological applications. Using the coarse-grained, bead-spring model, equilibrium molecular dynamics based on the Langevin equation in a quiescent flow was first employed to examine the nanostructure of PFPE. Further, by integrating the modified Langevin equation and imposing the Lees-Edwards boundary condition, nonequilibrium molecular dynamics of steady shear was investigated. We observe that the shear viscosity of PFPE system depends strongly on molecular architecture (e.g., molecular weight and endgroup functionality) and external conditions (e.g., temperature and shear rate). Our study of the flow activation energy/entropy and their correlations with nanostructure visualization showed that the PFPE structure was substantially modified.
Molecular dynamics on hypercube parallel computers
NASA Astrophysics Data System (ADS)
Smith, W.
1991-03-01
The implementation of molecular dynamics on parallel computers is described, with particular reference to hypercube computers. Three particular algorithms are described: replicated data (RD); systolic loop (SLS-G), and parallelised link-cells (PLC), all of which have good load balancing. The performance characteristics of each algorithm and the factors affecting their scaling properties are discussed. The article is pedagogic in intent, to introduce a novice to the main aspects of parallel computing in molecular dynamics.
Modeling the Hydrogen Bond within Molecular Dynamics
ERIC Educational Resources Information Center
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular 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.
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.
Modeling the Hydrogen Bond within Molecular Dynamics
ERIC Educational Resources Information Center
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular Dynamics Simulations of Simple Liquids
ERIC Educational Resources Information Center
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Fermionic Molecular Dynamics for Nuclear Dynamics and Thermodynamics
NASA Astrophysics Data System (ADS)
Hasnaoui, K. H. O.; Chomaz, Ph; Gulminelli, F.
A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented.
A computer code for beam dynamics simulations in SFRFQ structure
NASA Astrophysics Data System (ADS)
Wang, Z.; Chen, J. E.; Lu, Y. R.; Yan, X. Q.; Zhu, K.; Fang, J. X.; Guo, Z. Y.
2007-03-01
A computer code (SFRFQCODEv1.0) is developed to analyze the beam dynamics of Separated Function Radio Frequency Quadruples (SFRFQ) structure. Calculations show that the transverse and longitudinal stability can be ensured by selecting proper dynamic and structure parameters. This paper describes the beam dynamical mechanism of SFRFQ, and presents a design example of SFRFQ cavity, which will be used as a post accelerator of a 26 MHz 1 MeV O + Integrated Split Ring (ISR) RFQ and accelerate O + from 1 to 1.5 MeV. Three electrostatic quadruples are adopted to realize the transverse beam matching from ISR RFQ to SFRFQ cavity. This setting is also useful for the beam size adjustment and its applications.
Molecular dynamics simulations of nanostructures
NASA Astrophysics Data System (ADS)
Yuan, Zaoshi
This dissertation is focused on multimillion-atom molecular dynamics (MD) simulations of nanoscale materials. In the past decade, nanoscale materials have made significant commercial impacts, which will potentially lead to the next industrial revolution. The interest lies in the novel and promising features nanoscale materials exhibit due to their confined sizes. However, not all novel behaviors are understood or controllable. Many uncontrollable parameters, e.g. defects and dangling bonds, are known to hinder the performance of nanodevices. Solutions to these problems rely on our understanding of fundamental elements in nanoscience: isolated individual nanostructures and their assemblies. In this dissertation, we will address atomistic foundations of several problems of technological importance in nanoscience. Specifically, three basic problems are discussed: (1) embrittlement of nanocrystalline metal; (2) novel thermo-mechanical behaviors of nanowires (NWs); and (3) planar defect generation in NWs. With a scalable algorithm implemented on massively parallel computing platforms and various data mining methods, MD simulations can provide valuable insights into these problems. An essential role of sulfur segregation-induced amorphization of crystalline nickel was recently discovered experimentally, but the atomistic mechanism of the amorphization remains unexplained. Our MD simulations reveal that the large steric size of sulfur impurity causes strong sulfur-sulfur interaction mediated by lattice distortion, which leads to amorphization near the percolation threshold at the sulfur-sulfur network in nickel crystal. The generality of the mechanism due to the percolation of an impurity network is further confirmed by a model binary system. In our study of novel behaviors of semiconductor NWs, MD simulations construct a rich size-temperature `phase diagram' for the mechanical response of a zinc-oxide NW under tension. For smaller diameters and higher temperatures, novel
Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams
NASA Astrophysics Data System (ADS)
Ohya, Kaoru
2017-03-01
The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.
Modeling hybrid perovskites by molecular dynamics.
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Modeling hybrid perovskites by molecular dynamics
NASA Astrophysics Data System (ADS)
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Molecular dynamics 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
Holkundkar, Amol R.
2013-11-15
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of the experiments reported in the literature. Scaling laws for the computational time is established by varying the number of processor cores and number of macroparticles used. The capabilities of the code are highlighted by implementing various diagnostic tools. To study the dynamics of the laser-cluster interactions, the executable version of the code is available from the author.
Molecular Dynamics Studies of Matrix Metalloproteases.
Díaz, Natalia; Suárez, Dimas
2017-01-01
Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.
Dynamic molecular crystals with switchable physical properties.
Sato, Osamu
2016-06-21
The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials.
Mechanic: The MPI/HDF code framework for dynamical astronomy
NASA Astrophysics Data System (ADS)
Słonina, Mariusz; Goździewski, Krzysztof; Migaszewski, Cezary
2015-01-01
We introduce the Mechanic, a new open-source code framework. It is designed to reduce the development effort of scientific applications by providing unified API (Application Programming Interface) for configuration, data storage and task management. The communication layer is based on the well-established Message Passing Interface (MPI) standard, which is widely used on variety of parallel computers and CPU-clusters. The data storage is performed within the Hierarchical Data Format (HDF5). The design of the code follows core-module approach which allows to reduce the user’s codebase and makes it portable for single- and multi-CPU environments. The framework may be used in a local user’s environment, without administrative access to the cluster, under the PBS or Slurm job schedulers. It may become a helper tool for a wide range of astronomical applications, particularly focused on processing large data sets, such as dynamical studies of long-term orbital evolution of planetary systems with Monte Carlo methods, dynamical maps or evolutionary algorithms. It has been already applied in numerical experiments conducted for Kepler-11 (Migaszewski et al., 2012) and νOctantis planetary systems (Goździewski et al., 2013). In this paper we describe the basics of the framework, including code listings for the implementation of a sample user’s module. The code is illustrated on a model Hamiltonian introduced by (Froeschlé et al., 2000) presenting the Arnold diffusion. The Arnold web is shown with the help of the MEGNO (Mean Exponential Growth of Nearby Orbits) fast indicator (Goździewski et al., 2008a) applied onto symplectic SABAn integrators family (Laskar and Robutel, 2001).
Code Verification of the HIGRAD Computational Fluid Dynamics Solver
Van Buren, Kendra L.; Canfield, Jesse M.; Hemez, Francois M.; Sauer, Jeremy A.
2012-05-04
The purpose of this report is to outline code and solution verification activities applied to HIGRAD, a Computational Fluid Dynamics (CFD) solver of the compressible Navier-Stokes equations developed at the Los Alamos National Laboratory, and used to simulate various phenomena such as the propagation of wildfires and atmospheric hydrodynamics. Code verification efforts, as described in this report, are an important first step to establish the credibility of numerical simulations. They provide evidence that the mathematical formulation is properly implemented without significant mistakes that would adversely impact the application of interest. Highly accurate analytical solutions are derived for four code verification test problems that exercise different aspects of the code. These test problems are referred to as: (i) the quiet start, (ii) the passive advection, (iii) the passive diffusion, and (iv) the piston-like problem. These problems are simulated using HIGRAD with different levels of mesh discretization and the numerical solutions are compared to their analytical counterparts. In addition, the rates of convergence are estimated to verify the numerical performance of the solver. The first three test problems produce numerical approximations as expected. The fourth test problem (piston-like) indicates the extent to which the code is able to simulate a 'mild' discontinuity, which is a condition that would typically be better handled by a Lagrangian formulation. The current investigation concludes that the numerical implementation of the solver performs as expected. The quality of solutions is sufficient to provide credible simulations of fluid flows around wind turbines. The main caveat associated to these findings is the low coverage provided by these four problems, and somewhat limited verification activities. A more comprehensive evaluation of HIGRAD may be beneficial for future studies.
Molecular dynamics analysis of a liquid explosive reaction zone
NASA Astrophysics Data System (ADS)
Soulard, Laurent
2005-07-01
We present in this work a detailed analysis by molecular dynamics of the reaction zone of a stationary planar detonation. In particular, we look at the influence of chemical characteristics such as the reactions reversibility and endothermicity. So, equilibrium and frozen Hugoniot of the reactive system are calculated by a specific molecular dynamics method. These results can be used to a predict the detonation characteristics such as the thermodynamic properties of ZND spike and the CJ point. We observe in particular the influence of the preliminary endothermic phase on the detonation velocity and its stability. The comparisons between these predictions and non equilibrium molecular dynamics results confirm the results of this first theoretical part. In a second step, the main hypotheses of a ZND model are extracted from the MD simulations (mainly the formalism of the reactive EOS in the reaction zone). The parameters of the corresponding model are then fitted on MD results. The final step is the implementation of the model in an hydrodynamic code. Direct comparisons between molecular dynamics simulations and hydrodynamics calculations for various 1D and 2D (in the hydrodynamics sens) configurations are presented.
Random Matrix Theory in molecular dynamics analysis.
Palese, Luigi Leonardo
2015-01-01
It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes.
Dynamics of excited molecular states
NASA Astrophysics Data System (ADS)
Meyer, Hans-Dieter
2005-01-01
The photo-excitation or photo-ionization of a polyatomic molecule is typically accompanied by a strong excitation of the vibrational modes. In particular when a conical intersection of the electronic potential energy surfaces involved lies within or close to the Frank-Condon zone, the nuclear motion becomes very complicated, often chaotic, and the spectra become irregular and dense. An accurate simulation of the dynamics of such excited molecules requires firstly that the multi-dimensional and multi-state potential energy surface - or a reliable model thereof - can be determined. Secondly, the multi-dimensional quantum dynamics have to be solved. This is a very difficult task, because of the high dimensionality of the problem (6 to 30 degrees of freedom, say). The multi-configuration time-dependent Hartree (MCTDH) method has proven to be very useful for the study of such problems. In fact, an accurate treatment of the quantal dynamics of molecules like the allene cation (C3 H+4, 15D), the butatriene cation (C4 H+4, 18D), or the pyrazine molecule (C4N2H4, 24D) in their full dimensionality, is - up to date - only possible with MCTDH. (The acronym n D denotes the dimensionality.) The construction of the vibronic model Hamiltonian and the MCTDH method will be briefly discussed. After this, the excited state dynamics of the butatriene and pyrazine molecules will be discussed.
Interactive computer code for dynamic and soil structure interaction analysis
Mulliken, J.S.
1995-12-01
A new interactive computer code is presented in this paper for dynamic and soil-structure interaction (SSI) analyses. The computer program FETA (Finite Element Transient Analysis) is a self contained interactive graphics environment for IBM-PC`s that is used for the development of structural and soil models as well as post-processing dynamic analysis output. Full 3-D isometric views of the soil-structure system, animation of displacements, frequency and time domain responses at nodes, and response spectra are all graphically available simply by pointing and clicking with a mouse. FETA`s finite element solver performs 2-D and 3-D frequency and time domain soil-structure interaction analyses. The solver can be directly accessed from the graphical interface on a PC, or run on a number of other computer platforms.
NASA Astrophysics Data System (ADS)
Jellali, Nabiha; Najjar, Monia; Ferchichi, Moez; Rezig, Houria
2017-07-01
In this paper, a new two-dimensional spectral/spatial codes family, named two dimensional dynamic cyclic shift codes (2D-DCS) is introduced. The 2D-DCS codes are derived from the dynamic cyclic shift code for the spectral and spatial coding. The proposed system can fully eliminate the multiple access interference (MAI) by using the MAI cancellation property. The effect of shot noise, phase-induced intensity noise and thermal noise are used to analyze the code performance. In comparison with existing two dimensional (2D) codes, such as 2D perfect difference (2D-PD), 2D Extended Enhanced Double Weight (2D-Extended-EDW) and 2D hybrid (2D-FCC/MDW) codes, the numerical results show that our proposed codes have the best performance. By keeping the same code length and increasing the spatial code, the performance of our 2D-DCS system is enhanced: it provides higher data rates while using lower transmitted power and a smaller spectral width.
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
2013-08-13
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.
The MOLDY short-range molecular dynamics package
NASA Astrophysics Data System (ADS)
Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.
2011-12-01
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as
Learning to Estimate Dynamical State with Probabilistic Population Codes
Sabes, Philip N.
2015-01-01
Tracking moving objects, including one’s own body, is a fundamental ability of higher organisms, playing a central role in many perceptual and motor tasks. While it is unknown how the brain learns to follow and predict the dynamics of objects, it is known that this process of state estimation can be learned purely from the statistics of noisy observations. When the dynamics are simply linear with additive Gaussian noise, the optimal solution is the well known Kalman filter (KF), the parameters of which can be learned via latent-variable density estimation (the EM algorithm). The brain does not, however, directly manipulate matrices and vectors, but instead appears to represent probability distributions with the firing rates of population of neurons, “probabilistic population codes.” We show that a recurrent neural network—a modified form of an exponential family harmonium (EFH)—that takes a linear probabilistic population code as input can learn, without supervision, to estimate the state of a linear dynamical system. After observing a series of population responses (spike counts) to the position of a moving object, the network learns to represent the velocity of the object and forms nearly optimal predictions about the position at the next time-step. This result builds on our previous work showing that a similar network can learn to perform multisensory integration and coordinate transformations for static stimuli. The receptive fields of the trained network also make qualitative predictions about the developing and learning brain: tuning gradually emerges for higher-order dynamical states not explicitly present in the inputs, appearing as delayed tuning for the lower-order states. PMID:26540152
Improvement of Basic Fluid Dynamics Models for the COMPASS Code
NASA Astrophysics Data System (ADS)
Zhang, Shuai; Morita, Koji; Shirakawa, Noriyuki; Yamamoto, Yuichi
The COMPASS code is a new next generation safety analysis code to provide local information for various key phenomena in core disruptive accidents of sodium-cooled fast reactors, which is based on the moving particle semi-implicit (MPS) method. In this study, improvement of basic fluid dynamics models for the COMPASS code was carried out and verified with fundamental verification calculations. A fully implicit pressure solution algorithm was introduced to improve the numerical stability of MPS simulations. With a newly developed free surface model, numerical difficulty caused by poor pressure solutions is overcome by involving free surface particles in the pressure Poisson equation. In addition, applicability of the MPS method to interactions between fluid and multi-solid bodies was investigated in comparison with dam-break experiments with solid balls. It was found that the PISO algorithm and free surface model makes simulation with the passively moving solid model stable numerically. The characteristic behavior of solid balls was successfully reproduced by the present numerical simulations.
A hybrid numerical fluid dynamics code for resistive magnetohydrodynamics
Johnson, Jeffrey
2006-04-01
Spasmos is a computational fluid dynamics code that uses two numerical methods to solve the equations of resistive magnetohydrodynamic (MHD) flows in compressible, inviscid, conducting media[1]. The code is implemented as a set of libraries for the Python programming language[2]. It represents conducting and non-conducting gases and materials with uncomplicated (analytic) equations of state. It supports calculations in 1D, 2D, and 3D geometry, though only the 1D configuation has received significant testing to date. Because it uses the Python interpreter as a front end, users can easily write test programs to model systems with a variety of different numerical and physical parameters. Currently, the code includes 1D test programs for hydrodynamics (linear acoustic waves, the Sod weak shock[3], the Noh strong shock[4], the Sedov explosion[5], magnetic diffusion (decay of a magnetic pulse[6], a driven oscillatory "wine-cellar" problem[7], magnetic equilibrium), and magnetohydrodynamics (an advected magnetic pulse[8], linear MHD waves, a magnetized shock tube[9]). Spasmos current runs only in a serial configuration. In the future, it will use MPI for parallel computation.
Molecular dynamics simulations of substitutional diffusion
Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob
2016-12-18
In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less
Molecular dynamics simulations of substitutional diffusion
Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob
2016-12-18
In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example, we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.
Discrete Molecular Dynamics Simulation of Biomolecules
NASA Astrophysics Data System (ADS)
Ding, Feng
2011-10-01
Discrete molecular dynamics (DMD) simulation of hard spheres was the first implementation of molecular dynamics (MD) in history. DMD simulations are computationally more efficient than continuous MD simulations due to simplified interaction potentials. However, also due to these simplified potentials, DMD has often been associated with coarse-grained modeling, and hence continuous MD has become the dominant approach used to study the internal dynamics of biomolecules. With the recent advances in DMD methodology, including the development of high-resolution models for biomolecules and approaches to increase DMD efficiency, DMD simulations are emerging as an important tool in the field of molecular modeling, including the study of protein folding, protein misfolding and aggregation, and protein engineering. Recently, DMD methodology has been applied to modeling RNA folding and protein-ligand recognition. With these improvements to DMD methodology and the continuous increase in available computational power, we expect a growing role of DMD simulations in our understanding of biology.
Liouville-von Neumann molecular dynamics.
Jakowski, Jacek; Morokuma, Keiji
2009-06-14
We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C(2) and retinal system.
Liouville-von Neumann molecular dynamics
NASA Astrophysics Data System (ADS)
Jakowski, Jacek; Morokuma, Keiji
2009-06-01
We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.
Wavelet Analysis for Molecular Dynamics
2015-06-01
factor of 1,000. Ultra-high-molecular-weight polyethylene offers a classic example of the scale challenge: despite its simple chemical makeup , CnH2n+2...below, but also disconnected graphs from individual molecules . 6 Linear homopolymers can be ordered to have block tridiagonal structure where each...solutions for this simple system; r̃(0)1 = √ 2rOH , r̃ (0) 2 = 0, which leads to a symmetric linear molecule , and r̃(0)1 = 0, r̃ (0) 2 = rOH √ 4+2mO
Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers
2017-01-01
Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition
Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-02-21
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular
Dynamic signature of molecular association in methanol.
Bertrand, C E; Self, J L; Copley, J R D; Faraone, A
2016-07-07
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.
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.
Molecular Scale Dynamics of Large Ring Polymers
NASA Astrophysics Data System (ADS)
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.
Molecular dynamic simulations of ocular tablet dissolution.
Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire
2013-11-25
Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies.
Understanding Modularity in Molecular Networks Requires Dynamics
Alexander, Roger P.; Kim, Philip M.; Emonet, Thierry; Gerstein, Mark B.
2014-01-01
The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology is to understand how cellular behavior emerges from the interaction in time and space of genetically encoded molecular parts, as well as non-genetically encoded small molecules. Networks provide a natural framework for the organization and quantitative representation of all the available data about molecular interactions. The structural and dynamic properties of molecular networks have been the subject of intense research. Despite major advances, bridging network structure to dynamics – and therefore to behavior – remains challenging. A key concept of modern engineering that recurs in the functional analysis of biological networks is modularity. Most approaches to molecular network analysis rely to some extent on the assumption that molecular networks are modular – that is, they are separable and can be studied to some degree in isolation. We describe recent advances in the analysis of modularity in biological networks, focusing on the increasing realization that a dynamic perspective is essential to grouping molecules into modules and determining their collective function. PMID:19638611
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.
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.
Lightweight computational steering of very large scale molecular dynamics simulations
Beazley, D.M.; Lomdahl, P.S.
1996-09-01
We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.
Sanville, Edward J; Bock, Nicolas; Challacombe, William M; Cawkwell, Marc J; Niklasson, Anders M N; Dattelbaum, Dana M; Sheffield, Stephen; Sewell, Thomas D
2010-01-01
A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.
Adaptively restrained molecular dynamics in LAMMPS
NASA Astrophysics Data System (ADS)
Kant Singh, Krishna; Redon, Stephane
2017-07-01
Adaptively restrained molecular dynamics (ARMD) is a recently introduced particles simulation method that switches positional degrees of freedom on and off during simulation in order to speed up calculations. In the NVE ensemble, ARMD allows users to trade between precision and speed while, in the NVT ensemble, it makes it possible to compute statistical averages faster. Despite the conceptual simplicity of the approach, however, integrating it in existing molecular dynamics packages is non-trivial, in particular since implemented potentials should a priori be rewritten to take advantage of frozen particles and achieve a speed-up. In this paper, we present novel algorithms for integrating ARMD in LAMMPS, a popular multi-purpose molecular simulation package. In particular, we demonstrate how to enable ARMD in LAMMPS without having to re-implement all available force fields. The proposed algorithms are assessed on four different benchmarks, and show how they allow us to speed up simulations up to one order of magnitude.
Excited State Quantum-Classical Molecular Dynamics
NASA Astrophysics Data System (ADS)
Krstic, Predrag
2005-05-01
The development of a new theoretical, algorithmic, and computational framework is reported describing the corresponding excited state many-body dynamics by applying multiphysics described by classical equations of motion for nuclei and Hartree-Fock/Multi-Configuration Hartree-Fock and multiresolution techniques for solving the quantum part of the problem (i.e. the motion of the electrons). We primarily have in mind reactive and electron-transition dynamics which involves molecular clusters, containing hundreds of atoms, perturbed by a slow ionic/atomic/molecular projectile, with possible applications in plasma-surface interactions, cluster physics, chemistry and biotechnology. The validation of the developed technique is performed at three-body systems. Application to the transition dynamics in small carbon clusters and hydrocarbons perturbed by slow carbon ions resolves some long-standing issues in the ion-surface interactions in fusion tokamaks.
Stuart, J.G.; Wright, A.D.; Butterfield, C.P.
1996-10-01
Mitigating the effects of damaging wind turbine loads and responses extends the lifetime of the turbine and, consequently, reduces the associated Cost of Energy (COE). Active control of aerodynamic devices is one option for achieving wind turbine load mitigation. Generally speaking, control system design and analysis requires a reasonable dynamic model of {open_quotes}plant,{close_quotes} (i.e., the system being controlled). This paper extends the wind turbine aileron control research, previously conducted at the National Wind Technology Center (NWTC), by presenting a more detailed development of the wind turbine dynamic model. In prior research, active aileron control designs were implemented in an existing wind turbine structural dynamics code, FAST (Fatigue, Aerodynamics, Structures, and Turbulence). In this paper, the FAST code is used, in conjunction with system identification, to generate a wind turbine dynamic model for use in active aileron control system design. The FAST code is described and an overview of the system identification technique is presented. An aileron control case study is used to demonstrate this modeling technique. The results of the case study are then used to propose ideas for generalizing this technique for creating dynamic models for other wind turbine control applications.
HYDRA, A finite element computational fluid dynamics code: User manual
Christon, M.A.
1995-06-01
HYDRA is a finite element code which has been developed specifically to attack the class of transient, incompressible, viscous, computational fluid dynamics problems which are predominant in the world which surrounds us. The goal for HYDRA has been to achieve high performance across a spectrum of supercomputer architectures without sacrificing any of the aspects of the finite element method which make it so flexible and permit application to a broad class of problems. As supercomputer algorithms evolve, the continuing development of HYDRA will strive to achieve optimal mappings of the most advanced flow solution algorithms onto supercomputer architectures. HYDRA has drawn upon the many years of finite element expertise constituted by DYNA3D and NIKE3D Certain key architectural ideas from both DYNA3D and NIKE3D have been adopted and further improved to fit the advanced dynamic memory management and data structures implemented in HYDRA. The philosophy for HYDRA is to focus on mapping flow algorithms to computer architectures to try and achieve a high level of performance, rather than just performing a port.
Promoter nucleosome dynamics regulated by signalling through the CTD code
Materne, Philippe; Anandhakumar, Jayamani; Migeot, Valerie; Soriano, Ignacio; Yague-Sanz, Carlo; Hidalgo, Elena; Mignion, Carole; Quintales, Luis; Antequera, Francisco; Hermand, Damien
2015-01-01
The phosphorylation of the RNA polymerase II C-terminal domain (CTD) plays a key role in delineating transcribed regions within chromatin by recruiting histone methylases and deacetylases. Using genome-wide nucleosome mapping, we show that CTD S2 phosphorylation controls nucleosome dynamics in the promoter of a subset of 324 genes, including the regulators of cell differentiation ste11 and metabolic adaptation inv1. Mechanistic studies on these genes indicate that during gene activation a local increase of phospho-S2 CTD nearby the promoter impairs the phospho-S5 CTD-dependent recruitment of Set1 and the subsequent recruitment of specific HDACs, which leads to nucleosome depletion and efficient transcription. The early increase of phospho-S2 results from the phosphorylation of the CTD S2 kinase Lsk1 by MAP kinase in response to cellular signalling. The artificial tethering of the Lsk1 kinase at the ste11 promoter is sufficient to activate transcription. Therefore, signalling through the CTD code regulates promoter nucleosomes dynamics. DOI: http://dx.doi.org/10.7554/eLife.09008.001 PMID:26098123
Ab initio molecular dynamics simulations of the adsorption of H2 on palladium surfaces.
Gross, Axel
2010-05-17
The interaction of hydrogen with palladium surfaces represents a model system for the study of the adsorption and absorption at metal surfaces. Theoretical gas-surface dynamics studies have usually concentrated on the adsorption dynamics on clean surfaces. Only recently has it become possible, based on advances in electronic structure codes and improvements in computer power, to address the much more complex problem of the adsorption dynamics on precovered surfaces. Herein, recent ab initio molecular dynamics studies are discussed that address the adsorption dynamics of hydrogen molecules on hydrogen- and sulfur-precovered Pd surfaces. In addition, the relaxation dynamics of the hydrogen atoms after the dissociation on clean Pd(100) are presented.
Dynamic assembly of molecularly imprinted polymer nanoparticles.
Gong, Haiyue; Hajizadeh, Solmaz; Jiang, Lingdong; Ma, Huiting; Ye, Lei
2017-09-11
Manipulation of specific binding and recycling of materials are two important aspects for practical applications of molecularly imprinted polymers. In this work, we developed a new approach to control the dynamic assembly of molecularly imprinted nanoparticles by surface functionalization. Molecularly imprinted polymer nanoparticles with a well-controlled core-shell structure were synthesized using precipitation polymerization. The specific binding sites were created in the core during the first step imprinting reaction. In the second polymerization step, epoxide groups were introduced into the particle shell to act asan intermediate linker to immobilize phenylboronic acids, as well as to introduce cis-diol structures on surface. The imprinted polymer nanoparticles modified with boronic acid and cis-diol structures maintained high molecular binding specificity, and the nanoparticles could be induced to form dynamic particle aggregation that responded to pH variation and chemical stimuli. The possibility of modulating molecular binding and nanoparticle assembly in a mutually independent fashion can be exploited in a number of applications where repeated use of precious nanoparticles is needed. Copyright © 2017 Elsevier Inc. All rights reserved.
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.
Dynamic strength of molecular adhesion bonds.
Evans, E; Ritchie, K
1997-04-01
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
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
Choice of timestep in molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Fincham, David
1986-06-01
In molecular dynamics computer simulation of liquids it is important to use as large a timestep as possible in order to sample phase space rapidly and save on computer expense. The effect of the resulting algorithm errors in the trajectories of the molecules is not well understood. An empirical investigation into this question is reported. Several simulations differing only in the timestep used are compared. It is found that much larger timesteps than usual can be employed without producing significant errors in observed thermodynamic, structural or dynamic properties.
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
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
Molecular dynamics studies of polyurethane nanocomposite hydrogels
NASA Astrophysics Data System (ADS)
Strankowska, J.; Piszczyk, Ł.; Strankowski, M.; Danowska, M.; Szutkowski, K.; Jurga, S.; Kwela, J.
2013-10-01
Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite® 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means of NMR spectroscopy, DMA and DSC analysis. The mechanical properties and thermal stability of the systems were improved by incorporation of clay and controlled by varying the clay content in polymeric matrix. Molecular dynamics of polymer chains depends on interaction of Cloisite® 30B nanoparticles with soft segments of polyurethanes. The characteristic nanosize effect is observed.
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.
Vacuum Ultraviolet Studies of Molecular Dynamics
1992-01-15
the Journal of Chemical Physics . Vacuum Ultraviolet Studies of Molecular Dynamics Page 4 B. Quenching of S(’D) by N2...An article on this work has been published in the Journal of Chemical Physics . E. The 157 am Photodissoclation of OCS The photodissociation of OCS...angular momentum vectors are perpendicular to one another. A report of this work has been published in the Journal of Chemical Physics . Vacuum
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
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.
Bead-Fourier path integral molecular dynamics.
Ivanov, Sergei D; Lyubartsev, Alexander P; Laaksonen, Aatto
2003-06-01
Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.
Monoamine transporters: insights from molecular dynamics simulations
Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit
2015-01-01
The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185
Equipartition Principle for Internal Coordinate Molecular Dynamics.
Jain, Abhinandan; Park, In-Hee; Vaidehi, Nagarajan
2012-08-14
The principle of equipartition of (kinetic) energy for all-atom Cartesian molecular dynamics states that each momentum phase space coordinate on the average has ½kT of kinetic energy in a canonical ensemble. This principle is used in molecular dynamics simulations to initialize velocities, and to calculate statistical properties such as entropy. Internal coordinate molecular dynamics (ICMD) models differ from Cartesian models in that the overall kinetic energy depends on the generalized coordinates and includes cross-terms. Due to this coupled structure, no such equipartition principle holds for ICMD models. In this paper we introduce non-canonical modal coordinates to recover some of the structural simplicity of Cartesian models and develop a new equipartition principle for ICMD models. We derive low-order recursive computational algorithms for transforming between the modal and physical coordinates. The equipartition principle in modal coordinates provides a rigorous method for initializing velocities in ICMD simulations thus replacing the ad hoc methods used until now. It also sets the basis for calculating conformational entropy using internal coordinates.
Bead-Fourier path integral molecular dynamics
NASA Astrophysics Data System (ADS)
Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto
2003-06-01
Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.
Learning generative models of molecular dynamics
2012-01-01
We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 reg-ularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories. PMID:22369071
Learning generative models of molecular dynamics.
Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J
2012-01-01
We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 regularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories.
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.
Andersen, Hans C.
2005-01-01
Supercooled liquids near the glass transition exhibit the phenomenon of heterogeneous relaxation; at any specific time, a nominally homogeneous equilibrium fluid undergoes dynamic fluctuations in its structure on a molecular distance scale with rates that are very different in different regions of the sample. Several theoretical and simulation studies have suggested a change in the nature of the dynamics of fluids as they are supercooled, leading to the concept of a dynamic crossover that is often associated with mode coupling theory. Here, we will review the use of molecular dynamics computer simulation methods to investigate heterogeneous dynamics and dynamic crossovers in models of atomic liquids. PMID:15870201
Fragment Molecular Orbital Nonadiabatic Molecular Dynamics for Condensed Phase Systems.
Nebgen, Ben; Prezhdo, Oleg V
2016-09-15
A method for efficiently simulating nonadiabatic molecular dynamics (NAMD) of nanoscale and condensed phase systems is developed and tested. The electronic structure, including force and nonadiabatic coupling, are obtained with the fragment molecular orbital (FMO) approximation, which provides significant computational savings by splitting the system into fragments and computing electronic properties of each fragment subject to the external field due to other all other fragments. The efficiency of the developed technique is demonstrated by studying the effect of explicit solvent molecules on excited state relaxation in the Fe(CO)4 complex. The relaxation in the gas phase occurs on a 50 fs time scale, which is in excellent agreement with previously recorded femtosecond pump-probe spectroscopy. Adding a solvation shell of ethanol molecules to the simulation results in an increase in the excited state lifetime to 100 fs, in agreement with recent femtosecond X-ray spectroscopy measurements.
Molecular Dynamics Studies of Caspase-3
Sulpizi, M.; Rothlisberger, U.; Carloni, P.
2003-01-01
Caspase-3 is a fundamental target for pharmaceutical interventions against a variety of diseases involving disregulated apoptosis. The enzyme is active as a dimer with two symmetry-related active sites, each featuring a Cys-His catalytic dyad and a selectivity loop, which recognizes the characteristic DEVD pattern of the substrate. Here, a molecular dynamics study of the enzyme in complex with two pentapeptide substrates DEVDG is presented, which provides a characterization of the dynamic properties of the active form in aqueous solution. The mobility of the substrate and that of the catalytic residues are rather low indicating a distinct preorganization effect of the Michaelis complex. An essential mode analysis permits us to identify coupled motions between the two monomers. In particular, it is found that the motions of the two active site loops are correlated and tend to steer the substrate toward the reactive center, suggesting that dimerization has a distinct effect on the dynamic properties of the active site regions. The selectivity loop of one monomer turns out to be correlated with the N-terminal region of the p12 subunit of the other monomer, an interaction that is also found to play a fundamental role in the electrostatic stabilization of the quaternary structure. To further characterize the specific influence of dimerization on the enzyme essential motions, a molecular dynamics analysis is also performed on the isolated monomer. PMID:12668429
Molecular dynamics simulations of magnetized dusty plasmas
NASA Astrophysics Data System (ADS)
Piel, Alexander; Reichstein, Torben; Wilms, Jochen
2012-10-01
The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)
Extra-coding RNAs regulate neuronal DNA methylation dynamics
Savell, Katherine E.; Gallus, Nancy V. N.; Simon, Rhiana C.; Brown, Jordan A.; Revanna, Jasmin S.; Osborn, Mary Katherine; Song, Esther Y.; O'Malley, John J.; Stackhouse, Christian T.; Norvil, Allison; Gowher, Humaira; Sweatt, J. David; Day, Jeremy J.
2016-01-01
Epigenetic mechanisms such as DNA methylation are essential regulators of the function and information storage capacity of neurons. DNA methylation is highly dynamic in the developing and adult brain, and is actively regulated by neuronal activity and behavioural experiences. However, it is presently unclear how methylation status at individual genes is targeted for modification. Here, we report that extra-coding RNAs (ecRNAs) interact with DNA methyltransferases and regulate neuronal DNA methylation. Expression of ecRNA species is associated with gene promoter hypomethylation, is altered by neuronal activity, and is overrepresented at genes involved in neuronal function. Knockdown of the Fos ecRNA locus results in gene hypermethylation and mRNA silencing, and hippocampal expression of Fos ecRNA is required for long-term fear memory formation in rats. These results suggest that ecRNAs are fundamental regulators of DNA methylation patterns in neuronal systems, and reveal a promising avenue for therapeutic targeting in neuropsychiatric disease states. PMID:27384705
Parallel molecular dynamics: Communication requirements for massively parallel machines
NASA Astrophysics Data System (ADS)
Taylor, Valerie E.; Stevens, Rick L.; Arnold, Kathryn E.
1995-05-01
Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems from large-scale computations of materials to the design and modeling of drug compounds. In this paper we address two major issues: a good decomposition method that can take advantage of future massively parallel processing systems for modest-sized problems in the range of 50,000 atoms and the communication requirements needed to achieve 30 to 40% efficiency on MPPs. We analyzed a scalable benchmark molecular dynamics program executing on the Intel Touchstone Deleta parallelized with an interaction decomposition method. Using a validated analytical performance model of the code, we determined that for an MPP with a four-dimensional mesh topology and 400 MHz processors the communication startup time must be at most 30 clock cycles and the network bandwidth must be at least 2.3 GB/s. This configuration results in 30 to 40% efficiency of the MPP for a problem with 50,000 atoms executing on 50,000 processors.
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.
Spectroscopy and molecular dynamics in nonpolar fluids
NASA Astrophysics Data System (ADS)
Everitt, Karl Frederick
This thesis considers the mechanisms by which molecular dynamics in nonpolar liquids influences solvation dynamics and vibrational energy relaxation. We use semiclassical molecular dynamics simulations to calculate photon echo signals for two simple fluids. We demonstrate that two new observables are directly related to the relevant molecular quantity, the frequency- frequency time correlation function (TCF), in contrast to the commonly measured 3PEPS, which cannot be simply related to this TCF at short times. We also present a semianalytic photon echo theory, based on an ansatz which determines the full time dependence from the short time expansion coefficients of the TCF. We demonstrate that this theory accurately predicts most photon echo observables, even when the theory's gaussian approximation is not accurate. We also consider vibrational energy relaxation (VER) in liquid oxygen. Using semiclassical molecular dynamics simulations and an intermolecular potential from the literature, we evaluate the required quantity (the spectral density of a certain force-force TCF) using the same ansatz described above. We demonstrate numerically that this procedure is accurate. Approximately relating this semiclassical rate to the fully quantum mechanical VER rate, using one of the more accurate ``quantum corrections'' available in the literature, yields a result which is in order-of-magnitude agreement with the experimental VER rate. We also calculate the VER rate for liquid oxygen/argon mixtures. The rotations of the solvent near a vibrationally excited molecule, and of that molecule itself, have important consequences for the short-time dynamics of the force-force TCF. We propose a simple statistical model which quantitatively explains the mole- fraction dependence of the observed VER rate. Next, we demonstrate that a newly-developed model for oxygen very accurately describes the liquid, by comparing to experimental measures of microscopic structure and dynamics. We also
Molecular Dynamics Simulations of Network Glasses
NASA Astrophysics Data System (ADS)
Drabold, David A.
The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References
Polymer Fluid Dynamics: Continuum and Molecular Approaches.
Bird, R B; Giacomin, A J
2016-06-07
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.
Plimpton, Steve; Thompson, Aidan; Crozier, Paul
LAMMPS (http://lammps.sandia.gov/index.html) stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a code that can be used to model atoms or, as the LAMMPS website says, as a parallel particle simulator at the atomic, meso, or continuum scale. This Sandia-based website provides a long list of animations from large simulations. These were created using different visualization packages to read LAMMPS output, and each one provides the name of the PI and a brief description of the work done or visualization package used. See also the static images produced from simulations at http://lammps.sandia.gov/pictures.html The foundation paper for LAMMPS is: S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995), but the website also lists other papers describing contributions to LAMMPS over the years.
MDVRY: a polarizable classical molecular dynamics package for biomolecules
NASA Astrophysics Data System (ADS)
Souaille, M.; Loirat, H.; Borgis, D.; Gaigeot, M. P.
2009-02-01
The MDVRY classical molecular dynamics package is presented for the study of biomolecules in the gas and liquid phase. Electrostatic polarization has been implemented in the formalism of point induced dipoles following the model of Thole. Two schemes have been implemented for the calculation of induced dipoles, i.e. resolution of the self-consistent equations and a 'Car-Parrinello' dynamical approach. In this latter, the induced dipoles are calculated at each time step of the dynamics through the dynamics of additional degrees of freedom associated with the dipoles. This method saves computer time and allows to study polarized solvated proteins at a very low CPU cost. The program is written in C-language and runs on LINUX machines. A detailed manual of the code is given. The main features of the package are illustrated taking on examples of proteins in the gas phase or immersed in liquid water. Program summaryProgram title: MDVRY Catalogue identifier: AEBY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBY_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.: 39 156 No. of bytes in distributed program, including test data, etc.: 277 197 Distribution format: tar.bz2 Programming language: C Computer: Linux machines with FFTW Fourier Transform package installed Operating system: Linux machines, SUSE & RedHat distributions Classification: 3, 16.13, 23 External routines: FFTW ( http://www.fftw.org/) Nature of problem: Molecular Dynamics Software package. Solution method: Velocity Verlet algorithm. The implemented force field is composed of intra-molecular interactions and inter-molecular interactions (electrostatics, polarization, van der Waals). Polarization is accounted through induced point dipoles at each atomic site. Supplementary degrees of freedom are
NASA Astrophysics Data System (ADS)
Dutt, Meenakshi; Hancock, Bruno; Bentham, Craig; Elliott, James
2005-02-01
We have modified Daresbury Laboratory's replicated data strategy (RDS) parallel molecular dynamics (MD) package DL_POLY (version 2.13) to study the granular dynamics of frictional elastic particles. DL_POLY [Smith and Forester, The DL_POLY_2 User Manual v2.13, 2001; Forester and Smith, The DL_POLY_2 Reference Manual v2.13, 2001] is a MD package originally developed to study liquid state and macromolecular systems by accounting for various molecular interaction forces. The particles of interest in this study are macroscopic grains in pharmaceutical powders, with sizes ranging from tens to hundreds of microns. We have therefore substituted the molecular interaction forces with contact forces (including linear-dashpot, HKK interaction forces and Coulombic friction) while taking advantage of the RDS scheme. In effect, we have created a parallel Discrete Element Simulation (DES) code. In this paper, we describe the modifications made to the original DL_POLY code and the results from the validation tests of the granular dynamics simulations for systems of monodisperse spherical particles settling under gravity. The code can also be utilized to study particle packings generated via uniaxial compaction and, in some cases, simultaneous application of shear, at constant strain.
Molecular codes defining rostrocaudal domains in the embryonic mouse hypothalamus.
Ferran, José L; Puelles, Luis; Rubenstein, John L R
2015-01-01
The prosomeric model proposes that the hypothalamus is a rostral forebrain entity, placed ventral to the telencephalon and rostral to the diencephalon. Gene expression markers differentially label molecularly distinct dorsoventral progenitor domains, which represent continuous longitudinal bands across the hypothalamic alar and basal regions. There is also circumstantial support for a rostrocaudal subdivision of the hypothalamus into transverse peduncular (caudal) and terminal (rostral) territories (PHy, THy). In addition, there is evidence for a specialized acroterminal domain at the rostral midline of the terminal hypothalamus (ATD). The PHy and THy transverse structural units are presently held to form part of two hypothalamo-telencephalic prosomeres (hp1 and hp2, respectively), which end dorsally at the telencephalic septocommissural roof. PHy and THy have distinct adult nuclei, at all dorsoventral levels. Here we report the results of data mining from the Allen Developing Mouse Brain Atlas database, looking for genes expressed differentially in the PHy, Thy, and ATD regions of the hypothalamus at several developmental stages. This search allowed us to identify additional molecular evidence supporting the postulated fundamental rostrocaudal bipartition of the mouse hypothalamus into the PHy and THy, and also corroborated molecularly the singularity of the ATD. A number of markers were expressed in Thy (Fgf15, Gsc, Nkx6.2, Otx1, Zic1/5), but were absent in PHy, while other genes showed the converse pattern (Erbb4, Irx1/3/5, Lmo4, Mfap4, Plagl1, Pmch). We also identified markers that selectively label the ATD (Fgf8/10/18, Otx2, Pomc, Rax, Six6). On the whole, these data help to explain why, irrespective of the observed continuity of all dorsoventral molecular hypothalamic subdivisions across PHy and THy, different nuclear structures originate within each of these two domains, and also why singular structures arise at the ATD, e.g., the suprachiasmatic nuclei, the
Molecular codes defining rostrocaudal domains in the embryonic mouse hypothalamus
Ferran, José L.; Puelles, Luis; Rubenstein, John L. R.
2015-01-01
The prosomeric model proposes that the hypothalamus is a rostral forebrain entity, placed ventral to the telencephalon and rostral to the diencephalon. Gene expression markers differentially label molecularly distinct dorsoventral progenitor domains, which represent continuous longitudinal bands across the hypothalamic alar and basal regions. There is also circumstantial support for a rostrocaudal subdivision of the hypothalamus into transverse peduncular (caudal) and terminal (rostral) territories (PHy, THy). In addition, there is evidence for a specialized acroterminal domain at the rostral midline of the terminal hypothalamus (ATD). The PHy and THy transverse structural units are presently held to form part of two hypothalamo-telencephalic prosomeres (hp1 and hp2, respectively), which end dorsally at the telencephalic septocommissural roof. PHy and THy have distinct adult nuclei, at all dorsoventral levels. Here we report the results of data mining from the Allen Developing Mouse Brain Atlas database, looking for genes expressed differentially in the PHy, Thy, and ATD regions of the hypothalamus at several developmental stages. This search allowed us to identify additional molecular evidence supporting the postulated fundamental rostrocaudal bipartition of the mouse hypothalamus into the PHy and THy, and also corroborated molecularly the singularity of the ATD. A number of markers were expressed in Thy (Fgf15, Gsc, Nkx6.2, Otx1, Zic1/5), but were absent in PHy, while other genes showed the converse pattern (Erbb4, Irx1/3/5, Lmo4, Mfap4, Plagl1, Pmch). We also identified markers that selectively label the ATD (Fgf8/10/18, Otx2, Pomc, Rax, Six6). On the whole, these data help to explain why, irrespective of the observed continuity of all dorsoventral molecular hypothalamic subdivisions across PHy and THy, different nuclear structures originate within each of these two domains, and also why singular structures arise at the ATD, e.g., the suprachiasmatic nuclei, the
Incoherent dynamics in the toric code subject to disorder
NASA Astrophysics Data System (ADS)
Röthlisberger, Beat; Wootton, James R.; Heath, Robert M.; Pachos, Jiannis K.; Loss, Daniel
2012-02-01
We numerically study the effects of two forms of quenched disorder on the anyons of the toric code. First, a class of codes based on random lattices of stabilizer operators is presented and shown to be superior to the standard square-lattice toric code for certain forms of biased noise. It is further argued that these codes are close to optimal, in that they tightly reach the upper bound of error thresholds beyond which no correctable Calderbank-Shore-Steane codes can exist. Additionally, we study the classical motion of anyons in toric codes with randomly distributed on-site potentials. In the presence of repulsive long-range interaction between the anyons, a surprising increase in the lifetime of encoded states with disorder strength is reported and explained by an entirely incoherent mechanism. Finally, the coherent transport of the anyons in the presence of both forms of disorder is investigated and a significant suppression of the anyon motion is found.
Molecular reconstruction of a fungal genetic code alteration.
Mateus, Denisa D; Paredes, João A; Español, Yaiza; Ribas de Pouplana, Lluís; Moura, Gabriela R; Santos, Manuel A S
2013-06-01
Fungi of the CTG clade translate the Leu CUG codon as Ser. This genetic code alteration is the only eukaryotic sense-to-sense codon reassignment known to date, is mediated by an ambiguous serine tRNA (tRNACAG(Ser)), exposes unanticipated flexibility of the genetic code and raises major questions about its selection and fixation in this fungal lineage. In particular, the origin of the tRNACAG(Ser) and the evolutionary mechanism of CUG reassignment from Leu to Ser remain poorly understood. In this study, we have traced the origin of the tDNACAG(Ser) gene and studied critical mutations in the tRNACAG(Ser) anticodon-loop that modulated CUG reassignment. Our data show that the tRNACAG(Ser) emerged from insertion of an adenosine in the middle position of the 5'-CGA-3'anticodon of a tRNACGA(Ser) ancestor, producing the 5'-CAG-3' anticodon of the tRNACAG(Ser), without altering its aminoacylation properties. This mutation initiated CUG reassignment while two additional mutations in the anticodon-loop resolved a structural conflict produced by incorporation of the Leu 5'-CAG-3'anticodon in the anticodon-arm of a tRNA(Ser). Expression of the mutant tRNACAG(Ser) in yeast showed that it cannot be expressed at physiological levels and we postulate that such downregulation was essential to maintain Ser misincorporation at sub-lethal levels during the initial stages of CUG reassignment. We demonstrate here that such low level CUG ambiguity is advantageous in specific ecological niches and we propose that misreading tRNAs are targeted for degradation by an unidentified tRNA quality control pathway.
Molecular reconstruction of a fungal genetic code alteration
Mateus, Denisa D.; Paredes, João A.; Español, Yaiza; Ribas de Pouplana, Lluís; Moura, Gabriela R.; Santos, Manuel A.S.
2013-01-01
Fungi of the CTG clade translate the Leu CUG codon as Ser. This genetic code alteration is the only eukaryotic sense-to-sense codon reassignment known to date, is mediated by an ambiguous serine tRNA (tRNACAGSer), exposes unanticipated flexibility of the genetic code and raises major questions about its selection and fixation in this fungal lineage. In particular, the origin of the tRNACAGSer and the evolutionary mechanism of CUG reassignment from Leu to Ser remain poorly understood. In this study, we have traced the origin of the tDNACAGSer gene and studied critical mutations in the tRNACAGSer anticodon-loop that modulated CUG reassignment. Our data show that the tRNACAGSer emerged from insertion of an adenosine in the middle position of the 5′-CGA-3′anticodon of a tRNACGASer ancestor, producing the 5′-CAG-3′ anticodon of the tRNACAGSer, without altering its aminoacylation properties. This mutation initiated CUG reassignment while two additional mutations in the anticodon-loop resolved a structural conflict produced by incorporation of the Leu 5′-CAG-3′anticodon in the anticodon-arm of a tRNASer. Expression of the mutant tRNACAGSer in yeast showed that it cannot be expressed at physiological levels and we postulate that such downregulation was essential to maintain Ser misincorporation at sub-lethal levels during the initial stages of CUG reassignment. We demonstrate here that such low level CUG ambiguity is advantageous in specific ecological niches and we propose that misreading tRNAs are targeted for degradation by an unidentified tRNA quality control pathway. PMID:23619021
NASA Astrophysics Data System (ADS)
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model
NASA Astrophysics Data System (ADS)
Scukins, Arturs; Bardik, Vitaliy; Pavlov, Evgen; Nerukh, Dmitry
2015-05-01
Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.
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.
Dynamic Molecular Invasion into Multiply Interlocked Catenane.
Yamada, Yasuyuki; Ito, Ryohei; Ogino, Sayaka; Kato, Tatsuhisa; Tanaka, Kentaro
2017-09-14
A multiply interlocked catenane with a novel molecular topology was synthesized; a phthalocyanine bearing four peripheral crown ethers was quadruply interlocked with a cofacial porphyrin dimer bridged with four alkylammonium chains. The supramolecular conjugate has two nanospaces surrounded by a porphyrin, a phthalocyanine, and four alkyl chains to accommodate guest molecules. Because the phthalocyanine is movable along the alkyl chains, it acts as an adjustable wall, permitting the invasion of large molecules to the nanospaces without spoiling the affinity of the association. The dynamic molecular invasion allowed the intercalation of dianionic porphyrins into both the nanospaces with a high affinity. A photometric titration experiment revealed the two-step inclusion phenomenon. The multiply interlocked catenane complexed with three Cu2+ ions, and the spin-spin interaction was switched off by the intercalation of dianionic porphyrins. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations
NASA Astrophysics Data System (ADS)
Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein
2015-12-01
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
NASA Astrophysics Data System (ADS)
Arntsen, Christopher; Chen, Chen; Voth, Gregory A.
2017-09-01
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.
Arntsen, Christopher; Chen, Chen; Voth, Gregory A
2017-09-01
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.
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.
Using RNA as Molecular Code for Programming Cellular Function.
Kushwaha, Manish; Rostain, William; Prakash, Satya; Duncan, John N; Jaramillo, Alfonso
2016-08-19
RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.
Exploring Hamiltonian dielectric solvent molecular dynamics
NASA Astrophysics Data System (ADS)
Bauer, Sebastian; Tavan, Paul; Mathias, Gerald
2014-09-01
Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an α-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.
Exchange frequency in replica exchange molecular dynamics
NASA Astrophysics Data System (ADS)
Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.
2008-01-01
The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.
8B structure in Fermionic Molecular Dynamics
NASA Astrophysics Data System (ADS)
Henninger, K. R.; Neff, T.; Feldmeier, H.
2015-04-01
The structure of the light exotic nucleus 8B is investigated in the Fermionic Molecular Dynamics (FMD) model. The decay of 8B is responsible for almost the entire high- energy solar-neutrino flux, making structure calculations of 8B important for determining the solar core temperature. 8B is a proton halo candidate thought to exhibit clustering. FMD uses a wave-packet basis and is well-suited for modelling clustering and halos. For a multiconfiguration treatment we construct the many-body Hilbert space from antisymmetrised angular-momentum projected 8-particle states. First results show formation of a proton halo.
Molecular Dynamics Simulations of Interface Failure
NASA Astrophysics Data System (ADS)
Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.
2007-03-01
The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.
Molecular beam studies of reaction dynamics
Lee, Y.T.
1987-03-01
Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.
Molecular dynamics simulations of dense plasmas
Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.
1993-12-31
We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.
Charge transport network dynamics in molecular aggregates
Jackson, Nicholas E.; Chen, Lin X.; Ratner, Mark A.
2016-07-20
Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ~100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed.
Collective dynamics of interacting molecular motors.
Campàs, O; Kafri, Y; Zeldovich, K B; Casademunt, J; Joanny, J-F
2006-07-21
The collective dynamics of N interacting processive molecular motors are considered theoretically when an external force is applied to the leading motor. We show, using a discrete lattice model, that the force-velocity curves strongly depend on the effective dynamic interactions between motors and differ significantly from those of a simple approach where the motors equally share the force. Moreover, they become essentially independent of the number of motors if N is large enough (N> or approximately 5 for conventional kinesin). We show that a two-state ratchet model has a very similar behavior to that of the coarse-grained lattice model with effective interactions. The general picture is unaffected by motor attachment and detachment events.
Charge transport network dynamics in molecular aggregates
Jackson, Nicholas E.; Chen, Lin X.; Ratner, Mark A.
2016-01-01
Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ∼100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed. PMID:27439871
NASA Astrophysics Data System (ADS)
Canning, A.; Galli, G.; Mauri, F.; De Vita, A.; Car, R.
1996-04-01
The implementation of an O( N) tight-binding molecular dynamics code on the Cray T3D parallel computer is discussed. The O( N) energy functional depends on non-orthogonal, localised orbitals and a chemical potential parameter which determines the number of electrons in the system. The localisation introduces a sparse nature to the orbital data and Hamiltonian matrix, greatly changing the coding on parallel machines compared to non-localised systems. The data distribution, communication routines and dynamic load-balancing scheme of the program are presented in detail together with the speed and scaling of the code on various homogeneous and inhomogeneous physical systems. Performance results will be presented for systems of 2048 to 32768 atoms on 32 to 512 processors. We discuss the relevance to quantum molecular dynamics simulations with localised orbitals, of techniques used for programming short-range classical molecular dynamics simulations on parallel machines. The absence of global communications and the localised nature of the orbitals makes these algorithms extremely scalable in terms of memory and speed on parallel systems with fast communications. The main aim of this article is to present in detail all the new concepts and programming techniques that localisation of the orbitals introduces which scientists, coming from a background in non-localised quantum molecular dynamics simulations, may be unfamiliar with.
Recent Progress on the Marylie/Impact Beam Dynamics Code
Ryne, R.D.; Qiang, J.; Bethel, E.W.; Pogorelov, I.; Shalf, J.; Siegerist, C.; Venturini, M.; Dragt, A.J.; Adelmann, A.; Abell, D.; Amundson, J.; Spentzouris, P.; Neri, F.; Walstrom, P.; Mottershead, C.T.; Samulyak, R.
2006-12-06
MARYLIE/IMPACT (ML/I) is a hybrid code that combines the beam optics capabilities of MARYLIE with the parallel Particle-In-Cell capabilities of IMPACT. In addition to combining the capabilities of these codes, ML/I has a number of powerful features, including a choice of Poisson solvers, a fifth-order rf cavity model, multiple reference particles for rf cavities, a library of soft-edge magnet models, representation of magnet systems in terms of coil stacks with possibly overlapping fields, and wakefield effects. The code allows for map production, map analysis, particle tracking, and 3D envelope tracking, all within a single, coherent user environment. ML/I has a front end that can read both MARYLIE input and MAD lattice descriptions. The code can model beams with or without acceleration, and with or without space charge. Developed under a US DOE Scientific Discovery through Advanced Computing (SciDAC) project, ML/I is well suited to large-scale modeling, simulations having been performed with up to 100M macroparticles. The code inherits the powerful fitting and optimizing capabilities of MARYLIE augmented for the new features of ML/I. The combination of soft-edge magnet models, high-order capability, space charge effects, and fitting/optimization capabilities, make ML/I a powerful code for a wide range of beam optics design problems. This paper provides a description of the code and its unique capabilities.
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.
2016-10-01
SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
An high performance Fortran implementation of a Tight-Binding Molecular Dynamics simulation
NASA Astrophysics Data System (ADS)
Di Martino, B.; Celino, M.; Rosato, V.
1999-08-01
Molecular Dynamics simulations in the Tight-Binding approach allow the study of the ionic and electronic structures of semiconductors. The Tight-Binding codes are characterized by inhomogeneous data distribution and require the repeated diagonalization of a large sparse matrix to compute the whole body of its eigenvalues and eigenvectors. We describe the porting of this code on a parallel computer: we show the parallelization strategy for both the Molecular Dynamics part of the code and for the diagonalization needed at each time step. The parallelization has been carried out within the High Performance Fortran (HPF) environment, and tested on IBM SP architectures. The integration of optimized parallel mathematical routines is also described.
Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample
NASA Technical Reports Server (NTRS)
Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)
2001-01-01
Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.
Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample
NASA Technical Reports Server (NTRS)
Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)
2001-01-01
Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.
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.
Coarse-grained protein molecular dynamics simulations.
Derreumaux, Philippe; Mousseau, Normand
2007-01-14
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Coarse-grained protein molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
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. Copyright 2009 Wiley Periodicals, Inc.
Accelerated molecular dynamics simulations of protein folding.
Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew
2015-07-30
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.
Flow and plasticity via nonequilibrium molecular dynamics
Hoover, W.G.
1984-06-11
The viscous flow of fluids and the plastic flow of solids, such as metals, are interesting from both the practical and the theoretical points of view. Atomistic molecular dynamics simulations provide a way of visualizing and understanding these flows in a detailed microscopic way. Simulations are necessarily carried out at relatively high rates of strain. For this reason they are ideally suited to the study of nonlinear flow phenomena: normal stresses induced by shear deformation, stress rotation, and the coupling of stress with heat flow, for instance. The simulations require appropriate boundary conditions, forces, and equations of motion. Newtonian mechanics is relatively inefficient for this simulation task. A modification, Nonequilibrium Molecular Dynamics, has been developed to simulate nonequilibrium flows. By now, many high-strain-rate rheological studies of flowing (viscous) fluids and (plastic) solids have been carried out. Here I describe the new methods used in the simulations and some results obtained in this way. A three-body shear-flow exercise is appended to make these ideas more concrete.
Exact dynamic properties of molecular motors.
Boon, N J; Hoyle, R B
2012-08-28
Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)] on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.
Exact dynamic properties of molecular motors
NASA Astrophysics Data System (ADS)
Boon, N. J.; Hoyle, R. B.
2012-08-01
Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.
Structure and Dynamics of Cellulose Molecular Solutions
NASA Astrophysics Data System (ADS)
Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert
Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.
Dynamic Wetting on Graphene-Coated Surface: Molecular Dynamics Investigation
NASA Astrophysics Data System (ADS)
Hung, Shih-Wei; Shiomi, Junichiro
2015-11-01
Wettability of graphene-coated surface gained significant attention recently due to discussion on the ``transparency'' (whether the wetting characteristics follow that of graphene or the underlying surface) and practical applications of graphene. In terms of static contact angle, the wettability of graphene-coated surfaces have been widely studied by experiments, simulations, and theory in recent years. However, the studies of dynamic wetting on graphene-coated surfaces are limited. In the present study, molecular dynamics simulation was performed to study the dynamic wetting of water droplet on graphene-coated surfaces from a microscopic point of view. The results show that the degree of similarity between the spreading behavior on graphene-coated surface and that on pure graphene (or that on the underlying surface) depends on time, i.e. how nonequilibrium the interface dynamics is. We also found that this feature can be altered by introducing defects into graphene. The work is partially supported by Grant-in-Aid for JSPS Fellows 26-04364 and JST CREST.
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.
Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor
NASA Astrophysics Data System (ADS)
Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.
2016-10-01
In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.
Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.
Luk, Hoi Ling; Feist, Johannes; Toppari, J Jussi; Groenhof, Gerrit
2017-09-12
When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model with which the effect of the light-matter coupling on the molecular dynamics can be predicted accurately. Here we present a multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons. Using this model we have performed simulations with up to 1600 Rhodamine molecules in a cavity. The results of these simulations reveal that the contributions of the molecules to the polariton are time-dependent due to thermal fluctuations that break symmetry. Furthermore, the simulations suggest that in addition to the cavity quality factor, also the Stokes shift and number of molecules control the lifetime of the polariton. Because large numbers of molecules interacting with confined light can now be simulated in atomic detail, we anticipate that our method will lead to a better understanding of the effects of strong coupling on chemical reactivity. Ultimately the method may even be used to systematically design cavities to control photochemistry.
Implementing molecular dynamics on hybrid high performance computers - short range forces
NASA Astrophysics Data System (ADS)
Brown, W. Michael; Wang, Peng; Plimpton, Steven J.; Tharrington, Arnold N.
2011-04-01
The use of accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages. In this work, we discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines - (1) choosing a hybrid parallel decomposition that works on central processing units (CPUs) with distributed memory and accelerator cores with shared memory, (2) minimizing the amount of code that must be ported for efficient acceleration, (3) utilizing the available processing power from both multi-core CPUs and accelerators, and (4) choosing a programming model for acceleration. We present our solution to each of these issues for short-range force calculation in the molecular dynamics package LAMMPS, however, the methods can be applied in many molecular dynamics codes. Specifically, we describe algorithms for efficient short range force calculation on hybrid high-performance machines. We describe an approach for dynamic load balancing of work between CPU and accelerator cores. We describe the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators. Finally, we present results on a parallel test cluster containing 32 Fermi GPUs and 180 CPU cores.
Molecular dynamics simulations of high speed rarefied gas flows
NASA Astrophysics Data System (ADS)
Dongari, Nishanth; Zhang, Yonghao; Reese, Jason M.
2012-11-01
To understand the molecular behaviour of gases in high speed rarefied conditions, we perform molecular dynamics (MD) numerical experiments using the open source code Open FOAM. We use shear-driven Couette flows as test cases, where the two parallel plates are moving with a speed of Uw in opposite directions with their temperatures set to Tw. The gas rarefaction conditions vary from slip to transition, and compressibility conditions vary from low speed isothermal to hypersonic flow regimes, i.e. Knudsen number (Kn) from 0.01 to 1 and Mach number (Ma) from 0.05 to 10. We measure the molecular velocity distribution functions, the spatial variation of gas mean free path profiles and other macroscopic properties. Our MD results convey that flow properties in the near-wall non-equilibrium region do not merely depend on Kn, but they are also significantly affected by Ma. These results may yield new insight into diffusive transport in rarefied gases at high speeds.
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
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. © 2016 Elsevier Inc. All rights reserved.
Molecular structures and intramolecular dynamics of pentahalides
NASA Astrophysics Data System (ADS)
Ischenko, A. A.
2017-03-01
This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.
Partial hydrodynamic representation of quantum molecular dynamics
NASA Astrophysics Data System (ADS)
Gu, Bing; Franco, Ignacio
2017-05-01
A hybrid method is proposed to propagate system-bath quantum dynamics that use both basis functions and coupled quantum trajectories. In it, the bath is represented with an ensemble of Bohmian trajectories while the system degrees of freedom are accounted through reduced density matrices. By retaining the Hilbert space structure for the system, the method is able to capture interference processes that are challenging to describe in Bohmian dynamics due to singularities that these processes introduce in the quantum potential. By adopting quantum trajectories to represent the bath, the method beats the exponential scaling of the computational cost with the bath size. This combination makes the method suitable for large-scale ground and excited state fully quantum molecular dynamics simulations. Equations of motion for the quantum trajectories and reduced density matrices are derived from the Schrödinger equation and a computational algorithm to solve these equations is proposed. Through computations in two-dimensional model systems, the method is shown to offer an accurate description of subsystem observables and of quantum decoherence, which is difficult to obtain when the quantum nature of the bath is ignored. The scaling of the method is demonstrated using a model with 21 degrees of freedom. The limit of independent trajectories is recovered when the mass of bath degrees of freedom is much larger than the one of the system, in agreement with mixed quantum-classical descriptions.
Engine dynamic analysis with general nonlinear finite element codes
NASA Technical Reports Server (NTRS)
Adams, M. L.; Padovan, J.; Fertis, D. G.
1991-01-01
A general engine dynamic analysis as a standard design study computational tool is described for the prediction and understanding of complex engine dynamic behavior. Improved definition of engine dynamic response provides valuable information and insights leading to reduced maintenance and overhaul costs on existing engine configurations. Application of advanced engine dynamic simulation methods provides a considerable cost reduction in the development of new engine designs by eliminating some of the trial and error process done with engine hardware development.
Hydration dynamics in water clusters via quantum molecular dynamics simulations
Turi, László
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of
Molecular dynamics simulations of cavitation bubble collapse and sonoluminescence
NASA Astrophysics Data System (ADS)
Schanz, Daniel; Metten, Burkhard; Kurz, Thomas; Lauterborn, Werner
2012-11-01
The dynamics of the medium within a collapsing and rebounding cavitation bubble is investigated by means of molecular dynamics (MD) simulations adopting a hard sphere model for the species inside the bubble. The dynamics of the surrounding liquid (water) is modelled using a Rayleigh-Plesset (RP)-type equation coupled to the bubble interior by the gas pressure at the wall obtained from the MD calculations. Water vapour and vapour chemistry are included in the RP-MD model as well as mass and energy transfer through the bubble wall. The calculations reveal the evolution of temperature, density and pressure within a bubble at conditions typical of single-bubble sonoluminescence and predict how the particle numbers and densities of different vapour dissociation and reaction products in the bubble develop in space and time. Among the parameters varied are the sound pressure amplitude of a sonoluminescence bubble in water, the noble gas mixture in the bubble and the accommodation coefficients for mass and energy exchange through the bubble wall. Simulation particle numbers up to 10 million are used; most calculations, however, are performed with one million particles to save computer run time. Validation of the MD code was done by comparing MD results with solutions obtained by continuum mechanics calculations for the Euler equations.
The study on dynamic cadastral coding rules based on kinship relationship
NASA Astrophysics Data System (ADS)
Xu, Huan; Liu, Nan; Liu, Renyi; Lu, Jingfeng
2007-06-01
Cadastral coding rules are an important supplement to the existing national and local standard specifications for building cadastral database. After analyzing the course of cadastral change, especially the parcel change with the method of object-oriented analysis, a set of dynamic cadastral coding rules based on kinship relationship corresponding to the cadastral change is put forward and a coding format composed of street code, block code, father parcel code, child parcel code and grandchild parcel code is worked out within the county administrative area. The coding rule has been applied to the development of an urban cadastral information system called "ReGIS", which is not only able to figure out the cadastral code automatically according to both the type of parcel change and the coding rules, but also capable of checking out whether the code is spatiotemporally unique before the parcel is stored in the database. The system has been used in several cities of Zhejiang Province and got a favorable response. This verifies the feasibility and effectiveness of the coding rules to some extent.
Molecular dynamics studies of nanofluidics and nanomechanics
NASA Astrophysics Data System (ADS)
Lee, Ki-Ho
Developing a membrane that can successfully filter molecules such as hydrocarbons, oxygen, and carbon dioxide from gaseous mixtures is an important issue for the environmental and economic industries. This potential selectivity can be predicted from atomistic simulations of the diffusion and adsorption of gases into and within carbon nanotubes. The computational nanofluidics of hydrocarbons, oxygen, and carbon dioxide have been studied with molecular dynamics simulations in the work reported here. The interactions in the system are modeled by a classical reactive empirical bond-order potential coupled to Lennard-Jones and Coulombic potentials. The transport of gas molecules for long time periods is characterized by initial non-equilibrium states followed by equilibrium states. The non-equilibrium state is induced by the diffusive motion of gas molecules from one end of the nanotubes into the vacuum or low-pressure region at the other end of the nanotubes, and lasts until the gases are evenly distributed in the nanotubes. During the non-equilibrium state, the gas molecules move back and forth through the nanotubes. It is found that this behavior, the time needed for the attainment of equilibrium, and the molecular motions at the openings of the nanotubes are affected by the density (or pressure) of gas molecules both inside and outside of the carbon nanotubes. When the gas molecules reach the end of the nanotubes, the attractive force between the tube end and the gas molecules prevents the molecules from exiting. The mechanical properties of carbon nanotubes have extended the potential applications of nanoelectromechanical systems (HEMS) such as nano-switches, nanosensors, nano-actuators, and nano-tweezers. In this study, the bending motion from externally incident Ar atom impacts on nanotubes with one firmly-fixed end is examined with classical molecular dynamics simulations. The deformation of the carbon nanotubes in the direction perpendicular to their axis is
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..
NASA Astrophysics Data System (ADS)
Pérez, Alejandro; Tuckerman, Mark E.
2011-08-01
Higher order factorization schemes are developed for path integral molecular dynamics in order to improve the convergence of estimators for physical observables as a function of the Trotter number. The methods are based on the Takahashi-Imada and Susuki decompositions of the Boltzmann operator. The methods introduced improve the averages of the estimators by using the classical forces needed to carry out the dynamics to construct a posteriori weighting factors for standard path integral molecular dynamics. The new approaches are straightforward to implement in existing path integral codes and carry no significant overhead. The Suzuki higher order factorization was also used to improve the end-to-end distance estimator in open path integral molecular dynamics. The new schemes are tested in various model systems, including an ab initio path integral molecular dynamics calculation on the hydrogen molecule and a quantum water model. The proposed algorithms have potential utility for reducing the cost of path integral molecular dynamics calculations of bulk systems.
Pérez, Alejandro; Tuckerman, Mark E
2011-08-14
Higher order factorization schemes are developed for path integral molecular dynamics in order to improve the convergence of estimators for physical observables as a function of the Trotter number. The methods are based on the Takahashi-Imada and Susuki decompositions of the Boltzmann operator. The methods introduced improve the averages of the estimators by using the classical forces needed to carry out the dynamics to construct a posteriori weighting factors for standard path integral molecular dynamics. The new approaches are straightforward to implement in existing path integral codes and carry no significant overhead. The Suzuki higher order factorization was also used to improve the end-to-end distance estimator in open path integral molecular dynamics. The new schemes are tested in various model systems, including an ab initio path integral molecular dynamics calculation on the hydrogen molecule and a quantum water model. The proposed algorithms have potential utility for reducing the cost of path integral molecular dynamics calculations of bulk systems.
Simulation of spacecraft attitude dynamics using TREETOPS and model-specific computer Codes
NASA Technical Reports Server (NTRS)
Cochran, John E.; No, T. S.; Fitz-Coy, Norman G.
1989-01-01
The simulation of spacecraft attitude dynamics and control using the generic, multi-body code called TREETOPS and other codes written especially to simulate particular systems is discussed. Differences in the methods used to derive equations of motion--Kane's method for TREETOPS and the Lagrangian and Newton-Euler methods, respectively, for the other two codes--are considered. Simulation results from the TREETOPS code are compared with those from the other two codes for two example systems. One system is a chain of rigid bodies; the other consists of two rigid bodies attached to a flexible base body. Since the computer codes were developed independently, consistent results serve as a verification of the correctness of all the programs. Differences in the results are discussed. Results for the two-rigid-body, one-flexible-body system are useful also as information on multi-body, flexible, pointing payload dynamics.
Kim, Daehee; Kim, Dongwan; An, Sunshin
2016-01-01
Code dissemination in wireless sensor networks (WSNs) is a procedure for distributing a new code image over the air in order to update programs. Due to the fact that WSNs are mostly deployed in unattended and hostile environments, secure code dissemination ensuring authenticity and integrity is essential. Recent works on dynamic packet size control in WSNs allow enhancing the energy efficiency of code dissemination by dynamically changing the packet size on the basis of link quality. However, the authentication tokens attached by the base station become useless in the next hop where the packet size can vary according to the link quality of the next hop. In this paper, we propose three source authentication schemes for code dissemination supporting dynamic packet size. Compared to traditional source authentication schemes such as μTESLA and digital signatures, our schemes provide secure source authentication under the environment, where the packet size changes in each hop, with smaller energy consumption. PMID:27409616
Kim, Daehee; Kim, Dongwan; An, Sunshin
2016-07-09
Code dissemination in wireless sensor networks (WSNs) is a procedure for distributing a new code image over the air in order to update programs. Due to the fact that WSNs are mostly deployed in unattended and hostile environments, secure code dissemination ensuring authenticity and integrity is essential. Recent works on dynamic packet size control in WSNs allow enhancing the energy efficiency of code dissemination by dynamically changing the packet size on the basis of link quality. However, the authentication tokens attached by the base station become useless in the next hop where the packet size can vary according to the link quality of the next hop. In this paper, we propose three source authentication schemes for code dissemination supporting dynamic packet size. Compared to traditional source authentication schemes such as μTESLA and digital signatures, our schemes provide secure source authentication under the environment, where the packet size changes in each hop, with smaller energy consumption.
NASA Astrophysics Data System (ADS)
Tringe, J. W.; Ileri, N.; Levie, H. W.; Stroeve, P.; Ustach, V.; Faller, R.; Renaud, P.
2015-08-01
We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.
Tringe, J. W.; Ileri, N.; Levie, H. W.; ...
2015-08-01
We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage.more » Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.« less
Nanodrop contact angles from molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim
2016-11-01
The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.
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.
Assessing Electrolyte Transport Properties with Molecular Dynamics
Jones, R. E.; Ward, D. K.; Gittleson, F. S.; ...
2017-04-15
Here in this work we use estimates of ionic transport properties obtained from molecular dynamics to rank lithium electrolytes of different compositions. We develop linear response methods to obtain the Onsager diffusivity matrix for all chemical species, its Fickian counterpart, and the mobilities of the ionic species. We apply these methods to the well-studied propylene carbonate/ethylene carbonate solvent with dissolved LiBF4 and O2. The results show that, over a range of lithium concentrations and carbonate mixtures, trends in the transport coefficients can be identified and optimal electrolytes can be selected for experimental focus; however, refinement of these estimation techniques ismore » necessary for a reliable ranking of a large set of electrolytes.« less
Molecular dynamics simulation of aluminium melting
NASA Astrophysics Data System (ADS)
Novak, Jakob
2016-06-01
Solid-liquid phase transition has been simulated by the molecular dynamics method, using isobaric-isoenthalpic ensemble. For interatomic potential, glue potential has been selected. The original algorithm for bookkeeping of the information on neighbouring relationships of the atoms has been developed and used in this research. Time consumption for calculation of interatomic forces has been reduced from o(N2) to o(N) by the use of this algorithm. Calculations show that phase transition from solid to liquid occurs between 1,000 K and 1,300 K. The simulated temperature of phase transition is higher than the experimental value due to the absence of crystal defects. If constant heat flux is supplied, temperature decreases during melting because the superheated state becomes unstable. During the cooling process, no significant changes of the observed variables were detected due to the high cooling rate, which prevents crystallisation.
Cell list algorithms for nonequilibrium molecular dynamics
NASA Astrophysics Data System (ADS)
Dobson, Matthew; Fox, Ian; Saracino, Alexandra
2016-06-01
We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.
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.
Cluster production within antisymmetrized molecular dynamics
NASA Astrophysics Data System (ADS)
Ono, Akira
2016-06-01
Clusters are quite important at various situations in heavy-ion collisions. Antisymmetrized molecular dynamics was improved to take into account the correlations to form light clusters, such as deuterons and α particles, and light nuclei composed of several clusters. The momentum fluctuations of emitted particles are also taken into account by a simple method. Formation of fragments and light clusters in a wide range of heavy-ion collisions was well described with a single set of model parameters. Fragmentation in a proton induced reaction was also well reproduced by introducing cluster correlations. Calculated results demonstrate strong impacts of clusters in various observables including those usually regarded as probes of the density dependence of symmetry energy.
Ion mobility analysis of molecular dynamics.
Wyttenbach, Thomas; Pierson, Nicholas A; Clemmer, David E; Bowers, Michael T
2014-01-01
The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.
Molecular Dynamics Simulations of Hypervelocity Impacts
NASA Astrophysics Data System (ADS)
Owens, Eli T.; Bachlechner, Martina E.
2007-03-01
Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.
Molecular-dynamics simulations of lead clusters
NASA Astrophysics Data System (ADS)
Hendy, S. C.; Hall, B. D.
2001-08-01
Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.
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
Molecular Dynamics Simulation of a RNA Aptasensor.
Ruan, Min; Seydou, Mahamadou; Noel, Vincent; Piro, Benoit; Maurel, François; Barbault, Florent
2017-04-14
Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.
NASA Astrophysics Data System (ADS)
Liu, Yuk Tung; Etienne, Zachariah; Shapiro, Stuart
2011-04-01
The Illinois relativity group has written and tested a new GRMHD code, which is compatible with adaptive-mesh refinement (AMR) provided by the widely-used Cactus/Carpet infrastructure. Our code solves the Einstein-Maxwell-MHD system of coupled equations in full 3+1 dimensions, evolving the metric via the BSSN formalism and the MHD and magnetic induction equations via a conservative, high-resolution shock-capturing scheme. The induction equations are recast as an evolution equation for the magnetic vector potential. The divergenceless constraint div(B) = 0 is enforced by the curl of the vector potential. In simulations with uniform grid spacing, our MHD scheme is numerically equivalent to a commonly used, staggered-mesh constrained-transport scheme. We will present numerical method and code validation tests for both Minkowski and curved spacetimes. The tests include magnetized shocks, nonlinear Alfven waves, cylindrical explosions, cylindrical rotating disks, magnetized Bondi tests, and the collapse of a magnetized rotating star. Some of the more stringent tests involve black holes. We find good agreement between analytic and numerical solutions in these tests, and achieve convergence at the expected order.
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.
Molecular beam studies of reaction dynamics
Lee, Y.T.
1990-03-01
The major thrust of this research project is to elucidate detailed dynamics of simple 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. 34 refs.
Molecular beam studies of reaction dynamics
Lee, Yuan T.
1991-03-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
A molecular dynamics approach to barrodiffusion
NASA Astrophysics Data System (ADS)
Cooley, James; Marciante, Mathieu; Murillo, Michael
2016-10-01
Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin
Molecular dynamics simulation in virus research
Ode, Hirotaka; Nakashima, Masaaki; Kitamura, Shingo; Sugiura, Wataru; Sato, Hironori
2012-01-01
Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique. PMID:22833741
Statistical Analysis of Coding for Molecular Properties in the Olfactory Bulb
Auffarth, Benjamin; Gutierrez-Galvez, Agustín; Marco, Santiago
2011-01-01
The relationship between molecular properties of odorants and neural activities is arguably one of the most important issues in olfaction and the rules governing this relationship are still not clear. In the olfactory bulb (OB), glomeruli relay olfactory information to second-order neurons which in turn project to cortical areas. We investigate relevance of odorant properties, spatial localization of glomerular coding sites, and size of coding zones in a dataset of [14C] 2-deoxyglucose images of glomeruli over the entire OB of the rat. We relate molecular properties to activation of glomeruli in the OB using a non-parametric statistical test and a support-vector machine classification study. Our method permits to systematically map the topographic representation of various classes of odorants in the OB. Our results suggest many localized coding sites for particular molecular properties and some molecular properties that could form the basis for a spatial map of olfactory information. We found that alkynes, alkanes, alkenes, and amines affect activation maps very strongly as compared to other properties and that amines, sulfur-containing compounds, and alkynes have small zones and high relevance to activation changes, while aromatics, alkanes, and carboxylics acid recruit very big zones in the dataset. Results suggest a local spatial encoding for molecular properties. PMID:21811447
GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES
MUCKERMAN,J.T.
1999-06-09
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.
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.
Vaidehi, Nagarajan; Jain, Abhinandan
2015-01-29
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.
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
NASA Technical Reports Server (NTRS)
Shapiro, Wilbur; Chupp, Raymond; Holle, Glenn; Scott, Thomas
2004-01-01
The objectives of the program were to develop computational fluid dynamics (CFD) codes and simpler industrial codes for analyzing and designing advanced seals for air-breathing and space propulsion engines. The CFD code SCISEAL is capable of producing full three-dimensional flow field information for a variety of cylindrical configurations. An implicit multidomain capability allow the division of complex flow domains to allow optimum use of computational cells. SCISEAL also has the unique capability to produce cross-coupled stiffness and damping coefficients for rotordynamic computations. The industrial codes consist of a series of separate stand-alone modules designed for expeditious parametric analyses and optimization of a wide variety of cylindrical and face seals. Coupled through a Knowledge-Based System (KBS) that provides a user-friendly Graphical User Interface (GUI), the industrial codes are PC based using an OS/2 operating system. These codes were designed to treat film seals where a clearance exists between the rotating and stationary components. Leakage is inhibited by surface roughness, small but stiff clearance films, and viscous pumping devices. The codes have demonstrated to be a valuable resource for seal development of future air-breathing and space propulsion engines
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver
2015-06-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
A quantum molecular dynamics study of aqueous solvation dynamics
NASA Astrophysics Data System (ADS)
Videla, Pablo E.; Rossky, Peter J.; Laria, D.
2013-10-01
Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.
Bubble Dynamics Calculations Using the DYSMAS/E Finite Difference Code
1988-07-01
NSWC TR 88-226 AD-A241 549 BUBBLE DYNAMICS CALCULATIONS USING THE DYSMAS/E FINITE DIFFERENCE CODE BY STEPHEN A. WILKERSON (NSWC) DR. HANS SCHITrKE...62314N RJ I4W27 1t. TITLE (include Securfry CJalssticdtti) Bubble Dynamics Calculations Using the l)YSMAS/E Finite D~ifference Code 12, PERSONAL AUTHOR...FIELD GROUP SUB. GR. bubble divnamics DN’SNAS/E, code 19 09 bubble collapse detonation 19. ABSTRACT (Continue on rovotse if noceisary and idenrty by block
BHARDWAJ, MANLJ K.; REESE,GARTH M.; DRIESSEN,BRIAN; ALVIN,KENNETH F.; DAY,DAVID M.
2000-04-06
As computational needs for structural finite element analysis increase, a robust implicit structural dynamics code is needed which can handle millions of degrees of freedom in the model and produce results with quick turn around time. A parallel code is needed to avoid limitations of serial platforms. Salinas is an implicit structural dynamics code specifically designed for massively parallel platforms. It computes the structural response of very large complex structures and provides solutions faster than any existing serial machine. This paper gives a current status of Salinas and uses demonstration problems to show Salinas' performance.
Structure and dynamics of layered molecular assemblies
NASA Astrophysics Data System (ADS)
Horne, Jennifer Conrad
This dissertation focuses on the goal of understanding and controlling layered material properties from a molecular perspective. With this understanding, materials can be synthetically tailored to exhibit predetermined bulk properties. This investigation describes the optical response of a family of metal-phosphonate (MP) monolayers and multilayers, materials that are potentially useful because the films are easy to synthesize and are chemically and thermally stable. MP films have shown potential in a variety of chemical sensing and optical applications, and in this dissertation, the suitability of MP films for optical information storage is explored For this application, the extent of photonic energy transport within and between optically active layers is an important factor in determining the stability and specificity of optical modifications made to a material. Intralayer and interlayer energy transport processes can be studied selectively in MP films because the composition, and thus the properties, of each layer are controlled synthetically. It was determined by fluorescence relaxation dynamics in conjunction with atomic force microscopy (AFM) that the substrate and layer morphologies are key factors in determining the layer optical and physical properties. The initial MP layers in a multilayer are structurally heterogeneous, characterized by randomly distributed islands that are ~50 A in diameter. The population dynamics measured for these layers are non-exponential, chromophore concentration-independent, and identical for two different chromophores. The data is explained in the context of an excitation hopping model in a system where the surface is characterized by islands of aggregated chromophores as well as non-aggregated monomers. Within a MP monolayer, the dynamics are dominated by intra-island excitation hopping. Forster (dipolar) energy transfer between the energetically overlapped chromophores does not play a significant role in determining the
Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators
Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.
1999-11-13
In this paper, we present an object-oriented three-dimensional parallel particle-in-cell code for beam dynamics simulation in linear accelerators. A two-dimensional parallel domain decomposition approach is employed within a message passing programming paradigm along with a dynamic load balancing. Implementing object-oriented software design provides the code with better maintainability, reusability, and extensibility compared with conventional structure based code. This also helps to encapsulate the details of communications syntax. Performance tests on SGI/Cray T3E-900 and SGI Origin 2000 machines show good scalability of the object-oriented code. Some important features of this code also include employing symplectic integration with linear maps of external focusing elements and using z as the independent variable, typical in accelerators. A successful application was done to simulate beam transport through three superconducting sections in the APT linac design.
Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure
2014-08-30
properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to
NASA Astrophysics Data System (ADS)
Pontoppidan, Klaus
Based on the observed distributions of exoplanets and dynamical models of their evolution, the primary planet-forming regions of protoplanetary disks are thought to span distances of 1-20 AU from typical stars. A key observational challenge of the next decade will be to understand the links between the formation of planets in protoplanetary disks and the chemical composition of exoplanets. Potentially habitable planets in particular are likely formed by solids growing within radii of a few AU, augmented by unknown contributions from volatiles formed at larger radii of 10-50 AU. The basic chemical composition of these inner disk regions is characterized by near- to far-infrared (2-200 micron) emission lines from molecular gas at temperatures of 50-1500 K. A critical step toward measuring the chemical composition of planet-forming regions is therefore to convert observed infrared molecular line fluxes, profiles and images to gas temperatures, densities and molecular abundances. However, current techniques typically employ approximate radiative transfer methods and assumptions of local thermodynamic equilibrium (LTE) to retrieve abundances, leading to uncertainties of orders of magnitude and inconclusive comparisons to chemical models. Ultimately, the scientific impact of the high quality spectroscopic data expected from the James Webb Space Telescope (JWST) will be limited by the availability of radiative transfer tools for infrared molecular lines. We propose to develop a numerically accurate, non-LTE 3D line radiative transfer code, needed to interpret mid-infrared molecular line observations of protoplanetary and debris disks in preparation for the James Webb Space Telescope (JWST). This will be accomplished by adding critical functionality to the existing Monte Carlo code LIME, which was originally developed to support (sub)millimeter interferometric observations. In contrast to existing infrared codes, LIME calculates the exact statistical balance of arbitrary
Molecular dynamics and spectra. II. Diatomic Raman
NASA Astrophysics Data System (ADS)
Berens, Peter H.; White, Steven R.; Wilson, Kent R.
1981-07-01
This paper and paper I in this series [P.H. Berens and K.R. Wilison, J. Chem. Phys. 74, 4872 (1981)] indicate that infrared and Raman rotational and fundamental vibrational-rotational spectra of dense systems (high pressure gases, liquids, and solids) are essentially classical, in that they can be computed and understood from a basically classical mechanical viewpoint, with some caveats for features in which anharmonicity is important, such as the detailed shape of Q branches. It is demonstrated here, using the diatomic case as an example, that ordinary, i.e., nonresonant, Raman band contours can be computed from classical mechanics plus simple quantum corrections. Classical versions of molecular dynamics, linear response theory, and ensemble averaging, followed by straightforward quantum corrections, are used to compute the pure rotational and fundamental vibration-rotational Raman band contours of N2 for the gas phase and for solutions of N2 in different densities of gas phase Ar and in liquid Ar. The evolution is seen from multiple peaked line shapes characteristic of free rotation in the gas phase to single peaks characteristic of hindered rotation in the liquid phase. Comparison is made with quantum and correspondence principle classical gas phase spectral calculations and with experimental measurements for pure N2 and N2 in liquid Ar. Three advantages are pointed out for a classical approach to infrared and Raman spectra. First, a classical approach can be used to compute the spectra of complex molecular systems, e.g., of large molecules, clusters, liquids, solutions, and solids. Second, this classical approach can be extended to compute the spectra of nonequilibrium and time-dependent systems, e.g., infrared and Raman spectra during the course of chemical reactions. Third, a classical viewpoint allows experimental infrared and Raman spectra to be understood and interpreted in terms of atomic motions with the considerable aid of classical models and of our
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
Nonlinear Resonance Artifacts in Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Schlick, Tamar; Mandziuk, Margaret; Skeel, Robert D.; Srinivas, K.
1998-02-01
The intriguing phenomenon of resonance, a pronounced integrator-induced corruption of a system's dynamics, is examined for simple molecular systems subject to the classical equations of motion. This source of timestep limitation is not well appreciated in general, and certainly analyses of resonance patterns have been few in connection to biomolecular dynamics. Yet resonances are present in the commonly used Verlet integrator, in symplectic implicit schemes, and also limit the scope of current multiple-timestep methods that are formulated as symplectic and reversible. The only general remedy to date has been to reduce the timestep. For this purpose, we derive method-dependent timestep thresholds (e.g., Tables 1 and 2) that serve as useful guidelines in practice for biomolecular simulations. We also devise closely related symplectic implicit schemes for which the limitation on the discretization stepsize is much less severe. Specifically, we design methods to remove third-order, or both the third- and fourth-order, resonances. These severe low-order resonances can lead to instability or very large energies. Our tests on two simple molecular problems (Morse and Lennard-Jones potentials), as well as a 22-atom molecule, N-acetylalanyl-N '-methylamide, confirm this prediction; our methods can delay resonances so that they occur only at larger timesteps (EW method) or are essentially removed (LIM2 method). Although stable for large timesteps by this approach, trajectories show large energy fluctuations, perhaps due to the coupling with other factors that induce instability in complex nonlinear systems. Thus, the methods developed here may be more useful for conformational sampling of biomolecular structures. The analysis presented here for the blocked alanine model emphasizes that one-dimensional analysis of resonances can be applied to a more complex, multimode system to analyze resonance behavior, but that resonance due to frequency coupling is more complex to pinpoint
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…
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…
Molecular dynamics simulations of glycoclusters and glycodendrimers.
von der Lieth, Claus W; Frank, Martin; Lindhorst, Thisbe K
2002-05-01
Protein-carbohydrate recognition plays a crucial role in a wide range of biological processes, required both for normal physiological functions and the onset of disease. Nature uses multivalency in carbohydrate-protein interactions as a strategy to overcome the low affinity found for singular binding of an individual saccharide epitope to a single carbohydrate recognition domain of a lectin. To mimic the complex multi-branched oligosaccharides found in glycoconjugates, which form the structural basis of multivalent carbohydrate-protein interactions, so-called glycoclusters and glycodendrimers have been designed to serve as high-affinity ligands of the respective receptor proteins. To allow a rational design of glycodendrimer-type molecules with regard to the receptor structures involved in carbohydrate recognition, a deeper knowledge of the dynamics of such molecules is desirable. Most glycodendrimers have to be considered highly flexible molecules with their conformational preferences most difficult to elucidate by experimental methods. Longtime molecular dynamics (MD) simulations with inclusion of explicit solvent molecules are suited to explore the conformational space accessible to glycodendrimers. Here, a detailed geometric and conformational analysis of 15 glycodendrimers and glycoclusters has been accomplished, which differ with regard to their core moieties, spacer characteristics and the type of terminal carbohydrate units. It is shown that the accessible conformational space depends strongly on the structural features of the core and spacer moieties and even on the type of terminating sugars. The obtained knowledge about possible spatial distributions of the sugar epitopes exposed on the investigated hyperbranched neoglycoconjugates is detailed for all examples and forms important information for the interpretation and prediction of affinity data, which can be deduced from biological testing of these multivalent neoglycoconjugates.
Microsecond Molecular Dynamics Simulations of Lipid Mixing
2015-01-01
Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na+ ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes. PMID:25237736
Molecular dynamics simulations of xDNA.
Varghese, Mathew K; Thomas, Renjith; Unnikrishnan, N V; Sudarsanakumar, C
2009-05-01
xDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force-field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5' G xT A xC xG C xA xG T3').(xA5' C T xG C G xT A xC A3') was explored using a 22 ns molecular dynamics simulation in explicit solvent. During the simulation, the duplex retained its Watson-Crick base-pairing and double helical structure, with deviations from the starting B-form geometry towards A-form; the deviations are mainly in the backbone torsion angles and in the helical parameters. The sugar pucker of the residues were distributed among a variety of modes; C2' endo, C1' exo, O4' endo, C4' exo, C2' exo, and C3' endo. The enhanced stacking interactions on account of the modification in the bases could help to retain the duplex nature of the helix with minor deviations from the ideal geometry. In our simulation, the xDNA showed a reduced minor groove width and an enlarged major groove width in comparison with the NMR structure. Both the grooves are larger than that of standard B-DNA, but major groove width is larger than that of A-DNA with almost equal minor groove width. The enlarged groove widths and the possibility of additional hydration in the grooves makes xDNA a potential molecule for various applications. Copyright (c) 2009 Wiley Periodicals, Inc.
Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code
Schiffgens, J.O.; Graves, N.J.; Oster, C.A.
1980-04-01
This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.
Early stage of critical clusters growth in phenomenological and molecular dynamics simulation models
NASA Astrophysics Data System (ADS)
Puzyrewski, Romuald; Rybicki, Jarosław; Białoskórski, Michał
2006-12-01
The growth of critical clusters is discussed in the paper according to the classical and molecular dynamics (MD) approaches. A new formula for molecule numbers in critical clusters has been derived within the framework of the classical approach. A set of equations controlling the early stage of growth in a neighborhood of a critical size is presented. As far as molecular dynamics simulation is concerned, a computational technique based on the DL_POLY code is described in brief. Computation results are presented concerning cluster formation of H 2O vapor, distribution of clusters versus time, cluster growth and radial density distribution of isolated clusters. A comparison with the classical results is made for a case of dense vapor, where the mechanism of strong condensation is predominant. The Hertz-Knudsen formula seems to be verified by the molecular dynamics results.
An evaluation and analysis of three dynamic watershed acidification codes (MAGIC, ETD, and ILWAS)
Jenne, E.A.; Eary, L.E.; Vail, L.W.; Girvin, D.C.; Liebetrau, A.M.; Hibler, L.F.; Miley, T.B.; Monsour, M.J.
1989-01-01
The US Environmental Protection Agency is currently using the dynamic watershed acidification codes MAGIC, ILWAS, and ETD to assess the potential future impact of the acidic deposition on surface water quality by simulating watershed acid neutralization processes. The reliability of forecasts made with these codes is of considerable concern. The present study evaluates the process formulations (i.e., conceptual and numerical representation of atmospheric, hydrologic geochemical and biogeochemical processes), compares their approaches to calculating acid neutralizing capacity (ANC), and estimates the relative effects (sensitivity) of perturbations in the input data on selected output variables for each code. Input data were drawn from three Adirondack (upstate New York) watersheds: Panther Lake, Clear Pond, and Woods Lake. Code calibration was performed by the developers of the codes. Conclusions focus on summarizing the adequacy of process formulations, differences in ANC simulation among codes and recommendations for further research to increase forecast reliability. 87 refs., 11 figs., 77 tabs.
ZEUS-MP/2: Computational Fluid Dynamics Code
NASA Astrophysics Data System (ADS)
Hayes, John C.; Norman, Michael L.; Fiedler, Robert A.; Bordner, James O.; Li, Pak Shing; Clark, Stephen E.; Ud-Doula, Asif; Mac Low, Mordecai-Mark
2011-02-01
ZEUS-MP is a multiphysics, massively parallel, message-passing implementation of the ZEUS code. ZEUS-MP offers an MHD algorithm that is better suited for multidimensional flows than the ZEUS-2D module by virtue of modifications to the method of characteristics scheme first suggested by Hawley & Stone. This MHD module is shown to compare quite favorably to the TVD scheme described by Ryu et al. ZEUS-MP is the first publicly available ZEUS code to allow the advection of multiple chemical (or nuclear) species. Radiation hydrodynamic simulations are enabled via an implicit flux-limited radiation diffusion (FLD) module. The hydrodynamic, MHD, and FLD modules can be used, singly or in concert, in one, two, or three space dimensions. In addition, so-called 1.5D and 2.5D grids, in which the "half-D'' denotes a symmetry axis along which a constant but nonzero value of velocity or magnetic field is evolved, are supported. Self-gravity can be included either through the assumption of a GM/r potential or through a solution of Poisson's equation using one of three linear solver packages (conjugate gradient, multigrid, and FFT) provided for that purpose. Point-mass potentials are also supported. Because ZEUS-MP is designed for large simulations on parallel computing platforms, considerable attention is paid to the parallel performance characteristics of each module in the code. Strong-scaling tests involving pure hydrodynamics (with and without self-gravity), MHD, and RHD are performed in which large problems (2563 zones) are distributed among as many as 1024 processors of an IBM SP3. Parallel efficiency is a strong function of the amount of communication required between processors in a given algorithm, but all modules are shown to scale well on up to 1024 processors for the chosen fixed problem size.
The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations
Boršnik, Urban; Miller, Benjamin T.; Brooks, Bernard R.; Janežič, Dušanka
2011-01-01
Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. PMID:21793007
Statistical coarse-graining of molecular dynamics into peridynamics.
Silling, Stewart Andrew; Lehoucq, Richard B.
2007-10-01
This paper describes an elegant statistical coarse-graining of molecular dynamics at finite temperature into peridynamics, a continuum theory. Peridynamics is an efficient alternative to molecular dynamics enabling dynamics at larger length and time scales. In direct analogy with molecular dynamics, peridynamics uses a nonlocal model of force and does not employ stress/strain relationships germane to classical continuum mechanics. In contrast with classical continuum mechanics, the peridynamic representation of a system of linear springs and masses is shown to have the same dispersion relation as the original spring-mass system.
Multimillion atom molecular dynamics simulations of glasses and ceramic materials
NASA Astrophysics Data System (ADS)
Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro
1999-11-01
Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed.
Eucb: A C++ program for molecular dynamics trajectory analysis
NASA Astrophysics Data System (ADS)
Tsoulos, Ioannis G.; Stavrakoudis, Athanassios
2011-03-01
Eucb is a standalone program for geometrical analysis of molecular dynamics trajectories of protein systems. The program is written in GNU C++ and it can be installed in any operating system running a C++ compiler. The program performs its analytical tasks based on user supplied keywords. The source code is freely available from http://stavrakoudis.econ.uoi.gr/eucb under LGPL 3 license. Program summaryProgram title:Eucb Catalogue identifier: AEIC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIC_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.: 31 169 No. of bytes in distributed program, including test data, etc.: 297 364 Distribution format: tar.gz Programming language: GNU C++ Computer: The tool is designed and tested on GNU/Linux systems Operating system: Unix/Linux systems RAM: 2 MB Supplementary material: Sample data files are available Classification: 3 Nature of problem: Analysis of molecular dynamics trajectories. Solution method: The program finds all possible interactions according to input files and the user instructions. Then it reads all the trajectory frames and finds those frames in which these interactions occur, under certain geometrical criteria. This is a blind search, without a priori knowledge if a certain interaction occurs or not. The program exports time series of these quantities (distance, angles, etc.) and appropriate descriptive statistics. Running time: Depends on the input data and the required options.
Strong scaling of general-purpose molecular dynamics simulations on GPUs
NASA Astrophysics Data System (ADS)
Glaser, Jens; Nguyen, Trung Dac; Anderson, Joshua A.; Lui, Pak; Spiga, Filippo; Millan, Jaime A.; Morse, David C.; Glotzer, Sharon C.
2015-07-01
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, 2013). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5 ×.
Molecular dynamics simulation of fractal aggregate diffusion
NASA Astrophysics Data System (ADS)
Pranami, Gaurav; Lamm, Monica H.; Vigil, R. Dennis
2010-11-01
The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)10.1088/0305-4470/27/9/012] comprised of Np spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D) , but these can be corrected by carrying out simulations using different simulation box sizes. Specifically, the diffusion coefficient is inversely proportional to the length of a cubic simulation box, and the constant of proportionality appears to be independent of the aggregate mass and fractal dimension. Using this result, it is possible to compute infinite dilution diffusion coefficients (Do) for aggregates of arbitrary size and fractal dimension, and it was found that Do∝Np-1/df , as is often assumed by investigators simulating Brownian aggregation of fractal aggregates. The ratio of hydrodynamic radius to radius of gyration is computed and shown to be independent of mass for aggregates of fixed fractal dimension, thus enabling an estimate of the diffusion coefficient for a fractal aggregate based on its radius of gyration.
Molecular Dynamics Simulations of Ferroelectric Phase Transitions
NASA Astrophysics Data System (ADS)
Yu, Rici; Krakauer, Henry
1997-03-01
Based on an analysis of the wavevector dependence of the lattice instabilities in KNbO_3, we proposed a real-space chain-like instability and a scenario of sequential freezing out or onset of coherence of these instabilities, which qualitatively explains the sequence of observed temperature-dependent ferroelectric phases.(R. Yu and H. Krakauer, Phys. Rev. Lett. 74), 4067 (1995). We suggested that this chain-like instability should also be found in BaTiO_3, and this has been subsequently confirmed by Ghosez et al.(P. Ghosez et al.), Proc. 4th Williamsburg Workshop on First-Principles Calculations for Ferroelectrics, to be published We will present molecular dynamics simulations on BaTiO_3, using effective Hamiltonians constructed from first-principles calculations,(W. Zhong, D. Vanderbilt, and K. M. Rabe, Phys. Rev. Lett. 73), 1861 (1994). that reproduce the essential features of diffuse x-ray scattering measurements in the cubic, tetragonal, orthorhombic, and rhombohedral phases. The good agreement supports the interpretation of real-space chain-formation. Simulations for KNbO3 may also be reported.
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
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.
Fundamental frequency from classical molecular dynamics.
Yamada, Tomonori; Aida, Misako
2015-02-07
We give a theoretical validation for calculating fundamental frequencies of a molecule from classical molecular dynamics (MD) when its anharmonicity is small enough to be treated by perturbation theory. We specifically give concrete answers to the following questions: (1) What is the appropriate initial condition of classical MD to calculate the fundamental frequency? (2) From that condition, how accurately can we extract fundamental frequencies of a molecule? (3) What is the benefit of using ab initio MD for frequency calculations? Our analytical approaches to those questions are classical and quantum normal form theories. As numerical examples we perform two types of MD to calculate fundamental frequencies of H2O with MP2/aug-cc-pVTZ: one is based on the quartic force field and the other one is direct ab initio MD, where the potential energies and the gradients are calculated on the fly. From those calculations, we show comparisons of the frequencies from MD with the post vibrational self-consistent field calculations, second- and fourth-order perturbation theories, and experiments. We also apply direct ab initio MD to frequency calculations of C-H vibrational modes of tetracene and naphthalene. We conclude that MD can give the same accuracy in fundamental frequency calculation as second-order perturbation theory but the computational cost is lower for large molecules.
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.
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.
Dynamics, flexibility, and allostery in molecular chaperonins.
Skjærven, Lars; Cuellar, Jorge; Martinez, Aurora; Valpuesta, José María
2015-09-14
The chaperonins are a family of molecular chaperones present in all three kingdoms of life. They are classified into Group I and Group II. Group I consists of the bacterial variants (GroEL) and the eukaryotic ones from mitochondria and chloroplasts (Hsp60), while Group II consists of the archaeal (thermosomes) and eukaryotic cytosolic variants (CCT or TRiC). Both groups assemble into a dual ring structure, with each ring providing a protective folding chamber for nascent and denatured proteins. Their functional cycle is powered by ATP binding and hydrolysis, which drives a series of structural rearrangements that enable encapsulation and subsequent release of the substrate protein. Chaperonins have elaborate allosteric mechanisms to regulate their functional cycle. Long-range negative cooperativity between the two rings ensures alternation of the folding chambers. Positive intra-ring cooperativity, which facilitates concerted conformational transitions within the protein subunits of one ring, has only been demonstrated for Group I chaperonins. In this review, we describe our present understanding of the underlying mechanisms and the structure-function relationships in these complex protein systems with a particular focus on the structural dynamics, allostery, and associated conformational rearrangements.
Parallel Molecular Dynamics of Coulomb Clusters
NASA Astrophysics Data System (ADS)
Kishimoto, Tokunari; Totsuji, Chieko; Tsuruta, Kenji; Totsuji, Hiroo
2000-10-01
Using parallel computers, we perform large-scale molecular dynamics (MD) simulations of Coulomb clusters in a spherical trapping field. Long-range Coulomb forces are calculated efficiently using the fast multipole method (FMM). Previously Hasse and Avilov [1] have performed numerical analysis of Coulomb clusters, and predicted a crossover between the energy curve of Coulomb clusters and that of finite bcc crystals around N = 10^6. Another prediction [2] has been reported around N = 10^5. Recently, experimental observation of Be^+ clusters in ion trap [3] indicated that structure of N = 8 *10^4 was similar to bcc single crystal. We perform direct simulations of Coulomb clusters of system sizes N = 10^5-10^6. We report preliminary results on 10^5 system: Radial distribution and the Laue-pattern analysis indicates structural evolution of the cluster. The correlation energy of the cluster is found to be lower than finite bcc crystal of the same size. We will show results for larger systems (10^6) and the N dependence of structure and energy of the Coulomb clusters around the crossover region. [1] R. W. Hasse and V. V. Avilov, Phys. Rev. A 44, 4506 (1991). [2] D. H. E. Dubin, Phys. Rev. A 40, 1140 (1989). [3] W. M. Itano et al., Science 279, 686 (1998).
Liquid Jet Cavitation via Molecular Dynamics
NASA Astrophysics Data System (ADS)
Ashurst, W. T.
1997-11-01
A two-dimensional molecular dynamics simulation of a liquid jet is used to investigate cavitation in a diesel-like fuel injector. A channel with a length four times its width has been examined at various system sizes (widths of 20 to 160 σ, where σ is the zero energy location in the Lennard-Jones potential). The wall boundary condition is Maxwell's diffuse reflection, similar to the work by Sun & Ebner (Phys. Rev A 46, 4813, 1992). Currently, the jet exhausts into a vacuum, but a second, low density gas will be incorporated to represent the compressed air in a diesel chamber. Four different flow rates are examined. With ρ U equal to √mɛ/σ^2 (the largest flow rate) the static pressure decreases by a factor of twenty between the channel entrance and exit. The largest flow rate has a parabolic velocity profile with almost constant density across the channel. The smallest flow rate has the same velocity profile but the density exhibits a large variation, with the minimum value in the channel center. Thus, the product ρ U is nearly constant across the channel at this flow rate. The discharge coefficient CD has a small variation with flow rate, but the velocity coefficient CV varies with the amount of two-phase fluid within the channel. The ratio of CV to CD varies from 1.3 (largest flow rate) to 2.0 (the smallest flow rate, which is one-eighth of the largest).
Direct anharmonic correction method by molecular dynamics
NASA Astrophysics Data System (ADS)
Liu, Zhong-Li; Li, Rui; Zhang, Xiu-Lu; Qu, Nuo; Cai, Ling-Cang
2017-04-01
The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties, the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI) method based on the temperature dependent phonon density of states (TD-PDOS) reduced from molecular dynamics simulations. Using the DFEI method, after anharmonic free energy corrections we reproduced the thermal expansion coefficients, the specific heat, the thermal pressure, the isothermal bulk modulus, and the Hugoniot P- V- T relationships of Cu easily and accurately. The extensive tests on other materials including metal, alloy, semiconductor and insulator also manifest that the DFEI method can easily uncover the rest anharmonicity that the quasi-harmonic approximation (QHA) omits. It is thus evidenced that the DFEI method is indeed a very efficient method used to conduct anharmonic effect corrections beyond QHA. More importantly it is much more straightforward and easier compared to previous anharmonic methods.
Molecular Dynamics Study of Helicobacter pylori Urease.
Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M
2014-05-13
Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc.2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.
Pattern-based video coding with dynamic background modeling
NASA Astrophysics Data System (ADS)
Paul, Manoranjan; Lin, Weisi; Lau, Chiew Tong; Lee, Bu-Sung
2013-12-01
The existing video coding standard H.264 could not provide expected rate-distortion (RD) performance for macroblocks (MBs) with both moving objects and static background and the MBs with uncovered background (previously occluded). The pattern-based video coding (PVC) technique partially addresses the first problem by separating and encoding moving area and skipping background area at block level using binary pattern templates. However, the existing PVC schemes could not outperform the H.264 with significant margin at high bit rates due to the least number of MBs classified using the pattern mode. Moreover, both H.264 and the PVC scheme could not provide the expected RD performance for the uncovered background areas due to the unavailability of the reference areas in the existing approaches. In this paper, we propose a new PVC technique which will use the most common frame in a scene (McFIS) as a reference frame to overcome the problems. Apart from the use of McFIS as a reference frame, we also introduce a content-dependent pattern generation strategy for better RD performance. The experimental results confirm the superiority of the proposed schemes in comparison with the existing PVC and the McFIS-based methods by achieving significant image quality gain at a wide range of bit rates.
Chroma sampling and modulation techniques in high dynamic range video coding
NASA Astrophysics Data System (ADS)
Dai, Wei; Krishnan, Madhu; Topiwala, Pankaj
2015-09-01
High Dynamic Range and Wide Color Gamut (HDR/WCG) Video Coding is an area of intense research interest in the engineering community, for potential near-term deployment in the marketplace. HDR greatly enhances the dynamic range of video content (up to 10,000 nits), as well as broadens the chroma representation (BT.2020). The resulting content offers new challenges in its coding and transmission. The Moving Picture Experts Group (MPEG) of the International Standards Organization (ISO) is currently exploring coding efficiency and/or the functionality enhancements of the recently developed HEVC video standard for HDR and WCG content. FastVDO has developed an advanced approach to coding HDR video, based on splitting the HDR signal into a smoothed luminance (SL) signal, and an associated base signal (B). Both signals are then chroma downsampled to YFbFr 4:2:0 signals, using advanced resampling filters, and coded using the Main10 High Efficiency Video Coding (HEVC) standard, which has been developed jointly by ISO/IEC MPEG and ITU-T WP3/16 (VCEG). Our proposal offers both efficient coding, and backwards compatibility with the existing HEVC Main10 Profile. That is, an existing Main10 decoder can produce a viewable standard dynamic range video, suitable for existing screens. Subjective tests show visible improvement over the anchors. Objective tests show a sizable gain of over 25% in PSNR (RGB domain) on average, for a key set of test clips selected by the ISO/MPEG committee.
Dynamic Response of a Pulse-Heated, Thick-Walled, Hollow Sphere: Validation of Code Numerics
Canaan, R.E.
2000-01-19
Volumetric pulse heating of a thick-walled hollow sphere is numerically investigated. The primary objective is to validate a variety of LLNL 30 hydrocodes for modeling the dynamic behavior of fissile/fissionable metals subject to rapid ''fission-heating'' transients. The 30 codes tested include both DYNA3D and NIKE3D, as well as the ''ASCI'' code, ALE3D. The codes are compared ''head-to-head'' and are benchmarked against a 1D finite difference solution to the problem that is derived from basic principles. Three pulse-heating transients are examined with full-width-half-maximum pulse durations of 41{micro}s, 85{micro}s, and 140{micro}s, respectively. These three transients produce a significant range of dynamic responses in the thermo-elastic regime. We present results for dynamic radial displacements and stresses for each pulse, and also discuss which code features/options worked best for these types of calculations. In general, the code results are in excellent agreement for the simple system considered. Validation of code numerics in simple systems is a key first step toward future application of the codes in more complicated geometries (U).
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.
Adaptive uniform grayscale coded aperture design for high dynamic range compressive spectral imaging
NASA Astrophysics Data System (ADS)
Diaz, Nelson; Rueda, Hoover; Arguello, Henry
2016-05-01
Imaging spectroscopy is an important area with many applications in surveillance, agriculture and medicine. The disadvantage of conventional spectroscopy techniques is that they collect the whole datacube. In contrast, compressive spectral imaging systems capture snapshot compressive projections, which are the input of reconstruction algorithms to yield the underlying datacube. Common compressive spectral imagers use coded apertures to perform the coded projections. The coded apertures are the key elements in these imagers since they define the sensing matrix of the system. The proper design of the coded aperture entries leads to a good quality in the reconstruction. In addition, the compressive measurements are prone to saturation due to the limited dynamic range of the sensor, hence the design of coded apertures must consider saturation. The saturation errors in compressive measurements are unbounded and compressive sensing recovery algorithms only provide solutions for bounded noise or bounded with high probability. In this paper it is proposed the design of uniform adaptive grayscale coded apertures (UAGCA) to improve the dynamic range of the estimated spectral images by reducing the saturation levels. The saturation is attenuated between snapshots using an adaptive filter which updates the entries of the grayscale coded aperture based on the previous snapshots. The coded apertures are optimized in terms of transmittance and number of grayscale levels. The advantage of the proposed method is the efficient use of the dynamic range of the image sensor. Extensive simulations show improvements in the image reconstruction of the proposed method compared with grayscale coded apertures (UGCA) and adaptive block-unblock coded apertures (ABCA) in up to 10 dB.
Stable and Dynamic Coding for Working Memory in Primate Prefrontal Cortex.
Spaak, Eelke; Watanabe, Kei; Funahashi, Shintaro; Stokes, Mark G
2017-07-05
Working memory (WM) provides the stability necessary for high-level cognition. Influential theories typically assume that WM depends on the persistence of stable neural representations, yet increasing evidence suggests that neural states are highly dynamic. Here we apply multivariate pattern analysis to explore the population dynamics in primate lateral prefrontal cortex (PFC) during three variants of the classic memory-guided saccade task (recorded in four animals). We observed the hallmark of dynamic population coding across key phases of a working memory task: sensory processing, memory encoding, and response execution. Throughout both these dynamic epochs and the memory delay period, however, the neural representational geometry remained stable. We identified two characteristics that jointly explain these dynamics: (1) time-varying changes in the subpopulation of neurons coding for task variables (i.e., dynamic subpopulations); and (2) time-varying selectivity within neurons (i.e., dynamic selectivity). These results indicate that even in a very simple memory-guided saccade task, PFC neurons display complex dynamics to support stable representations for WM.SIGNIFICANCE STATEMENT Flexible, intelligent behavior requires the maintenance and manipulation of incoming information over various time spans. For short time spans, this faculty is labeled "working memory" (WM). Dominant models propose that WM is maintained by stable, persistent patterns of neural activity in prefrontal cortex (PFC). However, recent evidence suggests that neural activity in PFC is dynamic, even while the contents of WM remain stably represented. Here, we explored the neural dynamics in PFC during a memory-guided saccade task. We found evidence for dynamic population coding in various task epochs, despite striking stability in the neural representational geometry of WM. Furthermore, we identified two distinct cellular mechanisms that contribute to dynamic population coding. Copyright © 2017
Stable and Dynamic Coding for Working Memory in Primate Prefrontal Cortex
Watanabe, Kei; Funahashi, Shintaro; Stokes, Mark G.
2017-01-01
Working memory (WM) provides the stability necessary for high-level cognition. Influential theories typically assume that WM depends on the persistence of stable neural representations, yet increasing evidence suggests that neural states are highly dynamic. Here we apply multivariate pattern analysis to explore the population dynamics in primate lateral prefrontal cortex (PFC) during three variants of the classic memory-guided saccade task (recorded in four animals). We observed the hallmark of dynamic population coding across key phases of a working memory task: sensory processing, memory encoding, and response execution. Throughout both these dynamic epochs and the memory delay period, however, the neural representational geometry remained stable. We identified two characteristics that jointly explain these dynamics: (1) time-varying changes in the subpopulation of neurons coding for task variables (i.e., dynamic subpopulations); and (2) time-varying selectivity within neurons (i.e., dynamic selectivity). These results indicate that even in a very simple memory-guided saccade task, PFC neurons display complex dynamics to support stable representations for WM. SIGNIFICANCE STATEMENT Flexible, intelligent behavior requires the maintenance and manipulation of incoming information over various time spans. For short time spans, this faculty is labeled “working memory” (WM). Dominant models propose that WM is maintained by stable, persistent patterns of neural activity in prefrontal cortex (PFC). However, recent evidence suggests that neural activity in PFC is dynamic, even while the contents of WM remain stably represented. Here, we explored the neural dynamics in PFC during a memory-guided saccade task. We found evidence for dynamic population coding in various task epochs, despite striking stability in the neural representational geometry of WM. Furthermore, we identified two distinct cellular mechanisms that contribute to dynamic population coding. PMID
Interpreting observations of molecular outflow sources: the MHD shock code mhd_vode
NASA Astrophysics Data System (ADS)
Flower, D. R.; Pineau des Forêts, G.
2015-06-01
The planar MHD shock code mhd_vode has been developed in order to simulate both continuous (C) type shock waves and jump (J) type shock waves in the interstellar medium. The physical and chemical state of the gas in steady-state may also be computed and used as input to a shock wave model. The code is written principally in FORTRAN 90, although some routines remain in FORTRAN 77. The documented program and its input data are described and provided as supplementary material, and the results of exemplary test runs are presented. Our intention is to enable the interested user to run the code for any sensible parameter set and to comprehend the results. With applications to molecular outflow sources in mind, we have computed, and are making available as supplementary material, integrated atomic and molecular line intensities for grids of C- and J-type models; these computations are summarized in the Appendices. Appendix tables, a copy of the current version of the code, and of the two model grids are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/578/A63
Ayyadurai, V A Shiva; Dewey, C Forbes
2011-03-01
A grand challenge of computational systems biology is to create a molecular pathway model of the whole cell. Current approaches involve merging smaller molecular pathway models' source codes to create a large monolithic model (computer program) that runs on a single computer. Such a larger model is difficult, if not impossible, to maintain given ongoing updates to the source codes of the smaller models. This paper describes a new system called CytoSolve that dynamically integrates computations of smaller models that can run in parallel across different machines without the need to merge the source codes of the individual models. This approach is demonstrated on the classic Epidermal Growth Factor Receptor (EGFR) model of Kholodenko. The EGFR model is split into four smaller models and each smaller model is distributed on a different machine. Results from four smaller models are dynamically integrated to generate identical results to the monolithic EGFR model running on a single machine. The overhead for parallel and dynamic computation is approximately twice that of a monolithic model running on a single machine. The CytoSolve approach provides a scalable method since smaller models may reside on any computer worldwide, where the source code of each model can be independently maintained and updated.
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.
Multiparticle Dynamics in the E-φ Tracking Code ESME
NASA Astrophysics Data System (ADS)
MacLachlan, James A.
2002-12-01
ESME has developed over a twenty year period from its origins as a program for modeling rf gymnastics to a rather general facility for that fraction of beam dynamics of synchrotrons and storage rings which can be properly treated in the two dimensional longitudinal phase space. The features of this program which serve particularly for multiparticle calculations are described, some uderlying principles are noted, and illustrative results are given.
Multiparticle dynamics in the E-phi tracking code ESME
James A. MacLachlan
2002-06-21
ESME has developed over a twenty year period from its origins as a program for modeling rf gymnastics to a rather general facility for that fraction of beam dynamics of synchrotrons and storage rings which can be properly treated in the two dimensional longitudinal phase space. The features of this program which serve particularly for multiparticle calculations are described, some underling principles are noted, and illustrative results are given.
Molecular cancer classification using a meta-sample-based regularized robust coding method
2014-01-01
Motivation Previous studies have demonstrated that machine learning based molecular cancer classification using gene expression profiling (GEP) data is promising for the clinic diagnosis and treatment of cancer. Novel classification methods with high efficiency and prediction accuracy are still needed to deal with high dimensionality and small sample size of typical GEP data. Recently the sparse representation (SR) method has been successfully applied to the cancer classification. Nevertheless, its efficiency needs to be improved when analyzing large-scale GEP data. Results In this paper we present the meta-sample-based regularized robust coding classification (MRRCC), a novel effective cancer classification technique that combines the idea of meta-sample-based cluster method with regularized robust coding (RRC) method. It assumes that the coding residual and the coding coefficient are respectively independent and identically distributed. Similar to meta-sample-based SR classification (MSRC), MRRCC extracts a set of meta-samples from the training samples, and then encodes a testing sample as the sparse linear combination of these meta-samples. The representation fidelity is measured by the l2-norm or l1-norm of the coding residual. Conclusions Extensive experiments on publicly available GEP datasets demonstrate that the proposed method is more efficient while its prediction accuracy is equivalent to existing MSRC-based methods and better than other state-of-the-art dimension reduction based methods. PMID:25473795
Molecular cancer classification using a meta-sample-based regularized robust coding method.
Wang, Shu-Lin; Sun, Liuchao; Fang, Jianwen
2014-01-01
Previous studies have demonstrated that machine learning based molecular cancer classification using gene expression profiling (GEP) data is promising for the clinic diagnosis and treatment of cancer. Novel classification methods with high efficiency and prediction accuracy are still needed to deal with high dimensionality and small sample size of typical GEP data. Recently the sparse representation (SR) method has been successfully applied to the cancer classification. Nevertheless, its efficiency needs to be improved when analyzing large-scale GEP data. In this paper we present the meta-sample-based regularized robust coding classification (MRRCC), a novel effective cancer classification technique that combines the idea of meta-sample-based cluster method with regularized robust coding (RRC) method. It assumes that the coding residual and the coding coefficient are respectively independent and identically distributed. Similar to meta-sample-based SR classification (MSRC), MRRCC extracts a set of meta-samples from the training samples, and then encodes a testing sample as the sparse linear combination of these meta-samples. The representation fidelity is measured by the l2-norm or l1-norm of the coding residual. Extensive experiments on publicly available GEP datasets demonstrate that the proposed method is more efficient while its prediction accuracy is equivalent to existing MSRC-based methods and better than other state-of-the-art dimension reduction based methods.
Molecular Dynamics Simulation of Disordered Zircon
Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin
2004-02-27
The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.
Eco-evolutionary dynamics, coding structure and the information threshold
2010-01-01
Background The amount of information that can be maintained in an evolutionary system of replicators is limited by genome length, the number of errors during replication (mutation rate) and various external factors that influence the selection pressure. To date, this phenomenon, known as the information threshold, has been studied (both genotypically and phenotypically) in a constant environment and with respect to maintenance (as opposed to accumulation) of information. Here we take a broader perspective on this problem by studying the accumulation of information in an ecosystem, given an evolvable coding structure. Moreover, our setup allows for individual based as well as ecosystem based solutions. That is, all functions can be performed by individual replicators, or complementing functions can be performed by different replicators. In this setup, where both the ecosystem and the individual genomes can evolve their structure, we study how populations cope with high mutation rates and accordingly how the information threshold might be alleviated. Results We observe that the first response to increased mutation rates is a change in coding structure. At moderate mutation rates evolution leads to longer genomes with a higher diversity than at high mutation rates. Thus, counter-intuitively, at higher mutation rates diversity is reduced and the efficacy of the evolutionary process is decreased. Therefore, moderate mutation rates allow for more degrees of freedom in exploring genotype space during the evolutionary trajectory, facilitating the emergence of solutions. When an individual based solution cannot be attained due to high mutation rates, spatial structuring of the ecosystem can accommodate the evolution of ecosystem based solutions. Conclusions We conclude that the evolutionary freedom (eg. the number of genotypes that can be reached by evolution) is increasingly restricted by higher mutation rates. In the case of such severe mutation rates that an individual
The development of an intelligent interface to a computational fluid dynamics flow-solver code
NASA Technical Reports Server (NTRS)
Williams, Anthony D.
1988-01-01
Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, 3-D, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.
The development of an intelligent interface to a computational fluid dynamics flow-solver code
NASA Technical Reports Server (NTRS)
Williams, Anthony D.
1988-01-01
Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, three-dimensional, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.
The development of an intelligent interface to a computational fluid dynamics flow-solver code
NASA Technical Reports Server (NTRS)
Williams, Anthony D.
1988-01-01
Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, three-dimensional, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.
Issues in computational fluid dynamics code verification and validation
Oberkampf, W.L.; Blottner, F.G.
1997-09-01
A broad range of mathematical modeling errors of fluid flow physics and numerical approximation errors are addressed in computational fluid dynamics (CFD). It is strongly believed that if CFD is to have a major impact on the design of engineering hardware and flight systems, the level of confidence in complex simulations must substantially improve. To better understand the present limitations of CFD simulations, a wide variety of physical modeling, discretization, and solution errors are identified and discussed. Here, discretization and solution errors refer to all errors caused by conversion of the original partial differential, or integral, conservation equations representing the physical process, to algebraic equations and their solution on a computer. The impact of boundary conditions on the solution of the partial differential equations and their discrete representation will also be discussed. Throughout the article, clear distinctions are made between the analytical mathematical models of fluid dynamics and the numerical models. Lax`s Equivalence Theorem and its frailties in practical CFD solutions are pointed out. Distinctions are also made between the existence and uniqueness of solutions to the partial differential equations as opposed to the discrete equations. Two techniques are briefly discussed for the detection and quantification of certain types of discretization and grid resolution errors.
Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.
NASA Astrophysics Data System (ADS)
Elliott, William Dewey
1995-01-01
A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over
MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.
Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver
2011-07-30
MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems.
Chiu, Matt; Herbordt, Martin C
2010-11-01
The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. In one part of the study, we systematically explore the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, and various other optimizations. We examine simplifications and find that some have little effect on simulation quality. In the other part, we present the first FPGA study of the filtering of particle pairs with nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA's resources. Overall, we find that, for an Altera Stratix-III EP3ES260, 8 force pipelines running at nearly 200 MHz can fit on the FPGA, and that they can perform at 95% efficiency. This results in an 80-fold per core speed-up for the short-range force, which is likely to make FPGAs highly competitive for MD.
Orbital-Free Molecular Dynamics Simulations at Extreme Conditions
NASA Astrophysics Data System (ADS)
Kress, J. D.; Collins, L. A.; Ticknor, C.
2015-06-01
Large-scale molecular dynamics (MD) simulations in an orbital-free (OF) density-functional theory (DFT) formulation have been performed for pure and mixed species over a broad range of temperatures (T) and densities (ρ) that includes the warm, dense matter and high-energy density physics regimes. A finite-temperature Thomas-Fermi-Dirac form with a local-density exchange-correlation potential and a regularized electron-ion interaction represents the quantum nature of the electrons. In particular, we examine the efficacy of the OFMD approach as an effective bridge between Kohn-Sham DFT MD at low temperatures and simple, fully-ionized plasma models at high temperatures. Comparisons against intermediate-range constructions such as the Yukawa and one-component plasmas are also made. We examine the mass transport (diffusion, viscosity) properties of various systems, ranging from light to heavy elements, including lithium hydride (LiH), mixtures of LiH with uranium, mixtures of deuterium-tritium (DT) with plutonium and mixtures of DT with plastic (CH). The OFMD mass transport results have been fitted to simple functions of ρ and T suitable for use in hydrodynamics simulation codes.
Modeling of aging in plutonium by molecular dynamics
NASA Astrophysics Data System (ADS)
Pochet, P.
2003-04-01
The origin of aging in plutonium lies in the extra formation of defects due to self-decay of 239Pu. The modeling of the formation of these defects is achieved by molecular dynamics (MD). In this work a simple EAM potential has been used to study defects formation in fcc plutonium and a 2 keV cascade is analyzed. A large pressure wave is generated around the cascade core. In the used MD code the pressure wave is not absorbed at the box boundaries and due to the periodic boundary conditions, the use of a very large box is crucial in order to avoid interaction of the cascade with itself. More than 800 000 atoms are needed to deal with this small 2 keV cascade without any artifacts. This effect comes from the very low bulk modulus of fcc Pu. The relative long time to achieve the annealing is also connected to the bulk modulus. These results are discussed in terms of large pressure wave: alloying effects are predicted using that viewpoint.
A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.
Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E
2017-06-20
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Thermal neutron scattering law calculations using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Wormald, Jonathan; Hawari, Ayman I.
2017-09-01
In recent years, methods for the calculation of the thermal scattering law (i.e. S(α,β), where α and β are dimensionless momentum and energy transfer variables, respectively) were developed based on ab initio lattice dynamics (AILD) and/or classical molecular dynamics (CMD). While these methods are now mature and efficient, further advancement in the application of such atomistic techniques is possible using ab initio molecular dynamics (AIMD) methods. In this case, temperature effects are inherently included in the calculation, e.g. phonon density of states (DOS), while using ab initio force fields that eliminate the need for parameterized semi-empirical force fields. In this work, AIMD simulations were performed to predict the phonon spectra as a function of temperature for beryllium and graphite, which are representative nuclear reactor moderator and reflector materials. Subsequently, the calculated phonon spectra were utilized to predict S(α,β) using the LEAPR module of the NJOY code. The AIMD models of beryllium and graphite were 5 × 5 × 5 crystal unit cells (250 atoms and 500 atoms respectively). Electronic structure calculations for the prediction of Hellman-Feynman forces were performed using density functional theory with a GGA exchange correlation functional and corresponding core electron pseudopotentials. AIMD simulations of 1000-10,000 time-steps were performed with the canonical ensemble (NVT thermostat) for several temperatures between 300 K and 900 K. The phonon DOS were calculated as the power spectrum of the AIMD predicted velocity autocorrelation functions. The resulting AIMD phonon DOS and corresponding inelastic thermal neutron scattering cross sections at 300 K, where anharmonic effects are expected to be small, were found to be in reasonable agreement with the results generated using traditional AILD. This illustrated the validity of the AIMD approach. However, since the impact of the temperature on the phonon DOS (e.g. broadening of
Spatial-temporal transcriptional dynamics of long non-coding RNAs in human brain.
Zhang, Xiao-Qin; Wang, Ze-Lin; Poon, Ming-Wai; Yang, Jian-Hua
2017-08-15
The functional architecture of the human brain is greatly determined by the temporal and spatial regulation of the transcription process. However, the spatial and temporal transcriptional landscape of long non-coding RNAs (lncRNAs) during human brain development remains poorly understood. Here, we report the genome-wide lncRNA transcriptional analysis in an extensive series of 1340 post-mortem human brain specimens collected from 16 regions spanning the period from early embryo development to late adulthood. We discovered that lncRNA transcriptome dramatically changed during fetal development, while transited to a surprisingly relatively stable state after birth till the late adulthood. We also discovered that the transcription map of lncRNAs was spatially different, and that this spatial difference was developmentally regulated. Of the 16 brain regions explored (cerebellar cortex, thalamus, striatum, amygdala, hippocampus and 11 neocortex areas), cerebellar cortex showed the most distinct lncRNA expression features from all remaining brain regions throughout the whole developmental period, reflecting its unique developmental and functional features. Furthermore, by characterizing the functional modules and cellular processes of the spatial-temporal dynamic lncRNAs, we found that they were significantly associated with the RNA processing, neuron differentiation and synaptic signal transportation processes. Furthermore, we found that many lncRNAs associated with the neurodegenerative Alzheimer and Parkinson diseases were co-expressed in the fetal development of the human brain, and affected the convergent biological processes. In summary, our study provides a comprehensive map for lncRNA transcription dynamics in human brain development, which might shed light on the understanding of the molecular underpinnings of human brain function and disease. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Capillary dynamics driven by molecular self-layering.
Wu, Pingkeng; Nikolov, Alex; Wasan, Darsh
2017-02-10
Capillary dynamics is a ubiquitous everyday phenomenon. It has practical applications in diverse fields, including ink-jet printing, lab-on-a-chip, biotechnology, and coating. Understanding capillary dynamics requires essential knowledge on the molecular level of how fluid molecules interact with a solid substrate (the wall). Recent studies conducted with the surface force apparatus (SFA), atomic force microscope (AFM), and statistical mechanics simulation revealed that molecules/nanoparticles confined into the film/wall surfaces tend to self-layer into 2D layer/s and even 2D in-layer with increased confinement and fluid volume fraction. Here, the capillary rise dynamics of simple molecular fluids in cylindrical capillary is explained by the molecular self-layering model. The proposed model considers the role of the molecular shape on self-layering and its effect on the molecularly thin film viscosity in regards to the advancing (dynamic) contact angle. The model was tested to explain the capillary rise dynamics of fluids of spherical, cylindrical, and disk shape molecules in borosilicate glass capillaries. The good agreement between the capillary rise data and SFA data from the literature for simple fluid self-layering shows the validity of the present model. The present model provides new insights into the design of many applications where dynamic wetting is important because it reveals the significant impact of molecular self-layering close to the wall on dynamic wetting.
Lehtinen, Arttu; Granberg, Fredric; Laurson, Lasse; Nordlund, Kai; Alava, Mikko J
2016-01-01
The stress-driven motion of dislocations in crystalline solids, and thus the ensuing plastic deformation process, is greatly influenced by the presence or absence of various pointlike defects such as precipitates or solute atoms. These defects act as obstacles for dislocation motion and hence affect the mechanical properties of the material. Here we combine molecular dynamics studies with three-dimensional discrete dislocation dynamics simulations in order to model the interaction between different kinds of precipitates and a 1/2〈111〉{110} edge dislocation in BCC iron. We have implemented immobile spherical precipitates into the ParaDis discrete dislocation dynamics code, with the dislocations interacting with the precipitates via a Gaussian potential, generating a normal force acting on the dislocation segments. The parameters used in the discrete dislocation dynamics simulations for the precipitate potential, the dislocation mobility, shear modulus, and dislocation core energy are obtained from molecular dynamics simulations. We compare the critical stresses needed to unpin the dislocation from the precipitate in molecular dynamics and discrete dislocation dynamics simulations in order to fit the two methods together and discuss the variety of the relevant pinning and depinning mechanisms.
Martínez-Rosell, Gerard; Giorgino, Toni; Harvey, Matt J; de Fabritiis, Gianni
2017-01-01
Bio-molecular dynamics (MD) simulations based on graphical processing units (GPUs) were first released to the public in the early 2009 with the code ACEMD. Almost 8 years after, applications now encompass a broad range of molecular studies, while throughput improvements have opened the way to millisecond sampling timescales. Based on an extrapolation of the amount of sampling in published literature, the second timescale will be reached by the year 2022, and therefore we predict that molecular dynamics is going to become one of the main tools in drug discovery in both academia and industry. Here, we review successful applications in the drug discovery domain developed over these recent years of GPU-based MD. We also retrospectively analyse limitations that have been overcome over the years and give a perspective on challenges that remain to be addressed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
NASA Astrophysics Data System (ADS)
Aeschliman, D. P.; Oberkampf, W. L.; Blottner, F. G.
Verification, calibration, and validation (VCV) of Computational Fluid Dynamics (CFD) codes is an essential element of the code development process. The exact manner in which code VCV activities are planned and conducted, however, is critically important. It is suggested that the way in which code validation, in particular, is often conducted--by comparison to published experimental data obtained for other purposes--is in general difficult and unsatisfactory, and that a different approach is required. This paper describes a proposed methodology for CFD code VCV that meets the technical requirements and is philosophically consistent with code development needs. The proposed methodology stresses teamwork and cooperation between code developers and experimentalists throughout the VCV process, and takes advantage of certain synergisms between CFD and experiment. A novel approach to uncertainty analysis is described which can both distinguish between and quantify various types of experimental error, and whose attributes are used to help define an appropriate experimental design for code VCV experiments. The methodology is demonstrated with an example of laminar, hypersonic, near perfect gas, 3-dimensional flow over a sliced sphere/cone of varying geometrical complexity.
Aeschliman, D.P.; Oberkampf, W.L.; Blottner, F.G.
1995-07-01
Verification, calibration, and validation (VCV) of Computational Fluid Dynamics (CFD) codes is an essential element of the code development process. The exact manner in which code VCV activities are planned and conducted, however, is critically important. It is suggested that the way in which code validation, in particular, is often conducted--by comparison to published experimental data obtained for other purposes--is in general difficult and unsatisfactory, and that a different approach is required. This paper describes a proposed methodology for CFD code VCV that meets the technical requirements and is philosophically consistent with code development needs. The proposed methodology stresses teamwork and cooperation between code developers and experimentalists throughout the VCV process, and takes advantage of certain synergisms between CFD and experiment. A novel approach to uncertainty analysis is described which can both distinguish between and quantify various types of experimental error, and whose attributes are used to help define an appropriate experimental design for code VCV experiments. The methodology is demonstrated with an example of laminar, hypersonic, near perfect gas, 3-dimensional flow over a sliced sphere/cone of varying geometrical complexity.
James, Scott Carlton; Roberts, Jesse D.
2014-03-01
This document describes the marine hydrokinetic (MHK) input file and subroutines for the Sandia National Laboratories Environmental Fluid Dynamics Code (SNL-EFDC), which is a combined hydrodynamic, sediment transport, and water quality model based on the Environmental Fluid Dynamics Code (EFDC) developed by John Hamrick [1], formerly sponsored by the U.S. Environmental Protection Agency, and now maintained by Tetra Tech, Inc. SNL-EFDC has been previously enhanced with the incorporation of the SEDZLJ sediment dynamics model developed by Ziegler, Lick, and Jones [2-4]. SNL-EFDC has also been upgraded to more accurately simulate algae growth with specific application to optimizing biomass in an open-channel raceway for biofuels production [5]. A detailed description of the input file containing data describing the MHK device/array is provided, along with a description of the MHK FORTRAN routine. Both a theoretical description of the MHK dynamics as incorporated into SNL-EFDC and an explanation of the source code are provided. This user manual is meant to be used in conjunction with the original EFDC [6] and sediment dynamics SNL-EFDC manuals [7]. Through this document, the authors provide information for users who wish to model the effects of an MHK device (or array of devices) on a flow system with EFDC and who also seek a clear understanding of the source code, which is available from staff in the Water Power Technologies Department at Sandia National Laboratories, Albuquerque, New Mexico.
Phantom of RAMSES (POR): A new Milgromian dynamicsN-body code
NASA Astrophysics Data System (ADS)
Lüghausen, Fabian; Famaey, Benoit; Kroupa, Pavel
2015-02-01
Since its first formulation in 1983, Milgromian dynamics (MOND) has been very successful in predicting the gravitational potential of galaxies from the distribution of baryons alone, including general scaling relations and detailed rotation curves of large statistical samples of individual galaxies covering a large range of masses and sizes. Most predictions however rely on static models, and only a handful of N-body codes have been developed over the years to investigate the consequences of the Milgromian framework for the dynamics of complex evolving dynamical systems. In this work, we present a new Milgromian N-body code, which is a customized version of the RAMSES code (Teyssier 2002) and thus comes with all its features: it includes particles and gas dynamics, and importantly allows for high spatial resolution of complex systems due to the adaptive mesh refinement (AMR) technique. It further allows the direct comparison between Milgromian simulations and standard Newtonian simulations with dark matter particles. We provide basic tests of this customized code and demonstrate its performance by presenting N-body computations of dark-matter-free spherical equilibrium models as well as dark-matter-free disk galaxies in Milgromian dynamics.
Dynamic Divisive Normalization Predicts Time-Varying Value Coding in Decision-Related Circuits
LoFaro, Thomas; Webb, Ryan; Glimcher, Paul W.
2014-01-01
Normalization is a widespread neural computation, mediating divisive gain control in sensory processing and implementing a context-dependent value code in decision-related frontal and parietal cortices. Although decision-making is a dynamic process with complex temporal characteristics, most models of normalization are time-independent and little is known about the dynamic interaction of normalization and choice. Here, we show that a simple differential equation model of normalization explains the characteristic phasic-sustained pattern of cortical decision activity and predicts specific normalization dynamics: value coding during initial transients, time-varying value modulation, and delayed onset of contextual information. Empirically, we observe these predicted dynamics in saccade-related neurons in monkey lateral intraparietal cortex. Furthermore, such models naturally incorporate a time-weighted average of past activity, implementing an intrinsic reference-dependence in value coding. These results suggest that a single network mechanism can explain both transient and sustained decision activity, emphasizing the importance of a dynamic view of normalization in neural coding. PMID:25429145
OOPSE: an object-oriented parallel simulation engine for molecular dynamics.
Meineke, Matthew A; Vardeman, Charles F; Lin, Teng; Fennell, Christopher J; Gezelter, J Daniel
2005-02-01
OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes. (c) 2004 Wiley Periodicals, Inc.
Laser ablation and spallation of crystalline aluminum simulated by molecular dynamics
NASA Astrophysics Data System (ADS)
Zhakhovskii, V.; Inogamov, N.; Nishihara, K.
2008-05-01
The mechanical action of femtosecond laser pulse on a target may result in ablation of the irradiated frontal layer and spallation of the target rear side as well. The dynamics of expansion of the solid Al film after laser heating is studied by means of molecular dynamics (MD) simulations with the two EAM potentials (ours and Mishin et al.) and our parallel auto-balancing MPD3 code. It is found that the rear side spallation threshold is half as much again the frontal ablation threshold. The experimental and evaluated characteristics agree well in both crater depth and incident fluence on the ablation threshold.
High-Performance Java Codes for Computational Fluid Dynamics
NASA Technical Reports Server (NTRS)
Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)
2001-01-01
The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.
RPMDRATE: Bimolecular chemical reaction rates from ring polymer molecular dynamics
NASA Astrophysics Data System (ADS)
Suleimanov, Yu. V.; Allen, J. W.; Green, W. H.
2013-03-01
We present RPMDRATE, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH4, OH+CH4 and H+C2H6 reactions. Catalogue identifier: AENW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 94512 No. of bytes in distributed program, including test data, etc.: 1395674 Distribution format: tar.gz Programming language: Fortran 90/95, Python (version 2.6.x or later, including any version of Python 3, is recommended). Computer: Not computer specific. Operating system: Any for which Python, Fortran 90/95 compiler and the required external routines are available. Has the code been vectorized or parallelized?: The program can efficiently utilize 4096+ processors, depending on problem and available computer. At low temperatures, 110 processors are reasonable for a typical umbrella integration run with an analytic potential energy function and gradients on the latest x86-64 machines.
Molecular Dynamic Screening Sesquiterpenoid Pogostemon Herba as Suggested Cyclooxygenase Inhibitor.
Raharjo, Sentot Joko; Kikuchi, Takeshi
2016-10-01
Virtual molecular dynamic sesquiterpenoid Pogostemon Herba (CID56928117, CID94275, CID107152, and CID519743) have screening as cyclooxygenase (COX-1/COX-2) selective inhibitor. Molecular interaction studies sesquiterpenoid compounds with COX-1 and COX-2 were using the molecular docking tools by Hex 8.0 and interactions were further visualized using by Discovery Studio Client 3.5 software tool and Virtual Molecular Dynamic 1.9.1 software. The binding energy calculation of molecular dynamic interaction was calculated by AMBER12 software. The analysis of the sesquiterpenoid compounds showed that CID56928117, CID94275, CID107152, and CID519743 have suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor.
Dynamical analysis of highly excited molecular spectra
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.
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.
Next generation extended Lagrangian first principles molecular dynamics
NASA Astrophysics Data System (ADS)
Niklasson, Anders M. N.
2017-08-01
Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.
Special issue on ultrafast electron and molecular dynamics
NASA Astrophysics Data System (ADS)
Hishikawa, Akiyoshi; Martin, Fernando; Vrakking, Marc
2013-07-01
Your invitation to submit. Journal of Physics. B: Atomic Molecular and Optical Physics (JPhysB) is delighted to announce a forthcoming special issue on ultrafast electron and molecular dynamics to appear in 2014, and invites you to submit a paper. Within the last decade, a number of novel approaches have emerged, both experimental and theoretical, that allow the investigation of (time-resolved) molecular dynamics in novel ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain. Along the way, particular types of molecular dynamics, such as dynamics around conical intersections, have gained an increased prominence, sparked by an emerging realization about the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of some of the most important developments in the field, while at the same time indicating how studies of (time-resolved) molecular dynamics are likely to evolve in the coming
Next generation extended Lagrangian first principles molecular dynamics.
Niklasson, Anders M N
2017-08-07
Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.
kspectrum: an open-source code for high-resolution molecular absorption spectra production
NASA Astrophysics Data System (ADS)
Eymet, V.; Coustet, C.; Piaud, B.
2016-01-01
We present the kspectrum, scientific code that produces high-resolution synthetic absorption spectra from public molecular transition parameters databases. This code was originally required by the atmospheric and astrophysics communities, and its evolution is now driven by new scientific projects among the user community. Since it was designed without any optimization that would be specific to any particular application field, its use could also be extended to other domains. kspectrum produces spectral data that can subsequently be used either for high-resolution radiative transfer simulations, or for producing statistic spectral model parameters using additional tools. This is a open project that aims at providing an up-to-date tool that takes advantage of modern computational hardware and recent parallelization libraries. It is currently provided by Méso-Star (http://www.meso-star.com) under the CeCILL license, and benefits from regular updates and improvements.
Force field development with GOMC, a fast new Monte Carlo molecular simulation code
NASA Astrophysics Data System (ADS)
Mick, Jason Richard
In this work GOMC (GPU Optimized Monte Carlo) a new fast, flexible, and free molecular Monte Carlo code for the simulation atomistic chemical systems is presented. The results of a large Lennard-Jonesium simulation in the Gibbs ensemble is presented. Force fields developed using the code are also presented. To fit the models a quantitative fitting process is outlined using a scoring function and heat maps. The presented n-6 force fields include force fields for noble gases and branched alkanes. These force fields are shown to be the most accurate LJ or n-6 force fields to date for these compounds, capable of reproducing pure fluid behavior and binary mixture behavior to a high degree of accuracy.
The Role and Molecular Mechanism of Non-Coding RNAs in Pathological Cardiac Remodeling
Gao, Jinning; Xu, Wenhua; Wang, Jianxun; Wang, Kun; Li, Peifeng
2017-01-01
Non-coding RNAs (ncRNAs) are a class of RNA molecules that do not encode proteins. Studies show that ncRNAs are not only involved in cell proliferation, apoptosis, differentiation, metabolism and other physiological processes, but also involved in the pathogenesis of diseases. Cardiac remodeling is the main pathological basis of a variety of cardiovascular diseases. Many studies have shown that the occurrence and development of cardiac remodeling are closely related with the regulation of ncRNAs. Recent research of ncRNAs in heart disease has achieved rapid development. Thus, we summarize here the latest research progress and mainly the molecular mechanism of ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), in cardiac remodeling, aiming to look for new targets for heart disease treatment. PMID:28287427
Benchmark of the IMPACT Code for High Intensity Beam DynamicsSimulation
Qiang, J.; Ryne, R.D.
2006-11-16
, an envelope matching and analysis code, and a number of pre- and post-processing codes were also developed to form the IMPACT code suite. The IMPACT code suite has been used to study beam dynamics in the SNS linac, the J-PARC linac commissioning, the CERN superconducting linac design, the Los Alamos Low Energy Demonstration Accelerator (LEDA) halo experiment, the Rare Isotope Accelerator (RIA) driver linac design, and the FERMI{at}Elettra FEL linac design [3-8]. It has also been used to study space-charge resonance in anisotropic beams [9-11].
Greenland Flow Dynamics: (De)coding Process Understanding
NASA Astrophysics Data System (ADS)
Alley, R. B.; Parizek, B. R.; Anandakrishnan, S.; Applegate, P. J.; Christianson, K. A.; Dixon, T. H.; Holland, D. M.; Holschuh, N.; Keller, K.; Koellner, S. J.; Lampkin, D. J.; Muto, A.; Nicholas, R.; Stevens, N. T.; Voytenko, D.; Walker, R. T.
2015-12-01
Extensive modeling informed by the growing body of observational data yields important insights to the controlling processes operating across a range of spatiotemporal scales that have influenced the dynamic variability of the Greenland ice sheet. Pressurized basal lubrication enhances ice flow. This lubricating water is largely produced by basal and/or surface melt. For the North East Greenland Ice Stream, elevated geothermal heat flux (GHF) near its onset helps initiate the streaming flow. We suggest that the elevated GHF is likely caused by melt production and migration due to cyclical loading of the lithosphere over glacial timescales. On sub-seasonal timescales, surface meltwater production and transmission to the subglacial environment can enhance flow for pressurized, distributed hydraulic systems and diminish regional sliding for lower-pressure, channelized systems. However, in a warming climate, this lubricating source occurs across an expanding ablation zone, possibly softening shear margins and triggering basal sliding over previously frozen areas. Yet, the existence of active englacial conduits can lead to a plumbing network that helps preserve ice tongues and limit the loss of important buttressing of outlet glacier flow. Ocean forcing has been implicated in the variability of outlet glacier speeds around the periphery of Greenland. The extent and timescale over which those marginal changes influence inland flow depends on the basal rheology that, on a local scale, also influences the concentration of englacial stresses. Detailed observations of a calving event on Helheim Glacier have helped constrain diagnostic simulations of the pre- and post-calving stress states conducted in hopes of informing improved calving relationships. Furthermore, warm-water-mass variability within Irminger/Atlantic Waters off Greenland may play an important role in the monthly modulation of outlet glacier flow speeds, as has been observed for an ice stream draining into
Elucidation of molecular dynamics of invasive species of rice
USDA-ARS?s Scientific Manuscript database
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...
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.
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.
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.
Visual TSUNAMI: A Versatile, User-Friendly, Multidimensional Ablation and Gas-Dynamics Design Code
Debonnel, C.S.; Wang, T.X.; Suzuki, M.; Garcia, E.; Peterson, P.F.
2005-05-15
Gas dynamics phenomena in thick-liquid protected inertial fusion target chambers have been explored since the early 1990's with the help of a series of simulation codes known as TSUNAMI. The code has been recently redesigned entirely to make use of modern programming techniques, languages and software; improve its user-friendliness; and refine its ability to model thick-liquid protected chambers, while expanding its capability to a larger variety of systems. The new code is named 'Visual Tsunami' to emphasize the programming language of its core, Fortran 95, as well as its graphics-based input file builder and output processors. It is aimed at providing a user-friendly design tool for complex systems for which transient gas dynamics phenomena play a key role.
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
Tlusty, Tsvi
2010-09-01
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the problem of the code's origin and discuss the results of a recent work that treats the code in terms of an evolving, error-prone information channel. Our model - which utilizes the rate-distortion theory of noisy communication channels - suggests that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources. The description of the code as an information channel allows us to mathematically identify the fitness of the code and locate its emergence at a second-order phase transition when the mapping of codons to amino-acids becomes nonrandom. The noise in the channel brings about an error-graph, in which edges connect codons that are likely to be confused. The emergence of the code is governed by the topology of the error-graph, which determines the lowest modes of the graph-Laplacian and is related to the map coloring problem. (c) 2010 Elsevier B.V. All rights reserved.
Sandia National Laboratories environmental fluid dynamics code : sediment transport user manual.
Grace, Matthew D.; Thanh, Phi Hung X.; James, Scott Carlton
2008-09-01
This document describes the sediment transport subroutines and input files for the Sandia National Laboratories Environmental Fluid Dynamics Code (SNL-EFDC). Detailed descriptions of the input files containing data from Sediment Erosion at Depth flume (SEDflume) measurements are provided along with the description of the source code implementing sediment transport. Both the theoretical description of sediment transport employed in SNL-EFDC and the source code are described. This user manual is meant to be used in conjunction with the EFDC manual (Hamrick 1996) because there will be no reference to the hydrodynamics in EFDC. Through this document, the authors aim to provide the necessary information for new users who wish to implement sediment transport in EFDC and obtain a clear understanding of the source code.
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
A computational fluid dynamics code for the investigation of ramjet-in-tube concepts
NASA Astrophysics Data System (ADS)
Bogdanoff, D. W.; Brackett, D. C.
1987-06-01
An inviscid computational fluid dynamics (CFD) code is presented which can handle multiple component species, simple chemical reactions, a completely general equation of state and velocities up to hundreds of km/sec. The code can also handle mutilple moving zones containing different media. Radiation effects are not included. The code uses third order spatial extrapolation/interpolation of the primitive variables to determine cell boundary values, applies limiting procedures to these values to maintain code stability and accuracy, and then uses Godunov procedures to calculate the cell boundary fluxes. The code numerical methods are presented in some detail and the results of benchmark test cases used to proof out the code are given. The agreement between the CFD and exact analytical calculations is found to be excellent. The code is used to investigate a ramjet-in-tube concept. In this concept, a projectile flies down a tube filled with combustible gas mixtures. The mixtures studied are H2 plus O2 plus excess H2 or N2 or CO2 as diluent. The projectile velocity range is 4 to 10 km/sec. Efficiencies up to 0.26 and ratios of effective projectile thrust pressure to maximum cycle pressure up to 0.12 are obtained. Plots of the pressure field around the projectile are presented.
A proposed framework for computational fluid dynamics code calibration/validation
Oberkampf, W.L.
1993-12-31
The paper reviews the terminology and methodology that have been introduced during the last several years for building confidence n the predictions from Computational Fluid Dynamics (CID) codes. Code validation terminology developed for nuclear reactor analyses and aerospace applications is reviewed and evaluated. Currently used terminology such as ``calibrated code,`` ``validated code,`` and a ``validation experiment`` is discussed along with the shortcomings and criticisms of these terms. A new framework is proposed for building confidence in CFD code predictions that overcomes some of the difficulties of past procedures and delineates the causes of uncertainty in CFD predictions. Building on previous work, new definitions of code verification and calibration are proposed. These definitions provide more specific requirements for the knowledge level of the flow physics involved and the solution accuracy of the given partial differential equations. As part of the proposed framework, categories are also proposed for flow physics research, flow modeling research, and the application of numerical predictions. The contributions of physical experiments, analytical solutions, and other numerical solutions are discussed, showing that each should be designed to achieve a distinctively separate purpose in building confidence in accuracy of CFD predictions. A number of examples are given for each approach to suggest methods for obtaining the highest value for CFD code quality assurance.
Aiming for Validation - The SCEC/USGS Dynamic Earthquake Rupture Code Comparison Exercise
NASA Astrophysics Data System (ADS)
Harris, R.
2016-12-01
The SCEC/USGS Dynamic Earthquake Rupture Code Group is an international collaboration among scientists who use 3D spontaneous rupture computer codes to numerically simulate physics-based earthquake rupture and the resulting ground motions. In the years to date, group members have tested the viability of their computer codes by comparing the results produced by each code, using an expansive set of benchmark exercises. These exercises implement the range of assumptions frequently used by modelers when they simulate earthquakes, including heterogeneity in initial stress conditions, a variety of formulations for fault friction, heterogeneous fault geometry including 3D rough faults, branched faults, and fault-stepovers, 1D and 3D velocity structures, and off-fault yielding. Whereas each exercise has sharpened the abilities of the codes and enhanced our confidence in the results that they produce, we have not yet rigorously tested the products of these codes against observations from real earthquakes. In 2016 we have started on this path toward code-validation, and our first test is the 2000 Mw6.6 Tottori, Japan earthquake. For more information, please also view our website scecdata.usc.edu/cvws
IllinoisGRMHD: an open-source, user-friendly GRMHD code for dynamical spacetimes
NASA Astrophysics Data System (ADS)
Etienne, Zachariah B.; Paschalidis, Vasileios; Haas, Roland; Mösta, Philipp; Shapiro, Stuart L.
2015-09-01
In the extreme violence of merger and mass accretion, compact objects like black holes and neutron stars are thought to launch some of the most luminous outbursts of electromagnetic and gravitational wave energy in the Universe. Modeling these systems realistically is a central problem in theoretical astrophysics, but has proven extremely challenging, requiring the development of numerical relativity codes that solve Einstein's equations for the spacetime, coupled to the equations of general relativistic (ideal) magnetohydrodynamics (GRMHD) for the magnetized fluids. Over the past decade, the Illinois numerical relativity (ILNR) group's dynamical spacetime GRMHD code has proven itself as a robust and reliable tool for theoretical modeling of such GRMHD phenomena. However, the code was written ‘by experts and for experts’ of the code, with a steep learning curve that would severely hinder community adoption if it were open-sourced. Here we present IllinoisGRMHD, which is an open-source, highly extensible rewrite of the original closed-source GRMHD code of the ILNR group. Reducing the learning curve was the primary focus of this rewrite, with the goal of facilitating community involvement in the code's use and development, as well as the minimization of human effort in generating new science. IllinoisGRMHD also saves computer time, generating roundoff-precision identical output to the original code on adaptive-mesh grids, but nearly twice as fast at scales of hundreds to thousands of cores.
Analysis and compensation for code Doppler effect of BDS II signal under high dynamics
NASA Astrophysics Data System (ADS)
Ouyang, Xiaofeng; Zeng, Fangling
2016-01-01
In high dynamic circumstances, the acquisition of BDS (BeiDou Navigation Satellite System) signal would be affected by the pseudo-code Doppler. The pseudo-code frequency shift is more prominent and complex when BOC modulation has been adopted by BDS-II, but is not yet involved in current compensation algorithm. In addition, the most frequently used code Doppler compensation algorithm is modifying the sampling rate or local bit rate, which not only increases the complexity of the acquisition and tracking, but also is barely realizable for the hardware receiver to modify the local frequency. Therefore, this paper proposes a code Doppler compensation method based on double estimator receiver, which simultaneously controls NCO delay of code tracking loop and subcarrier tracking loop to compensate for pseudo-code frequency shift. The simulation and test are implemented with BDS-II BOC signal. The test results demonstrate that the proposed algorithm can effectively compensate for pseudo-code Doppler of BOC signal and has detection probability 3dB higher than the uncompensated situation when the false alarm rate is under 0.01 and the coherent integration time is 1ms.
A Molecular Dynamics Simulation of C60-C60 Collision
NASA Astrophysics Data System (ADS)
Liu, Lei; Chen, Kaitai; Li, Yufen
1993-12-01
The formation process of C120-complex in C60-C60 collision has been clearly demonstrated by a molecular dynamics simulation. The complex, with a peanut-shell-like structure, is in a quite stable dynamical state. The results are consistent with recent observations.
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)
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.
Molecular Dynamics Simulations of Crystal Copper: Bulk Modulus and Shocks
NASA Astrophysics Data System (ADS)
Warrier, M.; Rawat, S.; Chaturvedi, S.
2011-07-01
Molecular dynamics is used to study the response of single crystal copper target to impacts by single crystal copper at velocities in the range 1 km/s to 3 km/s. The Embedded Atom Method (EAM) potential by Foiles et al. for Cu [1] was used in the simulation. The potential and its implementation in the open source, Large-scale Atomic Molecular Massively Parallel Simulator (LAMMPS) [2] was verified by reproducing the experimental values of bulk modulus of Cu. The shock velocity (us) as a function of particle velocity (up) matches published experimental and molecular dynamic simulations results.
Investigation of Ribosomes Using Molecular Dynamics Simulation Methods.
Makarov, G I; Makarova, T M; Sumbatyan, N V; Bogdanov, A A
2016-12-01
The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.
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.
Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles
2004-07-15
Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.
Molecular codes for neuronal individuality and cell assembly in the brain.
Yagi, Takeshi
2012-01-01
The brain contains an enormous, but finite, number of neurons. The ability of this limited number of neurons to produce nearly limitless neural information over a lifetime is typically explained by combinatorial explosion; that is, by the exponential amplification of each neuron's contribution through its incorporation into "cell assemblies" and neural networks. In development, each neuron expresses diverse cellular recognition molecules that permit the formation of the appropriate neural cell assemblies to elicit various brain functions. The mechanism for generating neuronal assemblies and networks must involve molecular codes that give neurons individuality and allow them to recognize one another and join appropriate networks. The extensive molecular diversity of cell-surface proteins on neurons is likely to contribute to their individual identities. The clustered protocadherins (Pcdh) is a large subfamily within the diverse cadherin superfamily. The clustered Pcdh genes are encoded in tandem by three gene clusters, and are present in all known vertebrate genomes. The set of clustered Pcdh genes is expressed in a random and combinatorial manner in each neuron. In addition, cis-tetramers composed of heteromultimeric clustered Pcdh isoforms represent selective binding units for cell-cell interactions. Here I present the mathematical probabilities for neuronal individuality based on the random and combinatorial expression of clustered Pcdh isoforms and their formation of cis-tetramers in each neuron. Notably, clustered Pcdh gene products are known to play crucial roles in correct axonal projections, synaptic formation, and neuronal survival. Their molecular and biological features induce a hypothesis that the diverse clustered Pcdh molecules provide the molecular code by which neuronal individuality and cell assembly permit the combinatorial explosion of networks that supports enormous processing capability and plasticity of the brain.
Mott Transition in a Metallic Liquid: Gutzwiller Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Chern, Gia-Wei; Barros, Kipton; Batista, Cristian D.; Kress, Joel D.; Kotliar, Gabriel
2017-06-01
We present a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. We use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ceriotti, Michele; More, Joshua; Manolopoulos, David E.
2014-03-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic
Enhanced sampling techniques in molecular dynamics simulations of biological systems.
Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus
2015-05-01
Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.
Single stock dynamics on high-frequency data: from a compressed coding perspective.
Fushing, Hsieh; Chen, Shu-Chun; Hwang, Chii-Ruey
2014-01-01
High-frequency return, trading volume and transaction number are digitally coded via a nonparametric computing algorithm, called hierarchical factor segmentation (HFS), and then are coupled together to reveal a single stock dynamics without global state-space structural assumptions. The base-8 digital coding sequence, which is capable of revealing contrasting aggregation against sparsity of extreme events, is further compressed into a shortened sequence of state transitions. This compressed digital code sequence vividly demonstrates that the aggregation of large absolute returns is the primary driving force for stimulating both the aggregations of large trading volumes and transaction numbers. The state of system-wise synchrony is manifested with very frequent recurrence in the stock dynamics. And this data-driven dynamic mechanism is seen to correspondingly vary as the global market transiting in and out of contraction-expansion cycles. These results not only elaborate the stock dynamics of interest to a fuller extent, but also contradict some classical theories in finance. Overall this version of stock dynamics is potentially more coherent and realistic, especially when the current financial market is increasingly powered by high-frequency trading via computer algorithms, rather than by individual investors.
Single Stock Dynamics on High-Frequency Data: From a Compressed Coding Perspective
Fushing, Hsieh; Chen, Shu-Chun; Hwang, Chii-Ruey
2014-01-01
High-frequency return, trading volume and transaction number are digitally coded via a nonparametric computing algorithm, called hierarchical factor segmentation (HFS), and then are coupled together to reveal a single stock dynamics without global state-space structural assumptions. The base-8 digital coding sequence, which is capable of revealing contrasting aggregation against sparsity of extreme events, is further compressed into a shortened sequence of state transitions. This compressed digital code sequence vividly demonstrates that the aggregation of large absolute returns is the primary driving force for stimulating both the aggregations of large trading volumes and transaction numbers. The state of system-wise synchrony is manifested with very frequent recurrence in the stock dynamics. And this data-driven dynamic mechanism is seen to correspondingly vary as the global market transiting in and out of contraction-expansion cycles. These results not only elaborate the stock dynamics of interest to a fuller extent, but also contradict some classical theories in finance. Overall this version of stock dynamics is potentially more coherent and realistic, especially when the current financial market is increasingly powered by high-frequency trading via computer algorithms, rather than by individual investors. PMID:24586235
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.
Force fields for classical molecular dynamics.
Monticelli, Luca; Tieleman, D Peter
2013-01-01
In this chapter we review the basic features and the principles underlying molecular mechanics force fields commonly used in molecular modeling of biological macromolecules. We start by summarizing the historical background and then describe classical pairwise additive potential energy functions. We introduce the problem of the calculation of nonbonded interactions, of particular importance for charged macromolecules. Different parameterization philosophies are then presented, followed by a section on force field validation. We conclude with a brief overview on future perspectives for the development of classical force fields.
Gas Diffusion in Polyethylene Terepthalate By Molecular Dynamics
NASA Astrophysics Data System (ADS)
Butler, Simon; Adolf, David
2006-03-01
Molecular dynamics simulations of the diffusion of small penetrants through PET have been performed utilising the anisotropic united atom model [1] and a virtual liquid technique. [2] The accuracy and reliability of these two approaches has been assessed in terms of the improvement in equation of state behaviour and of diffusion co-efficients and solubilities. The effect of the diffusion of nitrogen, carbon dioxide, and oxygen on the local dynamics of PET have been investigated as a result. Attention has been focused on the dual mode effect [3] observed during mixed gas diffusion. [1] Molecular dynamics calculation of the equation of state of alkanes, J. Chem. Phys. 93, 6 (1990) [2] Kikuchi, Kuwajima, Fukada, Novel method to estimate the solubility of small molecules in cis-polyisoprene by molecular dynamics simulations, J. Chem. Phys, 115, 13 (2001) [3] Lewis, Duckett, Ward, Fairclough, Ryan, The barrier properties of polyethylene terephthalate to mixtures of oxygen, carbon dioxide and nitrogen, Polymer, 1631, 44 (2003)
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.
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.
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.
A molecular bar-coded DNA repair resource for pooled toxicogenomic screens.
Rooney, John P; Patil, Ashish; Zappala, Maria R; Conklin, Douglas S; Cunningham, Richard P; Begley, Thomas J
2008-11-01
DNA damage from exogenous and endogenous sources can promote mutations and cell death. Fortunately, cells contain DNA repair and damage signaling pathways to reduce the mutagenic and cytotoxic effects of DNA damage. The identification of specific DNA repair proteins and the coordination of DNA repair pathways after damage has been a central theme to the field of genetic toxicology and we have developed a tool for use in this area. We have produced 99 molecular bar-coded Escherichia coli gene-deletion mutants specific to DNA repair and damage signaling pathways, and each bar-coded mutant can be tracked in pooled format using bar-code specific microarrays. Our design adapted bar-codes developed for the Saccharomyces cerevisiae gene-deletion project, which allowed us to utilize an available microarray product for pooled gene-exposure studies. Microarray-based screens were used for en masse identification of individual mutants sensitive to methyl methanesulfonate (MMS). As expected, gene-deletion mutants specific to direct, base excision, and recombinational DNA repair pathways were identified as MMS-sensitive in our pooled assay, thus validating our resource. We have demonstrated that molecular bar-codes designed for S. cerevisiae are transferable to E. coli, and that they can be used with pre-existing microarrays to perform competitive growth experiments. Further, when comparing microarray to traditional plate-based screens both overlapping and distinct results were obtained, which is a novel technical finding, with discrepancies between the two approaches explained by differences in output measurements (DNA content versus cell mass). The microarray-based classification of Deltatag and DeltadinG cells as depleted after MMS exposure, contrary to plate-based methods, led to the discovery that Deltatag and DeltadinG cells show a filamentation phenotype after MMS exposure, thus accounting for the discrepancy. A novel biological finding is the observation that while
Development of a CFD Code for Analysis of Fluid Dynamic Forces in Seals
NASA Technical Reports Server (NTRS)
Athavale, Mahesh M.; Przekwas, Andrzej J.; Singhal, Ashok K.
1991-01-01
The aim is to develop a 3-D computational fluid dynamics (CFD) code for the analysis of fluid flow in cylindrical seals and evaluation of the dynamic forces on the seals. This code is expected to serve as a scientific tool for detailed flow analysis as well as a check for the accuracy of the 2D industrial codes. The features necessary in the CFD code are outlined. The initial focus was to develop or modify and implement new techniques and physical models. These include collocated grid formulation, rotating coordinate frames and moving grid formulation. Other advanced numerical techniques include higher order spatial and temporal differencing and an efficient linear equation solver. These techniques were implemented in a 2D flow solver for initial testing. Several benchmark test cases were computed using the 2D code, and the results of these were compared to analytical solutions or experimental data to check the accuracy. Tests presented here include planar wedge flow, flow due to an enclosed rotor, and flow in a 2D seal with a whirling rotor. Comparisons between numerical and experimental results for an annular seal and a 7-cavity labyrinth seal are also included.
An improved version of the Green's function molecular dynamics method
NASA Astrophysics Data System (ADS)
Kong, Ling Ti; Denniston, Colin; Müser, Martin H.
2011-02-01
This work presents an improved version of the Green's function molecular dynamics method (Kong et al., 2009; Campañá and Müser, 2004 [1,2]), which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only atoms near the surface. In the previous implementation, the effective elastic coefficients measured at the Γ-point were altered to reduce finite size effects: their eigenvalues corresponding to the acoustic modes were set to zero. This scheme was found to work well for simple Bravais lattices as long as only atoms within the last layer were treated as Green's function atoms. However, it failed to function as expected in all other cases. It turns out that a violation of the acoustic sum rule for the effective elastic coefficients at Γ (Kong, 2010 [3]) was responsible for this behavior. In the new version, the acoustic sum rule is enforced by adopting an iterative procedure, which is found to be physically more meaningful than the previous one. In addition, the new algorithm allows one to treat lattices with bases and the Green's function slab is no longer confined to one layer. New version program summaryProgram title: FixGFC/FixGFMD v1.12 Catalogue identifier: AECW_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECW_v1_1.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.: 206 436 No. of bytes in distributed program, including test data, etc.: 4 314 850 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Yes. Code has been parallelized using MPI directives. RAM: Depends on the problem Classification: 7.7 External routines: LAMMPS ( http://lammps.sandia.gov/), MPI ( http
Development of a dynamic coupled hydro-geomechanical code and its application to induced seismicity
NASA Astrophysics Data System (ADS)
Miah, Md Mamun
This research describes the importance of a hydro-geomechanical coupling in the geologic sub-surface environment from fluid injection at geothermal plants, large-scale geological CO2 sequestration for climate mitigation, enhanced oil recovery, and hydraulic fracturing during wells construction in the oil and gas industries. A sequential computational code is developed to capture the multiphysics interaction behavior by linking a flow simulation code TOUGH2 and a geomechanics modeling code PyLith. Numerical formulation of each code is discussed to demonstrate their modeling capabilities. The computational framework involves sequential coupling, and solution of two sub-problems- fluid flow through fractured and porous media and reservoir geomechanics. For each time step of flow calculation, pressure field is passed to the geomechanics code to compute effective stress field and fault slips. A simplified permeability model is implemented in the code that accounts for the permeability of porous and saturated rocks subject to confining stresses. The accuracy of the TOUGH-PyLith coupled simulator is tested by simulating Terzaghi's 1D consolidation problem. The modeling capability of coupled poroelasticity is validated by benchmarking it against Mandel's problem. The code is used to simulate both quasi-static and dynamic earthquake nucleation and slip distribution on a fault from the combined effect of far field tectonic loading and fluid injection by using an appropriate fault constitutive friction model. Results from the quasi-static induced earthquake simulations show a delayed response in earthquake nucleation. This is attributed to the increased total stress in the domain and not accounting for pressure on the fault. However, this issue is resolved in the final chapter in simulating a single event earthquake dynamic rupture. Simulation results show that fluid pressure has a positive effect on slip nucleation and subsequent crack propagation. This is confirmed by
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.
SCISEAL: A CFD code for analysis of fluid dynamic forces in seals
NASA Technical Reports Server (NTRS)
Athavale, Mahesh; Przekwas, Andrzej
1994-01-01
A viewgraph presentation is made of the objectives, capabilities, and test results of the computer code SCISEAL. Currently, the seal code has: a finite volume, pressure-based integration scheme; colocated variables with strong conservation approach; high-order spatial differencing, up to third-order; up to second-order temporal differencing; a comprehensive set of boundary conditions; a variety of turbulence models and surface roughness treatment; moving grid formulation for arbitrary rotor whirl; rotor dynamic coefficients calculated by the circular whirl and numerical shaker methods; and small perturbation capabilities to handle centered and eccentric seals.
Visualizing global properties of a molecular dynamics trajectory.
Zhou, Hao; Li, Shangyang; Makowski, Lee
2016-01-01
Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule. © 2015 Wiley Periodicals, Inc.
Modeling ramp compression experiments using large-scale molecular dynamics simulation.
Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I.; Winey, J. Michael; Gupta, Yogendra Mohan; Lane, J. Matthew D.; Ditmire, Todd; Quevedo, Hernan J.
2011-10-01
Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.
Electron-Nuclear Dynamics of Molecular Systems
1994-04-18
approach with a completely general form of trial function yields the time - dependent Schr ~ dinger equation . Restricting the...dynamical equations approximating the time - dependent SchrOdinger equation . These equations govern the time evolution of the relevant state vector parameters... equations that apprximate the Apuit 18, 1994 time - dependent Schradinger equation and govern the time evolution of
Molecular Dynamics and Spectra. II. Diatomic Raman.
1981-02-01
applicable to many molecular geometries, and we will use a somewhat more general form than needed for our ’Y diatomic in an attempt to clarify the... aCeit M rach Offta* Naval Pastgraduara SchooI. .4C:i: at. - d. ’eeb.es lontrore’ Calirnia 93940 0300 Sumer 3treec Dr- A. L. SliU:1osk7 3CStOn
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.
Yi, Zheng; Lindner, Benjamin; Prinz, Jan -Hendrik; Noe, Frank; Smith, Jeremy C.
2013-11-01
Here, neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.
Impact of dynamic rate coding aspects of mobile phone networks on forensic voice comparison.
Alzqhoul, Esam A S; Nair, Balamurali B T; Guillemin, Bernard J
2015-09-01
Previous studies have shown that landline and mobile phone networks are different in their ways of handling the speech signal, and therefore in their impact on it. But the same is also true of the different networks within the mobile phone arena. There are two major mobile phone technologies currently in use today, namely the global system for mobile communications (GSM) and code division multiple access (CDMA) and these are fundamentally different in their design. For example, the quality of the coded speech in the GSM network is a function of channel quality, whereas in the CDMA network it is determined by channel capacity (i.e., the number of users sharing a cell site). This paper examines the impact on the speech signal of a key feature of these networks, namely dynamic rate coding, and its subsequent impact on the task of likelihood-ratio-based forensic voice comparison (FVC). Surprisingly, both FVC accuracy and precision are found to be better for both GSM- and CDMA-coded speech than for uncoded. Intuitively one expects FVC accuracy to increase with increasing coded speech quality. This trend is shown to occur for the CDMA network, but, surprisingly, not for the GSM network. Further, in respect to comparisons between these two networks, FVC accuracy for CDMA-coded speech is shown to be slightly better than for GSM-coded speech, particularly when the coded-speech quality is high, but in terms of FVC precision the two networks are shown to be very similar. Copyright © 2015 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.
Semiconductor nanostructure properties. Molecular Dynamic Simulations
NASA Astrophysics Data System (ADS)
Podolska, N. I.; Zhmakin, A. I.
2013-08-01
The need for research is based on the fact that development of non-planar semiconductor nanosystems and nanomaterials with controlled properties is an important scientific and industrial problem. So, final scientific and technological problem is the creation of adequate modern methods and software for growth and properties simulation and optimization of various III-V (GaAs, InAs, InP, InGaAs etc.) nanostructures (e.g. nanowires) with controlled surface morphology, crystal structure, optical, transport properties etc. Accordingly, now we are developing a specialized computer code for atomistic simulation of structural (distribution of atoms and impurities, elastic and force constants, strain distribution etc.) and thermodynamic (mixing energy, interaction energy, surface energy etc.) properties of the nanostructures. Some simulation results are shown too.
Reflecting boundary conditions for classical molecular dynamics simulations of nonideal plasmas
NASA Astrophysics Data System (ADS)
Lavrinenko, Ya S.; Morozov, I. V.; Valuev, I. A.
2016-11-01
The influence of boundary conditions on results of the classical molecular dynamics simulations of nonideal electron-ion plasma is analyzed. A comprehensive study is performed for the convergence of per-particle potential energy and pressure with the number of particles using both the nearest image method (periodic boundaries) and harmonic reflective boundaries. As a result an error caused by finiteness of the simulation box is estimated. Moreover the electron oscillations given by the spectra of the current autocorrelation function are analyzed for both types of the boundary conditions. Nonideal plasmas with the nonideality parameter in range 0.26-2.6 is considered. To speed up the classical molecular dynamics simulations the graphics accelerators code is used.
Equation of State of Al Based on Quantum Molecular Dynamics Calculations
NASA Astrophysics Data System (ADS)
Minakov, Dmitry V.; Levashov, Pavel R.; Khishchenko, Konstantin V.
2011-06-01
In this work, we present quantum molecular dynamics calculations of the shock Hugoniots of solid and porous samples as well as release isentropes and values of isentropic sound velocity behind the shock front for aluminum. We use the VASP code with an ultrasoft pseudopotential and GGA exchange-correlation functional. Up to 108 particles have been used in calculations. For the Hugoniots of Al we solve the Hugoniot equation numerically. To calculate release isentropes, we use Zel'dovich's approach and integrate an ordinary differential equation for the temperature thus restoring all thermodynamic parameters. Isentropic sound velocity is calculated by differentiation along isentropes. The results of our calculations are in good agreement with experimental data. Thus, quantum molecular dynamics results can be effectively used for verification or calibration of semiempirical equations of state under conditions of lack of experimental information at high energy densities. This work is supported by RFBR, grants 09-08-01129 and 11-08-01225.
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.
Script, code, information: how to differentiate analogies in the "prehistory" of molecular biology.
Kogge, Werner
2012-01-01
The remarkable fact that twentieth-century molecular biology developed its conceptual system on the basis of sign-like terms has been the object of numerous studies and debates. Throughout these, the assumption is made that this vocabulary's emergence should be seen in the historical context of mathematical communication theory and cybernetics. This paper, in contrast, sets out the need for a more differentiated view: whereas the success of the terms "code" and "information" would probably be unthinkable outside that historical context, general semiotic and especially scriptural concepts arose far earlier in the "prehistory" of molecular biology, and in close association with biological research and phenomena. This distinction, established through a reconstruction of conceptual developments between 1870 and 1950, makes it possible to separate off a critique of the reductive implications of particular information-based concepts from the use of semiotic and scriptural concepts, which is fundamental to molecular biology. Gene-centrism and determinism are not implications of semiotic and scriptural analogies, but arose only when the vocabulary of information was superimposed upon them.
Research on verification and validation strategy of detonation fluid dynamics code of LAD2D
NASA Astrophysics Data System (ADS)
Wang, R. L.; Liang, X.; Liu, X. Z.
2017-07-01
The verification and validation (V&V) is an important approach in the software quality assurance of code in complex engineering application. Reasonable and efficient V&V strategy can achieve twice the result with half the effort. This article introduces the software-Lagrangian adaptive hydrodynamics code in 2D space (LAD2D), which is self-developed software in detonation CFD with plastic-elastic structure. The V&V strategy of this detonation CFD code is presented based on the foundation of V&V methodology for scientific software. The basic framework of the module verification and the function validation is proposed, composing the detonation fluid dynamics model V&V strategy of LAD2D.
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.
Real-world predictions from ab initio molecular dynamics simulations.
Kirchner, Barbara; di Dio, Philipp J; Hutter, Jürg
2012-01-01
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
Theoretical analysis of dynamic processes for interacting molecular motors
NASA Astrophysics Data System (ADS)
Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem
2015-02-01
Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.
Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.
Teimouri, Hamid; Kolomeisky, Anatoly B; Mehrabiani, Kareem
2015-02-13
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.
Molecular dynamics study of atomic displacements in disordered solid alloys
NASA Astrophysics Data System (ADS)
Puzyrev, Yevgeniy S.
The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.
The SCEC-USGS Dynamic Earthquake Rupture Code Verification Exercise - Recent Progress
NASA Astrophysics Data System (ADS)
Harris, R.
2013-12-01
I summarize recent progress by the SCEC-USGS Dynamic Rupture Code Verification Group, that examines if the results produced by researchers' earthquake simulation codes agree with each other when computing benchmark scenarios of dynamically propagating earthquake ruptures. To date we have tested the codes against benchmarks that incorporate a range of features, including a single planar vertical fault, a single planar dipping fault, slip-weakening, rate-state, and thermal pressurization friction, elastic and plastic off-fault behavior, complete stress drops that lead to supershear rupture velocities and extreme ground motion, and, heterogeneous initial stresses. Our most recent benchmarks have involved complexities in fault geometry, with computationally simulated earthquakes spontaneously propagating on parallel non-co-planar vertical strike-slip faults and on branching vertical strike-slip faults. The parallel strike-slip fault case has been discussed in the published literature over the past decades, from both observational and theoretical perspectives, and the results are sometimes used in hazard estimates for multi-fault earthquake ruptures. The branching fault case has been a focus of study due to its potential application to a number of geologically hazardous settings. Group members used their individual computer codes and achieved satisfactory agreement among the codes' results for both sets of these recent benchmarks, the parallel faults and the branched faults. Our next benchmark exercise will continue on the theme of complex fault geometry and investigate the case of a geometrical asperity on an otherwise planar fault. We also plan to work on developing suitable quantitative metrics for our code comparisons. For more information about our group and our work, please see our website and our group's overview papers, Harris et al., Seismological Research Letters, 2009, and Harris et al., Seismological Research Letters, 2011.
Zachariah, M; Romanini, M; Tripathi, P; Tamarit, J Ll; Macovez, R
2015-06-28
We probe the ionic conduction and the molecular dynamics in a pure and lithium-salt doped dinitrile molecular plastic crystal. While the diffusion of the Li(+) ions is decoupled from the molecular reorientational dynamics, in the undoped plastic crystal the temperature dependence of the mobility of dinitrile ions and thus of the conductivity is virtually identical to that of on-site molecular rotations. The undoped material is found to obey the Walden and Stokes-Einstein rules typical of ideal liquid electrolytes, implying that an effective viscosity against diffusion can be defined even for a plastic crystalline phase. These surprising results, never reported before in a translationally ordered solid, indicate that in this dinitrile plastic crystalline material the timescale of translational diffusion is perfectly correlated with that of the purely reorientational on-site dynamics.
Dynamic molecular oxygen production in cometary comae
NASA Astrophysics Data System (ADS)
Yao, Yunxi; Giapis, Konstantinos P.
2017-05-01
Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2-. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.
Dynamic molecular oxygen production in cometary comae
Yao, Yunxi; Giapis, Konstantinos P.
2017-01-01
Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov–Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind–surface interactions and gas-phase collisions. Here we report an original Eley–Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2−. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets. PMID:28480881
LETTER TO THE EDITOR: Retrieval dynamics of neural networks for sparsely coded sequential patterns
NASA Astrophysics Data System (ADS)
Kitano, Katsunori; Aoyagi, Toshio
1998-09-01
It is well known that a sparsely coded network in which the activity level is extremely low has intriguing equilibrium properties. In this work, we study the dynamical properties of a neural network designed to store sparsely coded sequential patterns rather than static ones. Applying the theory of statistical neurodynamics, we derive the dynamical equations governing the retrieval process which are described by some macroscopic order parameters such as the overlap. It is found that our theory provides good predictions for the storage capacity and the basin of attraction obtained through numerical simulations. The results indicate that the nature of the basin of attraction depends on the methods of activity control employed. Furthermore, it is found that robustness against random synaptic dilution slightly deteriorates with the degree of sparseness.
Laminar and temporal expression dynamics of coding and noncoding RNAs in the mouse neocortex.
Fertuzinhos, Sofia; Li, Mingfeng; Kawasawa, Yuka Imamura; Ivic, Vedrana; Franjic, Daniel; Singh, Darshani; Crair, Michael; Sestan, Nenad
2014-03-13
The hallmark of the cerebral neocortex is its organization into six layers, each containing a characteristic set of cell types and synaptic connections. The transcriptional events involved in laminar development and function still remain elusive. Here, we employed deep sequencing of mRNA and small RNA species to gain insights into transcriptional differences among layers and their temporal dynamics during postnatal development of the mouse primary somatosensory neocortex. We identify a number of coding and noncoding transcripts with specific spatiotemporal expression and splicing patterns. We also identify signature trajectories and gene coexpression networks associated with distinct biological processes and transcriptional overlap between these processes. Finally, we provide data that allow the study of potential miRNA and mRNA interactions. Overall, this study provides an integrated view of the laminar and temporal expression dynamics of coding and noncoding transcripts in the mouse neocortex and a resource for studies of neurodevelopment and transcriptome.
Sandia National Laboratories environmental fluid dynamics code : pH effects user manual.
Janardhanam, Vijay; James, Scott Carlton
2012-02-01
This document describes the implementation level changes in the source code and input files of Sandia National Laboratories Environmental Fluid Dynamics Code (SNL-EFDC) that are necessary for including pH effects into algae-growth dynamics. The document also gives a brief introduction to how pH effects are modeled into the algae-growth model. The document assumes that the reader is aware of the existing algae-growth model in SNL-EFDC. The existing model is described by James, Jarardhanam and more theoretical considerations behind modeling pH effects are presented therein. This document should be used in conjunction with the original EFDC manual and the original water-quality manual.
A dynamic code for economic object valuation in prefrontal cortex neurons
Tsutsui, Ken-Ichiro; Grabenhorst, Fabian; Kobayashi, Shunsuke; Schultz, Wolfram
2016-01-01
Neuronal reward valuations provide the physiological basis for economic behaviour. Yet, how such valuations are converted to economic decisions remains unclear. Here we show that the dorsolateral prefrontal cortex (DLPFC) implements a flexible value code based on object-specific valuations by single neurons. As monkeys perform a reward-based foraging task, individual DLPFC neurons signal the value of specific choice objects derived from recent experience. These neuronal object values satisfy principles of competitive choice mechanisms, track performance fluctuations and follow predictions of a classical behavioural model (Herrnstein's matching law). Individual neurons dynamically encode both, the updating of object values from recently experienced rewards, and their subsequent conversion to object choices during decision-making. Decoding from unselected populations enables a read-out of motivational and decision variables not emphasized by individual neurons. These findings suggest a dynamic single-neuron and population value code in DLPFC that advances from reward experiences to economic object values and future choices. PMID:27618960
ALEGRA -- A massively parallel h-adaptive code for solid dynamics
Summers, R.M.; Wong, M.K.; Boucheron, E.A.; Weatherby, J.R.
1997-12-31
ALEGRA is a multi-material, arbitrary-Lagrangian-Eulerian (ALE) code for solid dynamics designed to run on massively parallel (MP) computers. It combines the features of modern Eulerian shock codes, such as CTH, with modern Lagrangian structural analysis codes using an unstructured grid. ALEGRA is being developed for use on the teraflop supercomputers to conduct advanced three-dimensional (3D) simulations of shock phenomena important to a variety of systems. ALEGRA was designed with the Single Program Multiple Data (SPMD) paradigm, in which the mesh is decomposed into sub-meshes so that each processor gets a single sub-mesh with approximately the same number of elements. Using this approach the authors have been able to produce a single code that can scale from one processor to thousands of processors. A current major effort is to develop efficient, high precision simulation capabilities for ALEGRA, without the computational cost of using a global highly resolved mesh, through flexible, robust h-adaptivity of finite elements. H-adaptivity is the dynamic refinement of the mesh by subdividing elements, thus changing the characteristic element size and reducing numerical error. The authors are working on several major technical challenges that must be met to make effective use of HAMMER on MP computers.
Dynamics of electron solvation in molecular clusters.
Ehrler, Oli T; Neumark, Daniel M
2009-06-16
Solvated electrons, and hydrated electrons in particular, are important species in condensed phase chemistry, physics, and biology. Many studies have examined the formation mechanism, reactivity, spectroscopy, and dynamics of electrons in aqueous solution and other solvents, leading to a fundamental understanding of the electron-solvent interaction. However, key aspects of solvated electrons remain controversial, and the interaction between hydrated electrons and water is of central interest. For example, although researchers generally accept that hydrated electrons, eaq-, occupy solvent cavities, another picture suggests that the electron resides in a diffuse orbital localized on a H3O radical. In addition, researchers have proposed two physically distinct models for the relaxation mechanism when the electron is excited. These models, formulated to interpret condensed phase experiments, have markedly different timescales for the internal conversion from the excited p state to the ground s state.Studies of negatively charged clusters, such as (H2O)n- and I-(H2O)n, offer a complementary perspective for studying aqueous electron solvation. In this Account, we use time-resolved photoelectron spectroscopy (TRPES), a femtosecond pump-probe technique in which mass-selected anions are electronically excited and then photodetached at a series of delay times, to focus on time-resolved dynamics in these and similar species. In (H2O)n-,TRPES gives evidence for ultrafast internal conversion in clusters up to n=100. Extrapolation of these results yields a p-state lifetime of 50 fs in the bulk limit. This is in good agreement with the nonadiabatic solvation model, one of the models proposed for relaxation of eaq-. Similarly, experiments on (MeOH)n- up to n=450 give an extrapolated p-state lifetime of 150fs. TRPES investigations of I-(H2O)n and I-(CH3CN)n probe a different aspect of electron solvation dynamics. In these experiments,an ultraviolet pump pulse excites the cluster
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.
Molecular Dynamics Analysis of a Liquid Explosive Reaction Zone
NASA Astrophysics Data System (ADS)
Soulard, L.; Crouzet, B.
2006-07-01
We present an analysis of the reaction zone of a stationary planar detonation by a equilibrium molecular dynamics method (EMD). We particularly focus on the influence of chemical characteristics such as the reactions reversibility and endothermicity. First, equilibrium and unreacted Hugoniot of the reactive system are calculated by EMD. These results are then used to predict the detonation characteristics such as the thermodynamic properties of ZND spike and the sonic point. We observe in particular the influence of the preliminary endothermic phase on the detonation velocity and its stability. The comparison between these predictions and non equilibrium molecular dynamics calculations validate the EMD method.
Nonholonomic Hamiltonian method for molecular dynamics simulations of reacting shocks
NASA Astrophysics Data System (ADS)
Bass, Joseph; Fahrenthold, Eric P.
2017-01-01
Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general the potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new nonholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations, and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted parameters.
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.
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.
Cawkwell, M J; Niklasson, Anders M N
2012-10-07
Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.
Electron-phonon interaction within classical molecular dynamics
NASA Astrophysics Data System (ADS)
Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.
2016-07-01
We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e -ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.
Electron-phonon interaction within classical molecular dynamics
Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.
2016-07-14
Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.
Electron-phonon interaction within classical molecular dynamics
Tamm, A.; Samolyuk, G.; Correa, A. A.; ...
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
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 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.
CAVEAT: a computer code for fluid dynamics problems with large distortion and internal slip
Addessio, F.L.; Carroll, D.E.; Dukowicz, J.K.; Harlow, F.H.; Johnson, J.N.; Kashiwa, B.A.; Maltrud, M.E.; Ruppel, H.M.
1986-02-01
This report describes the CAVEAT computer code, which numerically solves the equations of transient, multimaterial, compressible fluid dynamics. General material equations of state are allowed by the use of the SESAME library. Of particular interest is the general capability to handle material interfaces, including slip, cavitation, or void closure. Also included is the capability to treat material strength and plasticity, high explosive (HE) detonations, and a k-epsilon model of turbulence. 62 refs., 60 figs., 6 tabs.
Multi-code analysis of scrape-off layer filament dynamics in MAST
NASA Astrophysics Data System (ADS)
Militello, F.; Walkden, N. R.; Farley, T.; Gracias, W. A.; Olsen, J.; Riva, F.; Easy, L.; Fedorczak, N.; Lupelli, I.; Madsen, J.; Nielsen, A. H.; Ricci, P.; Tamain, P.; Young, J.
2016-11-01
Four numerical codes are employed to investigate the dynamics of scrape-off layer filaments in tokamak relevant conditions. Experimental measurements were taken in the MAST device using visual camera imaging, which allows the evaluation of the perpendicular size and velocity of the filaments, as well as the combination of density and temperature associated with the perturbation. A new algorithm based on the light emission integrated along the field lines associated with the position of the filament is developed to ensure that it is properly detected and tracked. The filaments are found to have velocities of the order of 1~\\text{km}~{{\\text{s}}-1} , a perpendicular diameter of around 2-3 cm and a density amplitude 2-3.5 times the background plasma. 3D and 2D numerical codes (the STORM module of BOUT++, GBS, HESEL and TOKAM3X) are used to reproduce the motion of the observed filaments with the purpose of validating the codes and of better understanding the experimental data. Good agreement is found between the 3D codes. The seeded filament simulations are also able to reproduce the dynamics observed in experiments with accuracy up to the experimental errorbar levels. In addition, the numerical results showed that filaments characterised by similar size and light emission intensity can have quite different dynamics if the pressure perturbation is distributed differently between density and temperature components. As an additional benefit, several observations on the dynamics of the filaments in the presence of evolving temperature fields were made and led to a better understanding of the behaviour of these coherent structures.
Mathematical framework for the analysis of dynamic stochastic systems with the RAVEN code
Rabiti, C.; Mandelli, D.; Alfonsi, A.; Cogliati, J.; Kinoshita, R.
2013-07-01
RAVEN (Reactor Analysis and Virtual control Environment) is a software code under development at Idaho National Laboratory aimed at performing probabilistic risk assessment and uncertainty quantification using RELAP-7, for which it acts also as a simulation controller. In this paper we will present the equations characterizing a dynamic stochastic system and we will then discuss the behavior of each stochastic term and how it is accounted for in the RAVEN software design. Moreover we will present preliminary results of the implementation. (authors)
Sandia National Laboratories Environmental Fluid Dynamics Code V. 1 0.0 (Beta)
2015-10-20
The DOE has funded Sandia National Labs (SNL) to develop an open-source modeling tool to guide the design and layout of marine hydrokinetic (MHK) arrays to maximize power production while minimizing environmental effects. This modeling framework simulates flows through and around MHK arrays while quantifying environmental responses. As an augmented version of US EPA's Environmental Fluid Dynamics Code (EFDC), SNL-EFDC includes: (1) a new module that simulates energy conversion (momentum withdrawal) by MHK devices with commensurate changes in the turbulent kinetic energy and its dissipation rate, (2) new, advanced sediment dynamics routines, and (3) augmented water quality modules.
Particle-in-Cell Code BEAMPATH for Beam Dynamics Simulations in Linear Accelerators and Beamlines
Batygin, Y.
2004-10-28
A code library BEAMPATH for 2 - dimensional and 3 - dimensional space charge dominated beam dynamics study in linear particle accelerators and beam transport lines is developed. The program is used for particle-in-cell simulation of axial-symmetric, quadrupole-symmetric and z-uniform beams in a channel containing RF gaps, radio-frequency quadrupoles, multipole lenses, solenoids and bending magnets. The programming method includes hierarchical program design using program-independent modules and a flexible combination of modules to provide the most effective version of the structure for every specific case of simulation. Numerical techniques as well as the results of beam dynamics studies are presented.
Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems
Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus
2014-01-01
Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171
Multiple time step integrators in ab initio molecular dynamics
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-02-28
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.
Efficient molecular dynamics simulations with many-body potentials on graphics processing units
NASA Astrophysics Data System (ADS)
Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari
2017-09-01
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).
Verification of fluid-dynamic codes in the presence of shocks and other discontinuities
NASA Astrophysics Data System (ADS)
Nathan Woods, C.; Starkey, Ryan P.
2015-08-01
The verification that computer codes correctly solve their model equations is critical to the continued success of numerical simulation. The method of manufactured solutions (MMS) is the best method currently available for this kind of verification for differential equations. However, it cannot be used directly with discontinuous solutions, as is required for the verification of high-speed aerodynamic codes with shocks. An integrative approach can extend the applicability of MMS to both discontinuous solutions such as shocks or material interfaces, as well as integral equations. We present an implementation of integrative MMS based on intelligent subdivision of integration domains that is both highly accurate and fast, and results in a rigorous, one-step verification procedure for shock-capturing codes. Numerical integration is found to be accurate to machine precision when tested on exact solutions of the linear heat equation and the Euler equations, even in the presence of discontinuous flow features. Intelligent subdivision of integration domains also improves computational performance by approximately 60× compared to the same algorithm without intelligent subdivisions. We demonstrate the use of MMS in the verification of the BACL-Streamer inviscid gas dynamics code. Integral MMS is found to compute convergence rates that are equivalent to those computed using differential MMS, and comparable to those computed using discontinuous, exact solutions, suggesting integral MMS is a valid method for verification of both integral and shock-capturing codes.
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.
Imaging the molecular dynamics of dissociative electron attachment to water
Adaniya, Hidihito; Rudek, B.; Osipov, Timur; Haxton, Dan; Weber, Thorsten; Rescigno, Thomas N.; McCurdy, C.W.; Belkacem, Ali
2009-10-19
Momentum imaging experiments on dissociative electron attachment to the water molecule are combined with ab initio theoretical calculations of the angular dependence of the quantum mechanical amplitude for electron attachment to provide a detailed picture of the molecular dynamics of dissociation attachment via the two lowest energy Feshbach resonances. The combination of momentum imaging experiments and theory can reveal dissociation dynamics for which the axial recoil approximation breaks down and thus provides a powerful reaction microscope for DEA to polyatomics.
Coarse-Grained Molecular Dynamics: Dissipation Due to Internal Modes
Rudd, R E
2001-12-21
We describe progress on the issue of pathological elastic wave reflection in atomistic and multiscale simulation. First we briefly review Coarse-Grained Molecular Dynamics (CGMD). Originally CGMD was formulated as a Hamiltonian system in which energy is conserved. This formulation is useful for many applications, but recently CGMD has been extended to include generalized Langevin forces. Here we describe how Langevin dynamics arise naturally in CGMD, and we examine the implication for elastic wave scattering.
A fast recursive algorithm for molecular dynamics simulation
NASA Technical Reports Server (NTRS)
Jain, A.; Vaidehi, N.; Rodriguez, G.
1993-01-01
The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.
Neural dynamics of reward probability coding: a Magnetoencephalographic study in humans.
Thomas, Julie; Vanni-Mercier, Giovanna; Dreher, Jean-Claude
2013-01-01
Prediction of future rewards and discrepancy between actual and expected outcomes (prediction error) are crucial signals for adaptive behavior. In humans, a number of fMRI studies demonstrated that reward probability modulates these two signals in a large brain network. Yet, the spatio-temporal dynamics underlying the neural coding of reward probability remains unknown. Here, using magnetoencephalography, we investigated the neural dynamics of prediction and reward prediction error computations while subjects learned to associate cues of slot machines with monetary rewards with different probabilities. We showed that event-related magnetic fields (ERFs) arising from the visual cortex coded the expected reward value 155 ms after the cue, demonstrating that reward value signals emerge early in the visual stream. Moreover, a prediction error was reflected in ERF peaking 300 ms after the rewarded outcome and showing decreasing amplitude with higher reward probability. This prediction error signal was generated in a network including the anterior and posterior cingulate cortex. These findings pinpoint the spatio-temporal characteristics underlying reward probability coding. Together, our results provide insights into the neural dynamics underlying the ability to learn probabilistic stimuli-reward contingencies.
Mott metal-insulator transition in a metallic liquid - Gutzwiller molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Barros, Kipton; Chern, Gia-Wei; Batista, Cristian D.; Kress, Joel D.; Kotliar, Gabriel
2015-03-01
Molecular dynamics (MD) simulations are crucial to modern computational physics, chemistry, and materials science, especially when combined with potentials derived from density-functional theory. However, even in state of the art MD codes, the on-site Coulomb repulsion is only treated at the self-consistent Hartree-Fock level. This standard approximation may miss important effects due to electron correlations. The Gutzwiller variational method captures essential correlated-electron physics yet is much faster than, e.g., the dynamical-mean field theory approach. We present our efficient Gutzwiller-MD implementation. With it, we investigate the Mott metal-insulator transition in a metallic fluid and uncover several surprising static and dynamic properties of this system.
Mesoscopic Dynamics of Biopolymers and Protein Molecular Machines
NASA Astrophysics Data System (ADS)
Kapral, Raymond
2013-03-01
The dynamics of biopolymers in solution and in crowded molecular environments, which mimic some features of the interior of a biochemical cell, will be discussed. In particular, the dynamics of protein machines that utilize chemical energy to effect cyclic conformational changes to carry out their catalytic functions will be described. The investigation of the dynamics of such complex systems requires knowledge of the time evolution on physically relevant long distance and time scales. This often necessitates a coarse grained or mesoscopic treatment of the dynamics. A hybrid particle-based mesoscopic dynamical method, which combines molecular dynamics for a coarse-grain model of the proteins with multiparticle collision dynamics for the solvent, will be described and utilized to study the dynamics of such systems. See, C. Echeverria, Y. Togashi, A. S. Mikhailov, and R. Kapral, Phys. Chem. Chem. Phys 13, 10527 (2011); C. Echeverria and R. Kapral, Phys. Chem. Chem. Phys., 14, 6755 (2012); J. M. Schofield, P. Inder and R. Kapral, J. Chem. Phys. 136, 205101 (2012). Work was supported in part by a grant from the Natural Sciences and Engineering Research Council of Canada.
Cloutier, Philippe; Coulombe, Benoit
2013-05-01
Molecular chaperones and their associated cofactors form a group of highly specialized proteins that orchestrate the folding and unfolding of other proteins and the assembly and disassembly of protein complexes. Chaperones are found in all cell types and organisms, and their activity must be tightly regulated to maintain normal cell function. Indeed, deregulation of protein folding and protein complex assembly is the cause of various human diseases. Here, we present the results of an extensive review of the literature revealing that the post-translational modification (PTM) of chaperones has been selected during evolution as an efficient mean to regulate the activity and specificity of these key proteins. Because the addition and reciprocal removal of chemical groups can be triggered very rapidly, this mechanism provides an efficient switch to precisely regulate the activity of chaperones on specific substrates. The large number of PTMs detected in chaperones suggests that a combinatory code is at play to regulate function, activity, localization, and substrate specificity for this group of biologically important proteins. This review surveys the core information currently available as a starting point toward the more ambitious endeavor of deciphering the "chaperone code". Copyright © 2013 Elsevier B.V. All rights reserved.
The molecular and cellular basis of taste coding in the legs of Drosophila.
Ling, Frederick; Dahanukar, Anupama; Weiss, Linnea A; Kwon, Jae Young; Carlson, John R
2014-05-21
To understand the principles of taste coding, it is necessary to understand the functional organization of the taste organs. Although the labellum of the Drosophila melanogaster head has been described in detail, the tarsal segments of the legs, which collectively contain more taste sensilla than the labellum, have received much less attention. We performed a systematic anatomical, physiological, and molecular analysis of the tarsal sensilla of Drosophila. We construct an anatomical map of all five tarsal segments of each female leg. The taste sensilla of the female foreleg are systematically tested with a panel of 40 diverse compounds, yielding a response matrix of ∼500 sensillum-tastant combinations. Six types of sensilla are characterized. One type was tuned remarkably broadly: it responded to 19 of 27 bitter compounds tested, as well as sugars; another type responded to neither. The midleg is similar but distinct from the foreleg. The response specificities of the tarsal sensilla differ from those of the labellum, as do n-dimensional taste spaces constructed for each organ, enhancing the capacity of the fly to encode and respond to gustatory information. We examined the expression patterns of all 68 gustatory receptors (Grs). A total of 28 Gr-GAL4 drivers are expressed in the legs. We constructed a receptor-to-sensillum map of the legs and a receptor-to-neuron map. Fourteen Gr-GAL4 drivers are expressed uniquely in the bitter-sensing neuron of the sensillum that is tuned exceptionally broadly. Integration of the molecular and physiological maps provides insight into the underlying basis of taste coding.
The Molecular and Cellular Basis of Taste Coding in the Legs of Drosophila
Ling, Frederick; Dahanukar, Anupama; Weiss, Linnea A.; Kwon, Jae Young
2014-01-01
To understand the principles of taste coding, it is necessary to understand the functional organization of the taste organs. Although the labellum of the Drosophila melanogaster head has been described in detail, the tarsal segments of the legs, which collectively contain more taste sensilla than the labellum, have received much less attention. We performed a systematic anatomical, physiological, and molecular analysis of the tarsal sensilla of Drosophila. We construct an anatomical map of all five tarsal segments of each female leg. The taste sensilla of the female foreleg are systematically tested with a panel of 40 diverse compounds, yielding a response matrix of ∼500 sensillum–tastant combinations. Six types of sensilla are characterized. One type was tuned remarkably broadly: it responded to 19 of 27 bitter compounds tested, as well as sugars; another type responded to neither. The midleg is similar but distinct from the foreleg. The response specificities of the tarsal sensilla differ from those of the labellum, as do n-dimensional taste spaces constructed for each organ, enhancing the capacity of the fly to encode and respond to gustatory information. We examined the expression patterns of all 68 gustatory receptors (Grs). A total of 28 Gr–GAL4 drivers are expressed in the legs. We constructed a receptor-to-sensillum map of the legs and a receptor-to-neuron map. Fourteen Gr–GAL4 drivers are expressed uniquely in the bitter-sensing neuron of the sensillum that is tuned exceptionally broadly. Integration of the molecular and physiological maps provides insight into the underlying basis of taste coding. PMID:24849350
NASA Astrophysics Data System (ADS)
Ocaya, R. O.; Terblans, J. J.
Ab-initio molecular dynamics (MD) employs Newtonian mechanics to model and simulate the time evolution of particle trajectories in material science ensembles using a differentiable potential function. Although commercial and free packages exist for MD, their heuristic nature prevents dissection. This open-source C-language package arose out of the interest to study effects of embedded atoms in metallic face-centered cubic structures (fcc) on a standalone computer. The algorithms use velocity-time integration to output instantaneous particle parameters for up to several thousands of particles in the NVT ensemble. The functions are coded in a reusable and redistributable standalone header library file.
Applications of Langevin and Molecular Dynamics methods
NASA Astrophysics Data System (ADS)
Lomdahl, P. S.
Computer simulation of complex nonlinear and disordered phenomena from materials science is rapidly becoming an active and new area serving as a guide for experiments and for testing of theoretical concepts. This is especially true when novel massively parallel computer systems and techniques are used on these problems. In particular the Langevin dynamics simulation technique has proven useful in situations where the time evolution of a system in contact with a heat bath is to be studied. The traditional way to study systems in contact with a heat bath has been via the Monte Carlo method. While this method has indeed been used successfully in many applications, it has difficulty addressing true dynamical questions. Large systems of coupled stochastic ODE's (or Langevin equations) are commonly the end result of a theoretical description of higher dimensional nonlinear systems in contact with a heat bath. The coupling is often local in nature, because it reflects local interactions formulated on a lattice, the lattice for example represents the underlying discreteness of a substrate of atoms or discrete k-values in Fourier space. The fundamental unit of parallelism thus has a direct analog in the physical system the authors are interested in. In these lecture notes the authors illustrate the use of Langevin stochastic simulation techniques on a number of nonlinear problems from materials science and condensed matter physics that have attracted attention in recent years. First, the authors review the idea behind the fluctuation-dissipation theorem which forms that basis for the numerical Langevin stochastic simulation scheme. The authors then show applications of the technique to various problems from condensed matter and materials science.
Molecular circuits for dynamic noise filtering
Zechner, Christoph; Seelig, Georg; Rullan, Marc; Khammash, Mustafa
2016-01-01
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
New ways to boost molecular dynamics simulations.
Krieger, Elmar; Vriend, Gert
2015-05-15
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Theory of multiexciton dynamics in molecular chains
NASA Astrophysics Data System (ADS)
Wang, Luxia; May, Volkhard
2016-11-01
Ultrafast and strong optical excitation of a molecular system is considered which is formed by a regular one-dimensional arrangement of identical molecules. As it is typical for zinc chlorine-type molecules the transition energy from the ground state to the first excited singlet state is assumed to be smaller than the energy difference between the first excited state and the following one. This enables the creation of many excitons without their immediate quenching due to exciton-exciton annihilation. As a first step into the field of dense Frenkel-exciton systems the present approach stays at a mean-field type of description and ignores vibrational contributions. The resulting nonlinear kinetic equations mix Rabi-type oscillations with those caused by energy transfer and suggest an excitation-dependent narrowing of the exciton band. The indication of this effect in the framework of a two-color pump-probe experiment and of the detection of photon emission is discussed.
Superspreading: molecular dynamics simulations and experimental results
NASA Astrophysics Data System (ADS)
Theodorakis, Panagiotis; Kovalchuk, Nina; Starov, Victor; Muller, Erich; Craster, Richard; Matar, Omar
2015-11-01
The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Recently, we have observed that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. Here, we present the structural characteristics and kinetics of the droplet spreading during the different stages of this process, and we compare our results with experimental data for trisiloxane and poly oxy ethylene surfactants. In this way, we highlight and explore the differences between surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting. EPSRC Platform Grant MACIPh (EP/L020564/).
Müller, C.; Hughes, E. D.; Niederauer, G. F.; Wilkening, H.; Travis, J. R.; Spore, J. W.; Royl, P.; Baumann, W.
1998-10-01
Los Alamos National Laboratory (LANL) and Forschungszentrum Karlsruhe (FzK) are developing GASFLOW, a three-dimensional (3D) fluid dynamics field code as a best- estimate tool to characterize local phenomena within a flow field. Examples of 3D phenomena include circulation patterns; flow stratification; hydrogen distribution mixing and stratification; combustion and flame propagation; effects of noncondensable gas distribution on local condensation and evaporation; and aerosol entrainment, transport, and deposition. An analysis with GASFLOW will result in a prediction of the gas composition and discrete particle distribution in space and time throughout the facility and the resulting pressure and temperature loadings on the walls and internal structures with or without combustion. A major application of GASFLOW is for predicting the transport, mixing, and combustion of hydrogen and other gases in nuclear reactor containment and other facilities. It has been applied to situations involving transporting and distributing combustible gas mixtures. It has been used to study gas dynamic behavior in low-speed, buoyancy-driven flows, as well as sonic flows or diffusion dominated flows; and during chemically reacting flows, including deflagrations. The effects of controlling such mixtures by safety systems can be analyzed. The code version described in this manual is designated GASFLOW 2.1, which combines previous versions of the United States Nuclear Regulatory Commission code HMS (for Hydrogen Mixing Studies) and the Department of Energy and FzK versions of GASFLOW. The code was written in standard Fortran 90. This manual comprises three volumes. Volume I describes the governing physical equations and computational model. Volume II describes how to use the code to set up a model geometry, specify gas species and material properties, define initial and boundary conditions, and specify different outputs, especially graphical displays. Sample problems are included. Volume
Nichols, B. D.; Mueller, C.; Necker, G. A.; Travis, J. R.; Spore, J. W.; Lam, K. L.; Royl, P.; Wilson, T. L.
1998-10-01
Los Alamos National Laboratory (LANL) and Forschungszentrum Karlsruhe (FzK) are developing GASFLOW, a three-dimensional (3D) fluid dynamics field code as a best-estimate tool to characterize local phenomena within a flow field. Examples of 3D phenomena include circulation patterns; flow stratification; hydrogen distribution mixing and stratification; combustion and flame propagation; effects of noncondensable gas distribution on local condensation and evaporation; and aerosol entrainment, transport, and deposition. An analysis with GASFLOW will result in a prediction of the gas composition and discrete particle distribution in space and time throughout the facility and the resulting pressure and temperature loadings on the walls and internal structures with or without combustion. A major application of GASFLOW is for predicting the transport, mixing, and combustion of hydrogen and other gases in nuclear reactor containment and other facilities. It has been applied to situations involving transporting and distributing combustible gas mixtures. It has been used to study gas dynamic behavior in low-speed, buoyancy-driven flows, as well as sonic flows or diffusion dominated flows; and during chemically reacting flows, including deflagrations. The effects of controlling such mixtures by safety systems can be analyzed. The code version described in this manual is designated GASFLOW 2.1, which combines previous versions of the United States Nuclear Regulatory Commission code HMS (for Hydrogen Mixing Studies) and the Department of Energy and FzK versions of GASFLOW. The code was written in standard Fortran 90. This manual comprises three volumes. Volume I describes the governing physical equations and computational model. Volume II describes how to use the code to set up a model geometry, specify gas species and material properties, define initial and boundary conditions, and specify different outputs, especially graphical displays. Sample problems are included. Volume III
Tsukada, Minoru; Ichinose, Natsuhiro; Aihara, Kazuyuki; Ito, Hiroyuki; Fujii, Hiroshi
1996-11-01
This paper is an attempt to understand how knowledge and events are represented and processed in the brain. An important point is the question of what carries information in the brain - the mean firing rate or the timing of spikes? The idea we want to pursue is that, contrary to the traditional view, the brain might use higher order statistics, which means in essence that timing of spikes plays a critical role in encoding, representing, and processing knowledge and events in the brain.A recently revealed salient nature of cortical pyramidal cells, i.e., the high variability of inter-spike intervals suggests that a cortical neuron may function effectively as a coincidence detector. At the same time, non-classical experimental phenomena of task-related, short time-scaled dynamical modulations of temporal correlations between neurons suggest a non-classical view on the dynamics working in the brain. In response to contexts or external events, a group of neurons, a dynamical cell assembly, spontaneously organizes, linked temporarily by coincident timing of incident spikes, showing correlated firing with each other. This is an emergent property of neuronal populations in the cortex.We make a theoretical exploration on issues as (1) the description of such emergent dynamics of dynamical cell assemblies based on the working hypothesis that a cortica neuron functions effectively as a coincidence detector, and (2) the principle of spatio-temporal coding based on the hypothetical emergent dynamics. Note that the conventional rate coding hypothesis does not give satisfactory answers to fundamental questions on the representation and processing of knowledge or events in the brain, e.g., the questions of cross-modular integration of information or the binding problem, and representation of hierarchical knowledge etc.The first goal is to give a non-encyclopedic review on (1) the temporal structure of spike sequences, focusing on the question of the basic code in the brain; (2
Investigation of neutral particle dynamics in Aditya tokamak plasma with DEGAS2 code
Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.; ...
2017-06-09
Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, Hα spectrum is also simulated which was matched with the experimental one. The dominantmore » contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~ 2.0 eV. Furthermore, the variation of neutral hydrogen density and Hα emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in Hα emission at the plasma edge with the variation of edge temperature (7 to 40 eV).« less
Investigation of neutral particle dynamics in Aditya tokamak plasma with DEGAS2 code
NASA Astrophysics Data System (ADS)
Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.; Manchanda, R.; Banerjee, S.; Ramaiya, N.; Sharma, Deepti; Srinivasan, R.; Stotler, D. P.; Aditya Team
2017-08-01
Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated and matched with the experimental one. The dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7-40 eV).
A molecular code dictates sequence-specific DNA recognition by homeodomains.
Damante, G; Pellizzari, L; Esposito, G; Fogolari, F; Viglino, P; Fabbro, D; Tell, G; Formisano, S; Di Lauro, R
1996-01-01
Most homeodomains bind to DNA sequences containing the motif 5'-TAAT-3'. The homeodomain of thyroid transcription factor 1 (TTF-1HD) binds to sequences containing a 5'-CAAG-3' core motif, delineating a new mechanism for differential DNA recognition by homeodomains. We investigated the molecular basis of the DNA binding specificity of TTF-1HD by both structural and functional approaches. As already suggested by the three-dimensional structure of TTF-1HD, the DNA binding specificities of the TTF-1, Antennapedia and Engrailed homeodomains, either wild-type or mutants, indicated that the amino acid residue in position 54 is involved in the recognition of the nucleotide at the 3' end of the core motif 5'-NAAN-3'. The nucleotide at the 5' position of this core sequence is recognized by the amino acids located in position 6, 7 and 8 of the TTF-1 and Antennapedia homeodomains. These data, together with previous suggestions on the role of amino acids in position 50, indicate that the DNA binding specificity of homeodomains can be determined by a combinatorial molecular code. We also show that some specific combinations of the key amino acid residues involved in DNA recognition do not follow a simple, additive rule. Images PMID:8890172
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.
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…
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
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.
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 simulations on PGLa using NMR orientational constraints.
Sternberg, Ulrich; Witter, Raiker
2015-11-01
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
Molecular dynamics simulation of aqueous solutions of glycine betaine
NASA Astrophysics Data System (ADS)
Civera, Monica; Fornili, Arianna; Sironi, Maurizio; Fornili, Sandro L.
2003-01-01
Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine- N-oxide, a bioprotectant closely related to glycine betaine.
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.
Molecular Dynamic Screening Sesquiterpenoid Pogostemon Herba as Suggested Cyclooxygenase Inhibitor
Raharjo, Sentot Joko; Kikuchi, Takeshi
2016-01-01
Objective: Virtual molecular dynamic sesquiterpenoid Pogostemon Herba (CID56928117, CID94275, CID107152, and CID519743) have screening as cyclooxygenase (COX-1/COX-2) selective inhibitor. Methods: Molecular interaction studies sesquiterpenoid compounds with COX-1 and COX-2 were using the molecular docking tools by Hex 8.0 and interactions were further visualized using by Discovery Studio Client 3.5 software tool and Virtual Molecular Dynamic 1.9.1 software. The binding energy calculation of molecular dynamic interaction was calculated by AMBER12 software. Result: The analysis of the sesquiterpenoid compounds showed that CID56928117, CID94275, CID107152, and CID519743 have suggested as inhibitor of COX-1 and COX-2. Conclusion: Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor. PMID:28077888
Natural image sequences constrain dynamic receptive fields and imply a sparse code.
Häusler, Chris; Susemihl, Alex; Nawrot, Martin P
2013-11-06
In their natural environment, animals experience a complex and dynamic visual scenery. Under such natural stimulus conditions, neurons in the visual cortex employ a spatially and temporally sparse code. For the input scenario of natural still images, previous work demonstrated that unsupervised feature learning combined with the constraint of sparse coding can predict physiologically measured receptive fields of simple cells in the primary visual cortex. This convincingly indicated that the mammalian visual system is adapted to the natural spatial input statistics. Here, we extend this approach to the time domain in order to predict dynamic receptive fields that can account for both spatial and temporal sparse activation in biological neurons. We rely on temporal restricted Boltzmann machines and suggest a novel temporal autoencoding training procedure. When tested on a dynamic multi-variate benchmark dataset this method outperformed existing models of this class. Learning features on a large dataset of natural movies allowed us to model spatio-temporal receptive fields for single neurons. They resemble temporally smooth transformations of previously obtained static receptive fields and are thus consistent with existing theories. A neuronal spike response model demonstrates how the dynamic receptive field facilitates temporal and population sparseness. We discuss the potential mechanisms and benefits of a spatially and temporally sparse representation of natural visual input.
Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics.
Vila Verde, Ana; Beltramo, Peter J; Maranas, Janna K
2011-05-17
We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala(10), Ser(10), Thr(10), Arg(10), Lys(10), and Gln(10)], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movement and flexibility of the peptide within a given conformation. Low conformational movement indicates stability of a given conformation and leads to less adsorption than homopolypeptides with faster conformational movement. Likewise, low flexibility within a given conformation also leads to less adsorption. Neither amino acid affinities nor dynamic considerations alone predict surface coverage; rather both quantities must be considered in peptide adsorption to gold surfaces.
Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response
Aitken, Stuart; Magi, Shigeyuki; Alhendi, Ahmad M. N.; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Daub, Carsten O.; Arner, Erik; Carninci, Piero; Forrest, Alistair R. R.; Hayashizaki, Yoshihide; Khachigian, Levon M.; Okada-Hatakeyama, Mariko; Semple, Colin A.
2015-01-01
The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers. However, the specificity of the response across stimuli and cell types, and the roles of non-coding RNAs are not well understood. Using a large collection of densely-sampled time series expression data we have examined the induction of the immediate-early response in unparalleled detail, across cell types and stimuli. We exploit cap analysis of gene expression (CAGE) time series datasets to directly measure promoter activities over time. Using a novel analysis method for time series data we identify transcripts with expression patterns that closely resemble the dynamics of known immediate-early genes (IEGs) and this enables a comprehensive comparative study of these genes and their chromatin state. Surprisingly, these data suggest that the earliest transcriptional responses often involve promoters generating non-coding RNAs, many of which are produced in advance of canonical protein-coding IEGs. IEGs are known to be capable of induction without de novo protein synthesis. Consistent with this, we find that the response of both protein-coding and non-coding RNA IEGs can be explained by their transcriptionally poised, permissive chromatin state prior to stimulation. We also explore the function of non-coding RNAs in the attenuation of the immediate early response in a small RNA sequencing dataset matched to the CAGE data: We identify a novel set of microRNAs responsible for the attenuation of the IEG response in an estrogen receptor positive cancer cell line. Our computational statistical method is well suited to meta-analyses as there is no requirement for transcripts to pass thresholds for significant differential expression between time points, and it is agnostic to the number of time points per dataset. PMID:25885578
Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.
Aitken, Stuart; Magi, Shigeyuki; Alhendi, Ahmad M N; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Daub, Carsten O; Arner, Erik; Carninci, Piero; Forrest, Alistair R R; Hayashizaki, Yoshihide; Khachigian, Levon M; Okada-Hatakeyama, Mariko; Semple, Colin A
2015-04-01
The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers. However, the specificity of the response across stimuli and cell types, and the roles of non-coding RNAs are not well understood. Using a large collection of densely-sampled time series expression data we have examined the induction of the immediate-early response in unparalleled detail, across cell types and stimuli. We exploit cap analysis of gene expression (CAGE) time series datasets to directly measure promoter activities over time. Using a novel analysis method for time series data we identify transcripts with expression patterns that closely resemble the dynamics of known immediate-early genes (IEGs) and this enables a comprehensive comparative study of these genes and their chromatin state. Surprisingly, these data suggest that the earliest transcriptional responses often involve promoters generating non-coding RNAs, many of which are produced in advance of canonical protein-coding IEGs. IEGs are known to be capable of induction without de novo protein synthesis. Consistent with this, we find that the response of both protein-coding and non-coding RNA IEGs can be explained by their transcriptionally poised, permissive chromatin state prior to stimulation. We also explore the function of non-coding RNAs in the attenuation of the immediate early response in a small RNA sequencing dataset matched to the CAGE data: We identify a novel set of microRNAs responsible for the attenuation of the IEG response in an estrogen receptor positive cancer cell line. Our computational statistical method is well suited to meta-analyses as there is no requirement for transcripts to pass thresholds for significant differential expression between time points, and it is agnostic to the number of time points per dataset.
Collisional dynamics in a gas of molecular super-rotors.
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh
2015-07-10
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.
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.
Molecular dynamics simulation of friction of hydrocarbon thin films
Tamura, Hiroyuki; Yoshida, Muneo; Kusakabe, Kenichi
1999-10-26
Molecular Dynamics (MD) simulations were performed to investigate the dynamic behavior of hydrocarbon molecules under shear conditions. Frictional properties of cyclohexane, n-hexane, and iso-hexane thin films confirmed between two solid surfaces were calculated. Because the affinity of the solid surfaces in these simulations is strong, slippages occurred at inner parts of the confined films, whereas no slippages were observed at the solid boundaries. The hexagonal closest packing structure was observed for the adsorbed cyclohexane molecular layers. The branched methyl groups in the iso-hexane molecules increase the shear stress between the molecular layers. For the n-hexane monolayer, molecules were observed to roll during the sliding simulations. Rolling of the n-hexane molecules decreased the shear stress.
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
Molecular Mechanism of Overhauser Dynamic Nuclear Polarization in Insulating Solids.
Pylaeva, Svetlana; Ivanov, Konstantin L; Baldus, Marc; Sebastiani, Daniel; Elgabarty, Hossam
2017-05-18
Dynamic nuclear polarization (DNP), a technique that significantly enhances NMR signals, is experiencing a renaissance owing to enormous methodological developments. In the heart of DNP is a polarization transfer mechanism that endows nuclei with much larger electronic spin polarization. Polarization transfer via the Overhauser effect (OE) is traditionally known to be operative only in liquids and conducting solids. Very recently, surprisingly strong OE-DNP in insulating solids has been reported, with a DNP efficiency that increases with the magnetic field strength. Here we offer an explanation for these perplexing observations using a combination of molecular dynamics and spin dynamics simulations. Our approach elucidates the underlying molecular stochastic motion, provides cross-relaxation rates, explains the observed sign of the NMR enhancement, and estimates the role of nuclear spin diffusion. The presented theoretical description opens the door for rational design of novel polarizing agents for OE-DNP in insulating solids.
Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.
Markegard, Cade B; Mazaheripour, Amir; Jocson, Jonah-Micah; Burke, Anthony M; Dickson, Mary N; Gorodetsky, Alon A; Nguyen, Hung D
2015-09-03
Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks.
Drugs That Target Dynamic Microtubules: A New Molecular Perspective
Stanton, Richard A.; Gernert, Kim M.; Nettles, James H.; Aneja, Ritu
2011-01-01
Microtubules have long been considered an ideal target for anticancer drugs because of the essential role they play in mitosis, forming the dynamic spindle apparatus. As such, there is a wide variety of compounds currently in clinical use and in development that act as antimitotic agents by altering microtubule dynamics. Although these diverse molecules are known to affect microtubule dynamics upon binding to one of the three established drug domains (taxane, vinca alkaloid, or colchicine site), the exact mechanism by which each drug works is still an area of intense speculation and research. In this study, we review the effects of microtubule-binding chemotherapeutic agents from a new perspective, considering how their mode of binding induces conformational changes and alters biological function relative to the molecular vectors of microtubule assembly or disassembly. These “biological vectors” can thus be used as a spatiotemporal context to describe molecular mechanisms by which microtubule-targeting drugs work. PMID:21381049
Digital micromirror device camera with per-pixel coded exposure for high dynamic range imaging.
Feng, Wei; Zhang, Fumin; Wang, Weijing; Xing, Wei; Qu, Xinghua
2017-05-01
In this paper, we overcome the limited dynamic range of the conventional digital camera, and propose a method of realizing high dynamic range imaging (HDRI) from a novel programmable imaging system called a digital micromirror device (DMD) camera. The unique feature of the proposed new method is that the spatial and temporal information of incident light in our DMD camera can be flexibly modulated, and it enables the camera pixels always to have reasonable exposure intensity by DMD pixel-level modulation. More importantly, it allows different light intensity control algorithms used in our programmable imaging system to achieve HDRI. We implement the optical system prototype, analyze the theory of per-pixel coded exposure for HDRI, and put forward an adaptive light intensity control algorithm to effectively modulate the different light intensity to recover high dynamic range images. Via experiments, we demonstrate the effectiveness of our method and implement the HDRI on different objects.
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.
2006-09-01
Therefore, dynamic quantities of reaction mixtures such as the velocity autocorrelation functions and the diffusion coefficients can be accurately...using the virial expression [25]. A standard NVT molecular dynamics method was em- ployed with the equations of motion solved using the Verlet leapfrog...configurational energy, pressure, and species concen- trations) are compared to quantities calculated by the RxMC approach. Second , the dynamic quantities
Lewis, Ashley G; Bastiaansen, Marcel
2015-07-01
There is a growing literature investigating the relationship between oscillatory neural dynamics measured using electroencephalography (EEG) and/or magnetoencephalography (MEG), and sentence-level language comprehension. Recent proposals have suggested a strong link between predictive coding accounts of the hierarchical flow of information in the brain, and oscillatory neural dynamics in the beta and gamma frequency ranges. We propose that findings relating beta and gamma oscillations to sentence-level language comprehension might be unified under such a predictive coding account. Our suggestion is that oscillatory activity in the beta frequency range may reflect both the active maintenance of the current network configuration responsible for representing the sentence-level meaning under construction, and the top-down propagation of predictions to hierarchically lower processing levels based on that representation. In addition, we suggest that oscillatory activity in the low and middle gamma range reflect the matching of top-down predictions with bottom-up linguistic input, while evoked high gamma might reflect the propagation of bottom-up prediction errors to higher levels of the processing hierarchy. We also discuss some of the implications of this predictive coding framework, and we outline ideas for how these might be tested experimentally. Copyright © 2015 Elsevier Ltd. All rights reserved.
NASA Astrophysics Data System (ADS)
Hanhart, Philippe; Řeřábek, Martin; Ebrahimi, Touradj
2015-09-01
This paper reports the details and results of the subjective evaluations conducted at EPFL to evaluate the responses to the Call for Evidence (CfE) for High Dynamic Range (HDR) and Wide Color Gamut (WCG) Video Coding issued by Moving Picture Experts Group (MPEG). The CfE on HDR/WCG Video Coding aims to explore whether the coding efficiency and/or the functionality of the current version of HEVC standard can be signi_cantly improved for HDR and WCG content. In total, nine submissions, five for Category 1 and four for Category 3a, were compared to the HEVC Main 10 Profile based Anchor. More particularly, five HDR video contents, compressed at four bit rates by each proponent responding to the CfE, were used in the subjective evaluations. Further, the side-by-side presentation methodology was used for the subjective experiment to discriminate small differences between the Anchor and proponents. Subjective results shows that the proposals provide evidence that the coding efficiency can be improved in a statistically noticeable way over MPEG CfE Anchors in terms of perceived quality within the investigated content. The paper further benchmarks the selected objective metrics based on their correlations with the subjective ratings. It is shown that PSNR-DE1000, HDRVDP- 2, and PSNR-Lx can reliably detect visible differences between the proposed encoding solutions and current HEVC standard.
Dynamic Population Coding of Category Information in Inferior Temporal and Prefrontal Cortex
Meyers, Ethan M.; Freedman, David J.; Kreiman, Gabriel; Miller, Earl K.; Poggio, Tomaso
2008-01-01
Most electrophysiology studies analyze the activity of each neuron separately. While such studies have given much insight into properties of the visual system, they have also potentially overlooked important aspects of information coded in changing patterns of activity that are distributed over larger populations of neurons. In this work, we apply a population decoding method to better estimate what information is available in neuronal ensembles and how this information is coded in dynamic patterns of neural activity in data recorded from inferior temporal cortex (ITC) and prefrontal cortex (PFC) as macaque monkeys engaged in a delayed match-to-category task. Analyses of activity patterns in ITC and PFC revealed that both areas contain “abstract” category information (i.e., category information that is not directly correlated with properties of the stimuli); however, in general, PFC has more task-relevant information, and ITC has more detailed visual information. Analyses examining how information coded in these areas show that almost all category information is available in a small fraction of the neurons in the population. Most remarkably, our results also show that category information is coded by a nonstationary pattern of activity that changes over the course of a trial with individual neurons containing information on much shorter time scales than the population as a whole. PMID:18562555
REBOUND: an open-source multi-purpose N-body code for collisional dynamics
NASA Astrophysics Data System (ADS)
Rein, H.; Liu, S.-F.
2012-01-01
REBOUND is a new multi-purpose N-body code which is freely available under an open-source license. It was designed for collisional dynamics such as planetary rings but can also solve the classical N-body problem. It is highly modular and can be customized easily to work on a wide variety of different problems in astrophysics and beyond. REBOUND comes with three symplectic integrators: leap-frog, the symplectic epicycle integrator (SEI) and a Wisdom-Holman mapping (WH). It supports open, periodic and shearing-sheet boundary conditions. REBOUND can use a Barnes-Hut tree to calculate both self-gravity and collisions. These modules are fully parallelized with MPI as well as OpenMP. The former makes use of a static domain decomposition and a distributed essential tree. Two new collision detection modules based on a plane-sweep algorithm are also implemented. The performance of the plane-sweep algorithm is superior to a tree code for simulations in which one dimension is much longer than the other two and in simulations which are quasi-two dimensional with less than one million particles. In this work, we discuss the different algorithms implemented in REBOUND, the philosophy behind the code's structure as well as implementation specific details of the different modules. We present results of accuracy and scaling tests which show that the code can run efficiently on both desktop machines and large computing clusters.
Siddick, M M; Ackland, G J; Morrison, C A
2006-08-14
We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
2014-01-01
Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585
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.