Introduction to Molecular Dynamics and Accelerated Molecular Dynamics
International Nuclear Information System (INIS)
Perez, Danny
2012-01-01
We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.
Accelerating convergence of molecular dynamics-based structural relaxation
DEFF Research Database (Denmark)
Christensen, Asbjørn
2005-01-01
We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...
Enhancing protein adsorption simulations by using accelerated molecular dynamics.
Directory of Open Access Journals (Sweden)
Christian Mücksch
Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.
On the application of accelerated molecular dynamics to liquid water simulations.
de Oliveira, César Augusto F; Hamelberg, Donald; McCammon, J Andrew
2006-11-16
Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.
Directory of Open Access Journals (Sweden)
Zeynab Mohammad Hosseini Naveh
Full Text Available Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP, a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD and Temperature Accelerated Molecular Dynamics (TAMD simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.
Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping
Lu, Jianfeng; Zhou, Zhennan
2018-02-01
To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limit, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer and thus connects the surface hopping approach to the mean-field path-integral molecular dynamics. A multiscale integrator for the infinite swapping limit is also proposed to enable efficient sampling based on the limiting dynamics. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path-integral molecular dynamics with surface hopping.
Voter, Arthur
Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.
Accelerated molecular dynamics methods: introduction and recent developments
Energy Technology Data Exchange (ETDEWEB)
Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO
2009-01-01
reaction pathways may be important, we return instead to a molecular dynamics treatment, in which the trajectory itself finds an appropriate way to escape from each state of the system. Since a direct integration of the trajectory would be limited to nanoseconds, while we are seeking to follow the system for much longer times, we modify the dynamics in some way to cause the first escape to happen much more quickly, thereby accelerating the dynamics. The key is to design the modified dynamics in a way that does as little damage as possible to the probability for escaping along a given pathway - i.e., we try to preserve the relative rate constants for the different possible escape paths out of the state. We can then use this modified dynamics to follow the system from state to state, reaching much longer times than we could reach with direct MD. The dynamics within any one state may no longer be meaningful, but the state-to-state dynamics, in the best case, as we discuss in the paper, can be exact. We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics. Each of these methods has its own advantages, and we and others have applied these methods to a wide range of problems. The purpose of this article is to give the reader a brief introduction to how these methods work, and discuss some of the recent developments that have been made to improve their power and applicability. Note that this brief review does not claim to be exhaustive: various other methods aiming at similar goals have been proposed in the literature. For the sake of brevity, our focus will exclusively be on the methods developed by the group.
Accelerated molecular dynamics methods: introduction and recent developments
International Nuclear Information System (INIS)
Uberuaga, Blas Pedro; Voter, Arthur F.; Perez, Danny; Shim, Y.; Amar, J.G.
2009-01-01
reaction pathways may be important, we return instead to a molecular dynamics treatment, in which the trajectory itself finds an appropriate way to escape from each state of the system. Since a direct integration of the trajectory would be limited to nanoseconds, while we are seeking to follow the system for much longer times, we modify the dynamics in some way to cause the first escape to happen much more quickly, thereby accelerating the dynamics. The key is to design the modified dynamics in a way that does as little damage as possible to the probability for escaping along a given pathway - i.e., we try to preserve the relative rate constants for the different possible escape paths out of the state. We can then use this modified dynamics to follow the system from state to state, reaching much longer times than we could reach with direct MD. The dynamics within any one state may no longer be meaningful, but the state-to-state dynamics, in the best case, as we discuss in the paper, can be exact. We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics. Each of these methods has its own advantages, and we and others have applied these methods to a wide range of problems. The purpose of this article is to give the reader a brief introduction to how these methods work, and discuss some of the recent developments that have been made to improve their power and applicability. Note that this brief review does not claim to be exhaustive: various other methods aiming at similar goals have been proposed in the literature. For the sake of brevity, our focus will exclusively be on the methods developed by the group
Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala
2018-06-01
Nano-drug delivery systems have proven to be an efficient formulation tool to overcome the challenges with current antibiotics therapy and resistance. A series of pH-responsive lipid molecules were designed and synthesized for future liposomal formulation as a nano-drug delivery system for vancomycin at the infection site. The structures of these lipids differ from each other in respect of hydrocarbon tails: Lipid1, 2, 3 and 4 have stearic, oleic, linoleic, and linolenic acid hydrocarbon chains, respectively. The impact of variation in the hydrocarbon chain in the lipid structure on drug encapsulation and release profile, as well as mode of drug interaction, was investigated using molecular modeling analyses. A wide range of computational tools, including accelerated molecular dynamics, normal molecular dynamics, binding free energy calculations and principle component analysis, were applied to provide comprehensive insight into the interaction landscape between vancomycin and the designed lipid molecules. Interestingly, both MM-GBSA and MM-PBSA binding affinity calculations using normal molecular dynamics and accelerated molecular dynamics trajectories showed a very consistent trend, where the order of binding affinity towards vancomycin was lipid4 > lipid1 > lipid2 > lipid3. From both normal molecular dynamics and accelerated molecular dynamics, the interaction of lipid3 with vancomycin is demonstrated to be the weakest (∆G binding = -2.17 and -11.57, for normal molecular dynamics and accelerated molecular dynamics, respectively) when compared to other complexes. We believe that the degree of unsaturation of the hydrocarbon chain in the lipid molecules may impact on the overall conformational behavior, interaction mode and encapsulation (wrapping) of the lipid molecules around the vancomycin molecule. This thorough computational analysis prior to the experimental investigation is a valuable approach to guide for predicting the encapsulation
Accelerating molecular dynamic simulation on the cell processor and Playstation 3.
Luttmann, Edgar; Ensign, Daniel L; Vaidyanathan, Vishal; Houston, Mike; Rimon, Noam; Øland, Jeppe; Jayachandran, Guha; Friedrichs, Mark; Pande, Vijay S
2009-01-30
Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors. (c) 2008 Wiley Periodicals, Inc.
Directory of Open Access Journals (Sweden)
Cameron Abrams
2013-12-01
Full Text Available We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.
Substructured multibody molecular dynamics.
Energy Technology Data Exchange (ETDEWEB)
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
Directory of Open Access Journals (Sweden)
Barry J Grant
2009-03-01
Full Text Available Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75 intermediate between GTP and GDP states, or distinct loop3 (46-49, loop7 (105-110, and alpha5 C-terminus (159-166 conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74 with alpha3-loop7 (93-110, loop2 (26-37 with loop10 (145-151, and loop3 (46-49 with alpha5 (152-167. The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD simulations, is a low-frequency motion intrinsic to the structure.
Czech Academy of Sciences Publication Activity Database
Klvana, M.; Pavlová, M.; Koudeláková, T.; Chaloupková, R.; Dvořák, P.; Prokop, Z.; Stsiapanava, A.; Kutý, Michal; Kutá-Smatanová, Ivana; Dohnálek, Jan; Kulhánek, P.; Damborský, J.
2009-01-01
Roč. 392, č. 5 (2009), s. 1339-1356 ISSN 0022-2836 R&D Projects: GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z60870520 Keywords : haloalkane dehalogenase * product release * random acceleration molecular dynamics Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.871, year: 2009
Directory of Open Access Journals (Sweden)
César Augusto F de Oliveira
2011-10-01
Full Text Available Chagas' disease, caused by the protozoan parasite Trypanosoma cruzi (T. cruzi, is a life-threatening illness affecting 11-18 million people. Currently available treatments are limited, with unacceptable efficacy and safety profiles. Recent studies have revealed an essential T. cruzi proline racemase enzyme (TcPR as an attractive candidate for improved chemotherapeutic intervention. Conformational changes associated with substrate binding to TcPR are believed to expose critical residues that elicit a host mitogenic B-cell response, a process contributing to parasite persistence and immune system evasion. Characterization of the conformational states of TcPR requires access to long-time-scale motions that are currently inaccessible by standard molecular dynamics simulations. Here we describe advanced accelerated molecular dynamics that extend the effective simulation time and capture large-scale motions of functional relevance. Conservation and fragment mapping analyses identified potential conformational epitopes located in the vicinity of newly identified transient binding pockets. The newly identified open TcPR conformations revealed by this study along with knowledge of the closed to open interconversion mechanism advances our understanding of TcPR function. The results and the strategy adopted in this work constitute an important step toward the rationalization of the molecular basis behind the mitogenic B-cell response of TcPR and provide new insights for future structure-based drug discovery.
Huang, Yu-Ming M; McCammon, J Andrew; Miao, Yinglong
2018-04-10
Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.
Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F.; Perez, Danny
2017-10-01
Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which have to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex accelerated molecular dynamics trajectories exhibiting shape fluctuations in Pt nanoclusters. This analysis provides an easily interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.
Donnan, Patrick H; Ngo, Phong D; Mansoorabadi, Steven O
2018-01-23
The bioluminescence reaction in dinoflagellates involves the oxidation of an open-chain tetrapyrrole by the enzyme dinoflagellate luciferase (LCF). The activity of LCF is tightly regulated by pH, where the enzyme is essentially inactive at pH ∼8 and optimally active at pH ∼6. Little is known about the mechanism of LCF or the structure of the active form of the enzyme, although it has been proposed that several intramolecularly conserved histidine residues in the N-terminal region are important for the pH regulation mechanism. Here, constant pH accelerated molecular dynamics was employed to gain insight into the conformational activation of LCF induced by acidification.
Accelerating Molecular Dynamic Simulation on Graphics Processing Units
Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.
2009-01-01
We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. PMID:19191337
Nonlinear dynamics in particle accelerators
Dilão, Rui
1996-01-01
This book is an introductory course to accelerator physics at the level of graduate students. It has been written for a large audience which includes users of accelerator facilities, accelerator physicists and engineers, and undergraduates aiming to learn the basic principles of construction, operation and applications of accelerators.The new concepts of dynamical systems developed in the last twenty years give the theoretical setting to analyse the stability of particle beams in accelerator. In this book a common language to both accelerator physics and dynamical systems is integrated and dev
Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces
International Nuclear Information System (INIS)
Brown, W. Michael; Wang, Peng; Plimpton, Steven J.; Tharrington, Arnold N.
2011-01-01
The use of accelerators such as general-purpose graphics processing units (GPGPUs) have 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 many-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. We describe algorithms for efficient short range force calculation on hybrid high performance machines. We describe a new 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 GPGPUs and 180 CPU cores.
Nonlinear dynamics aspects of particle accelerators
International Nuclear Information System (INIS)
Jowett, J.M.; Turner, S.; Month, M.
1986-01-01
These proceedings contain the lectures presented at the named winter school. They deal with the application of dynamical systems to accelerator theory. Especially considered are the statistical description of charged-beam plasmas, integrable and nonintegrable Hamiltonian systems, single particle dynamics and nonlinear resonances in circular accelerators, nonlinear dynamics aspects of modern storage rings, nonlinear beam-beam resonances, synchro-betatron resonances, observations of the beam-beam interactions, the dynamics of the beam-beam interactions, beam-beam simulations, the perturbation method in nonlinear dynamics, theories of statistical equilibrium in electron-positron storage rings, nonlinear dissipative phenomena in electron storage rings, the dynamical aperture, the transition to chaos for area-preserving maps, special processors for particle tracking, algorithms for tracking of charged particles in circular accelerators, the breakdown of stability, and a personal perspective of nonlinear dynamics. (HSI)
Chaotic dynamics in accelerator physics
International Nuclear Information System (INIS)
Cary, J.R.
1992-01-01
Substantial progress was in several areas of accelerator dynamics. For developing understanding of longitudinal adiabatic dynamics, and for creating efficiency enhancements of recirculating free-electron lasers, was substantially completed. A computer code for analyzing the critical KAM tori that bound the dynamic aperture in circular machines was developed. Studies of modes that arise due to the interaction of coating beams with a narrow-spectrum impedance have begun. During this research educational and research ties with the accelerator community at large have been strengthened
Multiple time step integrators in ab initio molecular dynamics
International Nuclear Information System (INIS)
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-01-01
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy
Dynamics and acceleration in linear structures
International Nuclear Information System (INIS)
Le Duff, J.
1985-06-01
Basic methods of linear acceleration are reviewed. Both cases of non relativistic and ultra relativistic particles are considered. Induction linac, radiofrequency quadrupole are mentioned. Fundamental parameters of accelerating structures are recalled; they are transit time factor, shunt impedance, quality factor and stored energy, phase velocity and group velocity, filling time, space harmonics in loaded waveguides. Energy gain in linear accelerating structures is considered through standing wave structures and travelling wave structures. Then particle dynamics in linear accelerators is studied: longitudinal motion, transverse motion and dynamics in RFQ
Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics.
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Denis Bucher
2011-04-01
Full Text Available Periplasmic binding proteins (PBPs are a large family of molecular transporters that play a key role in nutrient uptake and chemotaxis in Gram-negative bacteria. All PBPs have characteristic two-domain architecture with a central interdomain ligand-binding cleft. Upon binding to their respective ligands, PBPs undergo a large conformational change that effectively closes the binding cleft. This conformational change is traditionally viewed as a ligand induced-fit process; however, the intrinsic dynamics of the protein may also be crucial for ligand recognition. Recent NMR paramagnetic relaxation enhancement (PRE experiments have shown that the maltose binding protein (MBP - a prototypical member of the PBP superfamily - exists in a rapidly exchanging (ns to µs regime mixture comprising an open state (approx 95%, and a minor partially closed state (approx 5%. Here we describe accelerated MD simulations that provide a detailed picture of the transition between the open and partially closed states, and confirm the existence of a dynamical equilibrium between these two states in apo MBP. We find that a flexible part of the protein called the balancing interface motif (residues 175-184 is displaced during the transformation. Continuum electrostatic calculations indicate that the repacking of non-polar residues near the hinge region plays an important role in driving the conformational change. Oscillations between open and partially closed states create variations in the shape and size of the binding site. The study provides a detailed description of the conformational space available to ligand-free MBP, and has implications for understanding ligand recognition and allostery in related proteins.
Nonlinear dynamics aspects of particle accelerators. Proceedings
Energy Technology Data Exchange (ETDEWEB)
Jowett, J M; Turner, S; Month, M
1986-01-01
These proceedings contain the lectures presented at the named winter school. They deal with the application of dynamical systems to accelerator theory. Especially considered are the statistical description of charged-beam plasmas, integrable and nonintegrable Hamiltonian systems, single particle dynamics and nonlinear resonances in circular accelerators, nonlinear dynamics aspects of modern storage rings, nonlinear beam-beam resonances, synchro-betatron resonances, observations of the beam-beam interactions, the dynamics of the beam-beam interactions, beam-beam simulations, the perturbation method in nonlinear dynamics, theories of statistical equilibrium in electron-positron storage rings, nonlinear dissipative phenomena in electron storage rings, the dynamical aperture, the transition to chaos for area-preserving maps, special processors for particle tracking, algorithms for tracking of charged particles in circular accelerators, the breakdown of stability, and a personal perspective of nonlinear dynamics. (HSI).
Accelerating the convergence of path integral dynamics with a generalized Langevin equation
Ceriotti, Michele; Manolopoulos, David E.; Parrinello, Michele
2011-02-01
The quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that zero-point energy effects can be included comparatively cheaply in simulations of harmonic and quasiharmonic systems by augmenting classical molecular dynamics with a generalized Langevin equation (GLE). Here we describe how a similar approach can be used to accelerate the convergence of path integral (PI) molecular dynamics to the exact quantum mechanical result in more strongly anharmonic systems exhibiting both zero point energy and tunnelling effects. The resulting PI-GLE method is illustrated with applications to a double-well tunnelling problem and to liquid water.
Accelerating the convergence of path integral dynamics with a generalized Langevin equation.
Ceriotti, Michele; Manolopoulos, David E; Parrinello, Michele
2011-02-28
The quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that zero-point energy effects can be included comparatively cheaply in simulations of harmonic and quasiharmonic systems by augmenting classical molecular dynamics with a generalized Langevin equation (GLE). Here we describe how a similar approach can be used to accelerate the convergence of path integral (PI) molecular dynamics to the exact quantum mechanical result in more strongly anharmonic systems exhibiting both zero point energy and tunnelling effects. The resulting PI-GLE method is illustrated with applications to a double-well tunnelling problem and to liquid water.
An Examination of Resonance, Acceleration, and Particle Dynamics in the Micro-Accelerator Platform
International Nuclear Information System (INIS)
McNeur, Josh; Rosenzweig, J. B.; Travish, G.; Zhou, J.; Yoder, R.
2010-01-01
An effort to build a micron-scale dielectric-based slab-symmetric accelerator is underway at UCLA. The structure achieves acceleration via a resonant accelerating mode that is excited in an approximately 800 nm wide vacuum gap by a side coupled 800 nm laser. Detailed simulation results on structure fields and particle dynamics, using HFSS and VORPAL, are presented. We examine the quality factors of the accelerating modes for various structures and the excitations of non-accelerating destructive modes. Additionally, the results of an analytic and computational study of focusing, longitudinal dynamics and acceleration are described. Methods for achieving simultaneous transverse and longitudinal focusing are discussed, including modification of structure dimensions and slow variation of the coupling periodicity.
Iteration and accelerator dynamics
International Nuclear Information System (INIS)
Peggs, S.
1987-10-01
Four examples of iteration in accelerator dynamics are studied in this paper. The first three show how iterations of the simplest maps reproduce most of the significant nonlinear behavior in real accelerators. Each of these examples can be easily reproduced by the reader, at the minimal cost of writing only 20 or 40 lines of code. The fourth example outlines a general way to iteratively solve nonlinear difference equations, analytically or numerically
Use of molecular ion beams from a tandem accelerator
International Nuclear Information System (INIS)
Faibis, A.; Goldring, G.; Hass, M.; Kaim, R.; Plesser, I.; Vager, Z.
1981-01-01
A large variety of positive molecular ion beams can be produced by gaseous charge exchange in the terminal of a tandem accelerator. After acceleration the molecules are usually dissociated by passage through a thin foil. Measurements of the break-up products provide a way to study both the structure of incident ions and the effects of electronic potentials on the internuclear interaction inside the foil. Beam intensities of a few picoamperes are quite adequate for these measurements, and the relatively high energy obtained by use of a tandem accelerator has the advantage of minimizing multiple scattering effects in the foil. The main difficulty in using the molecular beams lies in the large magnetic rigidity of singly-charged heavy molecular ions
Single particle dynamics in circular accelerators
International Nuclear Information System (INIS)
Ruth, R.D.
1986-10-01
The purpose of this paper is to introduce the reader to the theory associated with the transverse dynamics of single particle, in circular accelerators. The discussion begins with a review of Hamiltonian dynamics and canonical transformations. The case of a single particle in a circular accelerator is considered with a discussion of non-linear terms and chromaticity. The canonical perturbation theory is presented and nonlinear resonances are considered. Finally, the concept of renormalization and residue criterion are examined. (FI)
Energy Technology Data Exchange (ETDEWEB)
Spellings, Matthew [Chemical Engineering, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Marson, Ryan L. [Materials Science & Engineering, University of Michigan, 2300 Hayward St., Ann Arbor, MI 48109 (United States); Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Anderson, Joshua A. [Chemical Engineering, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Glotzer, Sharon C., E-mail: sglotzer@umich.edu [Chemical Engineering, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Materials Science & Engineering, University of Michigan, 2300 Hayward St., Ann Arbor, MI 48109 (United States); Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States)
2017-04-01
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks–Chandler–Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method is a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.
A concurrent multiscale micromorphic molecular dynamics
International Nuclear Information System (INIS)
Li, Shaofan; Tong, Qi
2015-01-01
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation
Quantum optical device accelerating dynamic programming
Grigoriev, D.; Kazakov, A.; Vakulenko, S.
2005-01-01
In this paper we discuss analogue computers based on quantum optical systems accelerating dynamic programming for some computational problems. These computers, at least in principle, can be realized by actually existing devices. We estimate an acceleration in resolving of some NP-hard problems that can be obtained in such a way versus deterministic computers
Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann
Energy Technology Data Exchange (ETDEWEB)
Melenev, Petr, E-mail: melenev@icmm.ru [Ural Federal University, 4, Turgeneva str., 620000 Ekaterinburg (Russian Federation); Institute of Continuous Media Mechanics, 1, Koroleva str., 614013 Perm (Russian Federation)
2017-06-01
Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces. - Highlights: • The combination of molecular dynamics and lattice Boltzmann method is utilized for the reveal of the role of hydrodynamic interaction in rotational dynamics of colloid particles. • The verification of the model parameters is done based on the comparison with the results of Langevin dynamics. • For the task of free rotational diffusion of the pair of colloid particles the influence of the hydrodynamic interactions on the relaxation time is examined in the case of nonmagnetic particles and at the presence of weak dipolar interaction.
Efficient molecular dynamics simulations with many-body potentials on graphics processing units
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).
Parallel beam dynamics simulation of linear accelerators
International Nuclear Information System (INIS)
Qiang, Ji; Ryne, Robert D.
2002-01-01
In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity beams and to the study of beam transport in a proposed accelerator for the development of accelerator-driven waste transmutation technologies
Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; Ho, Kai-Ming; Travesset, Alex
2018-04-01
We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu64.5Zr35.5, and pair correlation function g (r) of liquid Ni3Al. Our code scales well with the size of the simulating system on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. The source code can be accessed through the HOOMD-blue web page for free by any interested user.
Accelerating transition dynamics in city regions: A qualitative modeling perspective
P.J. Valkering (Pieter); Yücel, G. (Gönenç); Gebetsroither-Geringer, E. (Ernst); Markvica, K. (Karin); Meynaerts, E. (Erika); N. Frantzeskaki (Niki)
2017-01-01
textabstractIn this article, we take stock of the findings from conceptual and empirical work on the role of transition initiatives for accelerating transitions as input for modeling acceleration dynamics. We applied the qualitative modeling approach of causal loop diagrams to capture the dynamics
Report of the workshop on accelerator-based atomic and molecular science
International Nuclear Information System (INIS)
Meyerhof, W.E.
1981-01-01
This Workshop, held in New London, NH on July 27-30, 1980, had a registration of 43, representing an estimated one-third of all principal investigators in the United States in this research subfield. The workshop was organized into 5 working groups for the purpose of (1) identifying some vital physics problems which experimental and theoretical atomic and molecular science can address with current and projected techniques; (2) establishing facilities and equipment needs required to realize solutions to these problems; (3) formulating suggestions for a coherent national policy concerning this discipline; (4) assessing and projecting the manpower situation; and (5) evaluating the relations of this interdisciplinary science to other fields. Recommedations deal with equipment and operating costs for small accelerator laboratories, especially at universities; instrumentation of ion beam lines dedicated to atomic and molecular science at some large accelerators; development of low-velocity, high charge-state ion sources; synchrotron light sources; improvement or replacement of tandem van de Graaff accelerators; high-energy beam lines for atomic physics; the needs for postdoctoral support in this subfield; new accelerator development; need for representatives from atomic and molecular science on program committees for large national accelerator facilities; and the contributions the field can make to applied physics problems
Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics
International Nuclear Information System (INIS)
Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.
1992-09-01
Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs
Acceleration of cluster and molecular ions by TIARA 3 MV tandem accelerator
Saitoh, Y; Tajima, S
2000-01-01
We succeeded in accelerating molecular and cluster ions (B sub 2 sub - sub 4 , C sub 2 sub - sub 1 sub 0 , O sub 2 , Al sub 2 sub - sub 4 , Si sub 2 sub - sub 4 , Cu sub 2 sub - sub 3 , Au sub 2 sub - sub 3 , LiF, and AlO) to MeV energies with high-intensity beam currents by means of a 3 MV tandem accelerator in the TIARA facility. These cluster ions were generated by a cesium sputter-type negative ion source. We tested three types of carbon sputter cathodes in which graphite powder was compressed with different pressures. The pressure difference affected the generating ratio of clusters generated to single atom ions extracted from the source and it appeared that the high-density cathode was suitable. We also investigated the optimum gas pressure for charge exchange in the tandem high-voltage terminal. Clusters of larger size tend to require lower pressure than do smaller ones. In addition, we were able to obtain doubly charged AlO molecular ions. (authors)
Molecular dynamics based enhanced sampling of collective variables with very large time steps
Chen, Pei-Yang; Tuckerman, Mark E.
2018-01-01
Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.
Beam dynamics simulation of a double pass proton linear accelerator
Directory of Open Access Journals (Sweden)
Kilean Hwang
2017-04-01
Full Text Available A recirculating superconducting linear accelerator with the advantage of both straight and circular accelerator has been demonstrated with relativistic electron beams. The acceleration concept of a recirculating proton beam was recently proposed [J. Qiang, Nucl. Instrum. Methods Phys. Res., Sect. A 795, 77 (2015NIMAER0168-900210.1016/j.nima.2015.05.056] and is currently under study. In order to further support the concept, the beam dynamics study on a recirculating proton linear accelerator has to be carried out. In this paper, we study the feasibility of a two-pass recirculating proton linear accelerator through the direct numerical beam dynamics design optimization and the start-to-end simulation. This study shows that the two-pass simultaneous focusing without particle losses is attainable including fully 3D space-charge effects through the entire accelerator system.
AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble.
Abdul-Wahid, Badi'; Feng, Haoyun; Rajan, Dinesh; Costaouec, Ronan; Darve, Eric; Thain, Douglas; Izaguirre, Jesús A
2014-10-27
A limitation of traditional molecular dynamics (MD) is that reaction rates are difficult to compute. This is due to the rarity of observing transitions between metastable states since high energy barriers trap the system in these states. Recently the weighted ensemble (WE) family of methods have emerged which can flexibly and efficiently sample conformational space without being trapped and allow calculation of unbiased rates. However, while WE can sample correctly and efficiently, a scalable implementation applicable to interesting biomolecular systems is not available. We provide here a GPLv2 implementation called AWE-WQ of a WE algorithm using the master/worker distributed computing WorkQueue (WQ) framework. AWE-WQ is scalable to thousands of nodes and supports dynamic allocation of computer resources, heterogeneous resource usage (such as central processing units (CPU) and graphical processing units (GPUs) concurrently), seamless heterogeneous cluster usage (i.e., campus grids and cloud providers), and support for arbitrary MD codes such as GROMACS, while ensuring that all statistics are unbiased. We applied AWE-WQ to a 34 residue protein which simulated 1.5 ms over 8 months with peak aggregate performance of 1000 ns/h. Comparison was done with a 200 μs simulation collected on a GPU over a similar timespan. The folding and unfolded rates were of comparable accuracy.
Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele
2003-01-01
The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metady- namics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.
Energy Technology Data Exchange (ETDEWEB)
Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)
2015-01-15
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.
Step by step parallel programming method for molecular dynamics code
International Nuclear Information System (INIS)
Orii, Shigeo; Ohta, Toshio
1996-07-01
Parallel programming for a numerical simulation program of molecular dynamics is carried out with a step-by-step programming technique using the two phase method. As a result, within the range of a certain computing parameters, it is found to obtain parallel performance by using the level of parallel programming which decomposes the calculation according to indices of do-loops into each processor on the vector parallel computer VPP500 and the scalar parallel computer Paragon. It is also found that VPP500 shows parallel performance in wider range computing parameters. The reason is that the time cost of the program parts, which can not be reduced by the do-loop level of the parallel programming, can be reduced to the negligible level by the vectorization. After that, the time consuming parts of the program are concentrated on less parts that can be accelerated by the do-loop level of the parallel programming. This report shows the step-by-step parallel programming method and the parallel performance of the molecular dynamics code on VPP500 and Paragon. (author)
Laser acceleration and nonlinear beam dynamics
International Nuclear Information System (INIS)
Pellegrini, C.
1991-01-01
This research contract covers the period April 1990, September 1991. The work to be done under the contract was theoretical research in the areas of nonlinear beam dynamics and laser acceleration. In this final report we will discuss the motivation for this work and the results obtained
Machine learning molecular dynamics for the simulation of infrared spectra.
Gastegger, Michael; Behler, Jörg; Marquetand, Philipp
2017-10-01
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.
Color molecular dynamics for dense matter
International Nuclear Information System (INIS)
Maruyama, Toshiki; Hatsuda, Tetsuo
2000-01-01
We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)
Lattice dynamics and molecular dynamics simulation of complex materials
International Nuclear Information System (INIS)
Chaplot, S.L.
1997-01-01
In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)
Molecular dynamics for irradiation driven chemistry
DEFF Research Database (Denmark)
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-01-01
A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...
Micro structure processing on plastics by accelerated hydrogen molecular ions
Hayashi, H.; Hayakawa, S.; Nishikawa, H.
2017-08-01
A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.
Multiscale implementation of infinite-swap replica exchange molecular dynamics.
Yu, Tang-Qing; Lu, Jianfeng; Abrams, Cameron F; Vanden-Eijnden, Eric
2016-10-18
Replica exchange molecular dynamics (REMD) is a popular method to accelerate conformational sampling of complex molecular systems. The idea is to run several replicas of the system in parallel at different temperatures that are swapped periodically. These swaps are typically attempted every few MD steps and accepted or rejected according to a Metropolis-Hastings criterion. This guarantees that the joint distribution of the composite system of replicas is the normalized sum of the symmetrized product of the canonical distributions of these replicas at the different temperatures. Here we propose a different implementation of REMD in which (i) the swaps obey a continuous-time Markov jump process implemented via Gillespie's stochastic simulation algorithm (SSA), which also samples exactly the aforementioned joint distribution and has the advantage of being rejection free, and (ii) this REMD-SSA is combined with the heterogeneous multiscale method to accelerate the rate of the swaps and reach the so-called infinite-swap limit that is known to optimize sampling efficiency. The method is easy to implement and can be trivially parallelized. Here we illustrate its accuracy and efficiency on the examples of alanine dipeptide in vacuum and C-terminal β-hairpin of protein G in explicit solvent. In this latter example, our results indicate that the landscape of the protein is a triple funnel with two folded structures and one misfolded structure that are stabilized by H-bonds.
Tang, Li; Liu, Jing-Ning; Feng, Dan; Tong, Wei
2008-12-01
Existing security solutions in network storage environment perform poorly because cryptographic operations (encryption and decryption) implemented in software can dramatically reduce system performance. In this paper we propose a cryptographic hardware accelerator on dynamically reconfigurable platform for the security of high performance network storage system. We employ a dynamic reconfigurable platform based on a FPGA to implement a PowerPCbased embedded system, which executes cryptographic algorithms. To reduce the reconfiguration latency, we apply prefetch scheduling. Moreover, the processing elements could be dynamically configured to support different cryptographic algorithms according to the request received by the accelerator. In the experiment, we have implemented AES (Rijndael) and 3DES cryptographic algorithms in the reconfigurable accelerator. Our proposed reconfigurable cryptographic accelerator could dramatically increase the performance comparing with the traditional software-based network storage systems.
Vectorization for Molecular Dynamics on Intel Xeon Phi Corpocessors
Yi, Hongsuk
2014-03-01
Many modern processors are capable of exploiting data-level parallelism through the use of single instruction multiple data (SIMD) execution. The new Intel Xeon Phi coprocessor supports 512 bit vector registers for the high performance computing. In this paper, we have developed a hierarchical parallelization scheme for accelerated molecular dynamics simulations with the Terfoff potentials for covalent bond solid crystals on Intel Xeon Phi coprocessor systems. The scheme exploits multi-level parallelism computing. We combine thread-level parallelism using a tightly coupled thread-level and task-level parallelism with 512-bit vector register. The simulation results show that the parallel performance of SIMD implementations on Xeon Phi is apparently superior to their x86 CPU architecture.
Molecular Dynamics Studies of Thermal Induced Chemistry in Tatb
Quenneville, J.; Germann, T. C.; Thompson, A. P.; Kober, E. M.
2007-12-01
A reactive force field (ReaxFF) is used with molecular dynamics to probe the chemistry induced by intense heating (`accelerated cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 32-molecule simulations, we calculate the reaction rate as a function of temperature and compare the Arrhenius-predicted activation energy with experiment. Decomposition product evolution (mainly N2, H2O, CO2 and graphitic carbon clusters) is followed using a 576-molecule larger simulation, which also illustrates the effect of system size on both carbon clustering and reaction rate.
Harnessing the crowd to accelerate molecular medicine research.
Smith, Robert J; Merchant, Raina M
2015-07-01
Crowdsourcing presents a novel approach to solving complex problems within molecular medicine. By leveraging the expertise of fellow scientists across the globe, broadcasting to and engaging the public for idea generation, harnessing a scalable workforce for quick data management, and fundraising for research endeavors, crowdsourcing creates novel opportunities for accelerating scientific progress. Copyright © 2015 Elsevier Ltd. All rights reserved.
Armen, Roger S; Chen, Jianhan; Brooks, Charles L
2009-10-13
Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.
International Nuclear Information System (INIS)
Caley, L.E.; Hoffman, D.M.
1981-01-01
The dynamic mechanical properties and molecular weight distribution of two experimental polymer bonded explosives, X-0287 and X-0298, maintained at 23, 60, and 74 0 C for 3 years were examined. X-0287 is 97% 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane explosive, 1.8% Kraton G-1650, and 1.2% B 2 was 170. X-0298 is 97.4% explosive, 1.4% Kraton G-1650, and 1.2% Cenco Hi-vac oil. The relaxation associated with the Kraton rubber block glass transition is observed in both X-0287 and X-0298. In the unaged X-0298 it occurs at -59 0 C and in the aged explosive at 50 0 C. This is caused by migration of the oil plasticizer out of the explosive. In X-0287 the Kraton rubber block T/sub g/ is weak and broad due to the presence of the wax plasticizer. X-0287 has a second broad relaxation associated with the melting of the wax from 10 to 65 0 C. The molecular weight of the Kraton binder decreased with increasing accelerated aging temperature. The oil plasticizer had no stabilizing effect, but below its melting point the wax reduced Kraton chain scission considerably. The simple random chain scission model predicted a 20.5 year use-life for X-0298, but X-0287 was stabilized against degradation below the wax melting point
Approximation of quantum observables by molecular dynamics simulations
Sandberg, Mattias
2016-01-01
In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.
Approximation of quantum observables by molecular dynamics simulations
Sandberg, Mattias
2016-01-06
In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.
Polymer friction Molecular Dynamics
DEFF Research Database (Denmark)
Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.
We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....
Computer codes for beam dynamics analysis of cyclotronlike accelerators
Smirnov, V.
2017-12-01
Computer codes suitable for the study of beam dynamics in cyclotronlike (classical and isochronous cyclotrons, synchrocyclotrons, and fixed field alternating gradient) accelerators are reviewed. Computer modeling of cyclotron segments, such as the central zone, acceleration region, and extraction system is considered. The author does not claim to give a full and detailed description of the methods and algorithms used in the codes. Special attention is paid to the codes already proven and confirmed at the existing accelerating facilities. The description of the programs prepared in the worldwide known accelerator centers is provided. The basic features of the programs available to users and limitations of their applicability are described.
Computer simulation of dynamic processes on accelerators
International Nuclear Information System (INIS)
Kol'ga, V.V.
1979-01-01
The problems of computer numerical investigation of motion of accelerated particles in accelerators and storages, an effect of different accelerator systems on the motion, determination of optimal characteristics of accelerated charged particle beams are considered. Various simulation representations are discussed which describe the accelerated particle dynamics, such as the enlarged particle method, the representation where a great number of discrete particle is substituted for a field of continuously distributed space charge, the method based on determination of averaged beam characteristics. The procedure is described of numerical studies involving the basic problems, viz. calculation of closed orbits, establishment of stability regions, investigation of resonance propagation determination of the phase stability region, evaluation of the space charge effect the problem of beam extraction. It is shown that most of such problems are reduced to solution of the Cauchy problem using a computer. The ballistic method which is applied to solution of the boundary value problem of beam extraction is considered. It is shown that introduction into the equation under study of additional members with the small positive regularization parameter is a general idea of the methods for regularization of noncorrect problems [ru
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.
Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics
Directory of Open Access Journals (Sweden)
Lin Lin
2013-12-01
Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.
A Molecular Dynamics Study of Lunasin | Singh | South African ...
African Journals Online (AJOL)
A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...
Energy Technology Data Exchange (ETDEWEB)
Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)
2014-10-15
The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.
Next Generation Extended Lagrangian Quantum-based Molecular Dynamics
Negre, Christian
2017-06-01
A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.
Molecular ion acceleration using tandem accelerator
Energy Technology Data Exchange (ETDEWEB)
Saito, Yuichi; Mizuhashi, Kiyoshi; Tajima, Satoshi [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment
1996-12-01
In TIARA compound beam radiation system, cluster beams have been produced using 3 MV tandem accelerator (9SDH-2) to supply them to various radiation on injection experiments. Till now, productions of C{sub 2-8}, Si{sub 2-4} and O{sub 2} and their accelerations up to 6 MeV have been succeeded. This study aimed at production and acceleration of B{sub 2-4} and LiF. Anion clusters were produced using the conventional ion source of cesium sputter type. The proportions of atoms, molecules and clusters elicited from the ion source were varied depending on the material`s properties and the operating conditions of ion source such as sample temperature, sputter voltage and the shape of sample. The anion clusters were accelerated toward the high voltage terminal in the center of tandem accelerator, leading to cations through losing their electrons by the collision to N{sub 2} gas in a charge conversion cell at the terminal. Positively charged cluster ions could be obtained by modulating the pressure of N{sub 2} gas. Thus, B{sub 2} (64 nA), B{sub 3} (4.4 nA) and B{sub 4} (2.7 nA) have been produced and their maximum survival probabilities were higher than those of carbon or silicon clusters. In addition, the relationship between beam current and gas pressure was investigated for Bn (n = 2-4) and LiF. (M.N.)
Thermally driven molecular linear motors - A molecular dynamics study
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence
2009-01-01
We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...
Symbolic mathematical computing: orbital dynamics and application to accelerators
International Nuclear Information System (INIS)
Fateman, R.
1986-01-01
Computer-assisted symbolic mathematical computation has become increasingly useful in applied mathematics. A brief introduction to such capabilitites and some examples related to orbital dynamics and accelerator physics are presented. (author)
International Nuclear Information System (INIS)
Wang Xiaojing; Wang Wei; Han Peilin; Kubo, Momoji; Miyamoto, Akira
2008-01-01
An accelerated quantum chemical molecular dynamical code 'Colors-Excite' was used to investigate the photolysis of alkyl nitrites series, RONO (R=CH 3 and C(CH 3 ) 3 ) on copper surfaces. Our calculations showed that the photo-dissociated processes are associated with the alkyl substituents of RONO when adsorbed on copper surfaces. For R=CH 3 , a two-step photolysis reaction occurred, yielding diverse intermediate products including RO radical, NO, and HNO, consistent with those reported in gas phase. While for R=C(CH 3 ) 3 , only one-step photolysis reaction occurred and gave intermediate products of RO radical and NO. Consequently, pure RO species were achieved to adsorb on metal surfaces by removing the NO species in photolysis reaction. The detailed photo-dissociated behaviors of RONO on copper surfaces with different alkyl substituents which are uncovered by the present simulation can be extended to explain the diverse dissociative mechanism experimentally observed. The quantum chemical molecular dynamical code 'Colors-Excite' is proved to be highly applicable to the photo-dissociations on metal surfaces
Beam-front dynamics and ion acceleration in drifting intense relativistic electron beams
International Nuclear Information System (INIS)
Alexander, K.F.; Hintze, W.
1976-01-01
Collective ion acceleration at the injection of a relativistic electron beam into a low-pressure gas or a plasma is discussed and its strong dependence on the beam-front dynamics is shown. A simple one-dimensional model taking explicitly into account the motion and ionizing action of the ions in the beam-front region is developed for the calculation of the beam drift velocity. The obtained pressure dependence is in good agreement with experimental data. The energy distribution is shown of the ions accelerated in the moving potential well of the space charge region. Scaling laws for the beam-front dynamics and ion acceleration are derived. (J.U.)
Sieberling, S.; Chu, Q.P.; Mulder, J.A.
2010-01-01
This paper presents a flight control strategy based on nonlinear dynamic inversion. The approach presented, called incremental nonlinear dynamic inversion, uses properties of general mechanical systems and nonlinear dynamic inversion by feeding back angular accelerations. Theoretically, feedback of
Energy-aware SQL query acceleration through FPGA-based dynamic partial reconfiguration
Becher, Andreas; Bauer, Florian; Ziener, Daniel; Teich, Jürgen
2014-01-01
In this paper, we propose an approach for energy-aware FPGA-based query acceleration for databases on embedded devices. After the analysis of an incoming query, a query-specific hardware accelerator is generated on-the-fly and loaded on the FPGA for subsequent query execution using partial dynamic
Current-driven dynamics in molecular-scale devices
International Nuclear Information System (INIS)
Seideman, Tamar
2003-01-01
We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)
DROIDS 1.20: A GUI-Based Pipeline for GPU-Accelerated Comparative Protein Dynamics.
Babbitt, Gregory A; Mortensen, Jamie S; Coppola, Erin E; Adams, Lily E; Liao, Justin K
2018-03-13
Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures. Our open-source pipeline, DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a "comparative computational microscope" for observing the biophysical effects of mutations and other chemical changes in proteins. DROIDS implements structural alignment and Benjamini-Hochberg-corrected Kolmogorov-Smirnov statistics to compare nanosecond-scale atom bond fluctuations on the protein backbone, color mapping the significant differences identified in protein MD with single-amino-acid resolution. DROIDS is simple to use, incorporating graphical user interface control for Amber16 MD simulations, cpptraj analysis, and the final statistical and visual representations in R graphics and UCSF Chimera. We demonstrate that DROIDS can be utilized to visually investigate molecular evolution and disease-related functional changes in MD due to genetic mutation and epigenetic modification. DROIDS can also be used to potentially investigate binding interactions of pharmaceuticals, toxins, or other biomolecules in a functional evolutionary context as well. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Molecular Dynamics Studies of Nanofluidic Devices
DEFF Research Database (Denmark)
Zambrano Rodriguez, Harvey Alexander
of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...
The peculiarities of particle dynamics in the Fermi acceleration scheme
International Nuclear Information System (INIS)
Buts, V.A.
2015-01-01
With examples of discrete and distributed mathematical models of the Fermi acceleration mechanism, a usefulness, or even necessity, of taking into account of singular solutions is demonstrated. Also the role is shown of those parts of phase space where the uniqueness theorem conditions to form the dynamics of physical systems are broken. It was found that the dynamics of particles in discrete and distributed mathematical schemes of Fermi acceleration can be significantly different. The difference is due to the fact that the distributed model takes into account the effects of phase space where conditions do not correspond to those necessary for application of the uniqueness theorem. The role of singular solutions is under discussion as well.
Theoretical Concepts in Molecular Photodissociation Dynamics
DEFF Research Database (Denmark)
Henriksen, Niels Engholm
1995-01-01
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...
First principles molecular dynamics without self-consistent field optimization
International Nuclear Information System (INIS)
Souvatzis, Petros; Niklasson, Anders M. N.
2014-01-01
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations
A self-learning algorithm for biased molecular dynamics
Tribello, Gareth A.; Ceriotti, Michele; Parrinello, Michele
2010-01-01
A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences. PMID:20876135
Molecular dynamics and diffusion a compilation
Fisher, David
2013-01-01
The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...
Extended Lagrangian Excited State Molecular Dynamics.
Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N
2018-02-13
An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).
Electron cloud dynamics in the Cornell Electron Storage Ring Test Accelerator wiggler
Directory of Open Access Journals (Sweden)
C. M. Celata
2011-04-01
Full Text Available The interference of stray electrons (also called “electron clouds” with accelerator beams is important in modern intense-beam accelerators, especially those with beams of positive charge. In magnetic wigglers, used, for instance, for transverse emittance damping, the intense synchrotron radiation produced by the beam can generate an electron cloud of relatively high density. In this paper the complicated dynamics of electron clouds in wigglers is examined using the example of a wiggler in the Cornell Electron Storage Ring Test Accelerator experiment at the Cornell Electron Storage Ring. Three-dimensional particle-in-cell simulations with the WARP-POSINST computer code show different density and dynamics for the electron cloud at locations near the maxima of the vertical wiggler field when compared to locations near the minima. Dynamics in these regions, the electron cloud distribution vs longitudinal position, and the beam coherent tune shift caused by the wiggler electron cloud will be discussed.
Advances in molecular vibrations and collision dynamics molecular clusters
Bacic, Zatko
1998-01-01
This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...
Nonlinear dynamics of autonomous vehicles with limits on acceleration
Davis, L. C.
2014-07-01
The stability of autonomous vehicle platoons with limits on acceleration and deceleration is determined. If the leading-vehicle acceleration remains within the limits, all vehicles in the platoon remain within the limits when the relative-velocity feedback coefficient is equal to the headway time constant [k=1/h]. Furthermore, if the sensitivity α>1/h, no collisions occur. String stability for small perturbations is assumed and the initial condition is taken as the equilibrium state. Other values of k and α that give stability with no collisions are found from simulations. For vehicles with non-negligible mechanical response, simulations indicate that the acceleration-feedback-control gain might have to be dynamically adjusted to obtain optimal performance as the response time changes with engine speed. Stability is demonstrated for some perturbations that cause initial acceleration or deceleration greater than the limits, yet do not cause collisions.
Radio Frequency Station - Beam Dynamics Interaction in Circular Accelerators
Energy Technology Data Exchange (ETDEWEB)
Mastoridis, Themistoklis [Stanford Univ., CA (United States)
2010-08-01
The longitudinal beam dynamics in circular accelerators is mainly defined by the interaction of the beam current with the accelerating Radio Frequency (RF) stations. For stable operation, Low Level RF (LLRF) feedback systems are employed to reduce coherent instabilities and regulate the accelerating voltage. The LLRF system design has implications for the dynamics and stability of the closed-loop RF systems as well as for the particle beam, and is very sensitive to the operating range of accelerator currents and energies. Stability of the RF loop and the beam are necessary conditions for reliable machine operation. This dissertation describes theoretical formalisms and models that determine the longitudinal beam dynamics based on the LLRF implementation, time domain simulations that capture the dynamic behavior of the RF station-beam interaction, and measurements from the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC) that validate the models and simulations. These models and simulations are structured to capture the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They also provide the opportunity to study diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Coupled-bunch instabilities and RF station power were the performance limiting effects for PEP-II. The sensitivity of the instabilities to individual LLRF parameters, the effectiveness of alternative operational algorithms, and the possible tradeoffs between RF loop and beam stability were studied. New algorithms were implemented, with significant performance improvement leading to a world record current during the last PEP-II run of 3212 mA for the Low Energy Ring. Longitudinal beam emittance growth due to RF noise is a major concern for LHC
Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...
Indian Academy of Sciences (India)
Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.
Study and realization of an electron linear accelerator. Dynamics of accelerated electrons
International Nuclear Information System (INIS)
Bernard, J.
1966-12-01
The theoretical characteristics of the electron linear accelerator are: 30 MeV for the energy W S and 250 mA for the peak current I c . The main utilization is the intense production of fast neutrons by the reactions (γ,n) and (γ,f) induced in a target of natural uranium by the accelerated electrons. In the first part of the thesis, relative to the study and the realization of the accelerator, a new equation of dispersion is established analytically when the guide is loaded with round-edged irises. The relation is compared with the equation established by CHU and Hansen, WALKINSHAW, KVASIL in the case of a guide loaded with flat-edged irises. The experimental and theoretical curves of dispersion are compared. The accuracy of every relation of dispersion is estimated. The second part of the thesis is relative to the theoretical study of the electrons dynamics in the guide; it allows the derivation of the parameters of the beam: dispersion of phase, energy, dispersion of energy and the relation W S = f (I c ). The results relative to the first experiments are given and compared with the theoretical expectations. (author) [fr
Charged beam dynamics, particle accelerators and free electron lasers
Dattoli, Giuseppe; Sabia, Elio; Artioli, Marcello
2017-01-01
Charged Beam Dynamics, Particle Accelerators and Free Electron Lasers summarises different topics in the field of accelerators and of Free Electron Laser (FEL) devices. It is intended as a reference manual for the different aspects of FEL devices, explaining how to design both a FEL device and the accelerator providing the driving beam. It covers both theoretical and experimental aspects, allowing researchers to attempt a first design of a FEL device in different operating conditions. It provides an analysis of what is already available, what is needed, and what the challenges are to determine new progress in this field. All chapters contain complements and exercises that are designed in such a way that the reader will gradually acquire self-confidence with the matter treated in the book.
Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions
Czech Academy of Sciences Publication Activity Database
Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel
2016-01-01
Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016
Strain-accelerated dynamics of soft colloidal glasses
Agarwal, Praveen
2011-04-11
We have investigated strain-accelerated dynamics of soft glasses theoretically and experimentally. Mechanical rheology measurements performed on a variety of systems reveal evidence for the speeding-up of relaxation at modest shear strains in both step and oscillatory shear flows. Using the soft glassy rheology (SGR) model framework, we show that the observed behavior is a fundamental, but heretofore unexplored attribute of soft glasses. © 2011 American Physical Society.
Visualizing Energy on Target: Molecular Dynamics Simulations
2017-12-01
ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target
Beam Dynamics Studies for a Laser Acceleration Experiment
Spencer, James; Noble, Robert; Palmer, Dennis T; Siemann, Robert
2005-01-01
The NLC Test Accelerator at SLAC was built to address various beam dynamics issues for the Next Linear Collider. An S-Band RF gun, originally proposed for the NLCTA, is being installed together with a large-angle extraction line at 60 MeV. This is followed by a matching section, final focus and buncher for the laser acceleration experiment, E163. The laser-electron interaction area is followed by a broad range, high resolution spectrometer (HES) for electron bunch analysis. The RF gun is discussed in another paper. We discuss only the beam dynamics and high resolution analysis system at 6 MeV based on using Parmela and high-order Transport for bunch charges from 50 pC to 1 nC. Beyond the diagnostics, this system uses the emittance compensating solenoids and a low energy, high resolution spectrometer (LES) to help tune for best operating point and match to the linac. Optical symmetries in the design of the 25.5° extraction line provide 1:1 phase space transfer without linear dispersion or use of sextu...
Nonadiabatic electron wavepacket dynamics behind molecular autoionization
Matsuoka, Takahide; Takatsuka, Kazuo
2018-01-01
A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.
Ultrafast molecular dynamics illuminated with synchrotron radiation
International Nuclear Information System (INIS)
Bozek, John D.; Miron, Catalin
2015-01-01
Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.
Rheology via nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference
Determination of molecular-ion structures through the use of accelerated beams
International Nuclear Information System (INIS)
Gemmell, D.S.
1987-01-01
In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the ''Coulomb-explosion'' technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, has been termed a ''Coulomb explosion.'' 4 refs., 2 figs
Dynamical Aperture Control in Accelerator Lattices With Multipole Potentials
Morozov, I
2017-01-01
We develop tools for symbolic representation of a non-linear accelerator model and analytical methods for description of non-linear dynamics. Information relevant to the dynamic aperture (DA) is then obtained from this model and can be used for indirect DA control or as a complement to direct numerical optimization. We apply two analytical methods and use multipole magnets to satisfy derived analytical constraints. The accelerator model is represented as a product of unperturbed and perturbed exponential operators with the exponent of the perturbed operator given as a power series in the perturbation parameter. Normal forms can be applied to this representation and the lattice parameters are used to control the normal form Hamiltonian and normal form transformation. Hamiltonian control is used to compute a control term or controlled operator. Lattice parameters are then fitted to satisfy the imposed control constraints. Theoretical results, as well as illustrative examples, are presented.
First-principles molecular dynamics for metals
International Nuclear Information System (INIS)
Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.
1989-01-01
A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases
Spin dynamics in storage rings and linear accelerators
Energy Technology Data Exchange (ETDEWEB)
Irwin, J. [Stanford Univ., CA (United States)
1994-12-01
The purpose of these lectures is to survey the subject of spin dynamics in accelerators: to give a sense of the underlying physics, the typical analytic and numeric methods used, and an overview of results achieved. Consideration will be limited to electrons and protons. Examples of experimental and theoretical results in both linear and circular machines are included.
Spin dynamics in storage rings and linear accelerators
International Nuclear Information System (INIS)
Irwin, J.
1994-04-01
The purpose of these lectures is to survey the subject of spin dynamics in accelerators: to give a sense of the underlying physics, the typical analytic and numeric methods used, and an overview of results achieved. Consideration will be limited to electrons and protons. Examples of experimental and theoretical results in both linear and circular machines are included
How Dynamic Visualization Technology Can Support Molecular Reasoning
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
Directory of Open Access Journals (Sweden)
Ly Le
2010-09-01
Full Text Available Oseltamivir (Tamiflu is currently the frontline antiviral drug employed to fight the flu virus in infected individuals by inhibiting neuraminidase, a flu protein responsible for the release of newly synthesized virions. However, oseltamivir resistance has become a critical problem due to rapid mutation of the flu virus. Unfortunately, how mutations actually confer drug resistance is not well understood. In this study, we employ molecular dynamics (MD and steered molecular dynamics (SMD simulations, as well as graphics processing unit (GPU-accelerated electrostatic mapping, to uncover the mechanism behind point mutation induced oseltamivir-resistance in both H5N1 "avian" and H1N1pdm "swine" flu N1-subtype neuraminidases. The simulations reveal an electrostatic binding funnel that plays a key role in directing oseltamivir into and out of its binding site on N1 neuraminidase. The binding pathway for oseltamivir suggests how mutations disrupt drug binding and how new drugs may circumvent the resistance mechanisms.
Physical adsorption and molecular dynamics
International Nuclear Information System (INIS)
Cohan, N.V.
1981-01-01
Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt
Thomas-Fermi molecular dynamics
International Nuclear Information System (INIS)
Clerouin, J.; Pollock, E.L.; Zerah, G.
1992-01-01
A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated
Molecular dynamics for dense matter
International Nuclear Information System (INIS)
Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)
Molecular dynamics for dense matter
Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi
2012-08-01
We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.
International Nuclear Information System (INIS)
Miyamoto, Akira; Sato, Etsuko; Sato, Ryo; Inaba, Kenji; Hatakeyama, Nozomu
2014-01-01
In collaboration with experimental experts we have reported in the present conference (Hatakeyama, N. et al., “Experiment-integrated multi-scale, multi-physics computational chemistry simulation applied to corrosion behaviour of BWR structural materials”) the results of multi-scale multi-physics computational chemistry simulations applied to the corrosion behaviour of BWR structural materials. In macro-scale, a macroscopic simulator of anode polarization curve was developed to solve the spatially one-dimensional electrochemical equations on the material surface in continuum level in order to understand the corrosion behaviour of typical BWR structural material, SUS304. The experimental anode polarization behaviours of each pure metal were reproduced by fitting all the rates of electrochemical reactions and then the anode polarization curve of SUS304 was calculated by using the same parameters and found to reproduce the experimental behaviour successfully. In meso-scale, a kinetic Monte Carlo (KMC) simulator was applied to an actual-time simulation of the morphological corrosion behaviour under the influence of an applied voltage. In micro-scale, an ultra-accelerated quantum chemical molecular dynamics (UA-QCMD) code was applied to various metallic oxide surfaces of Fe 2 O 3 , Fe 3 O 4 , Cr 2 O 3 modelled as same as water molecules and dissolved metallic ions on the surfaces, then the dissolution and segregation behaviours were successfully simulated dynamically by using UA-QCMD. In this paper we describe details of the multi-scale, multi-physics computational chemistry method especially the UA-QCMD method. This method is approximately 10,000,000 times faster than conventional first-principles molecular dynamics methods based on density-functional theory (DFT), and the accuracy was also validated for various metals and metal oxides compared with DFT results. To assure multi-scale multi-physics computational chemistry simulation based on the UA-QCMD method for
Energy Technology Data Exchange (ETDEWEB)
Lee, S. Y. [Indiana Univ., Bloomington, IN (United States)
2014-04-07
We had carried out a design of an ultimate storage ring with beam emittance less than 10 picometer for the feasibility of coherent light source at X-ray wavelength. The accelerator has an inherent small dynamic aperture. We study method to improve the dynamic aperture and collective instability for an ultimate storage ring. Beam measurement and accelerator modeling are an integral part of accelerator physics. We develop the independent component analysis (ICA) and the orbit response matrix method for improving accelerator reliability and performance. In collaboration with scientists in National Laboratories, we also carry out experimental and theoretical studies on beam dynamics. Our proposed research topics are relevant to nuclear and particle physics using high brightness particle and photon beams.
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
International Nuclear Information System (INIS)
Chiba, Satoshi; Niita, Koji; Maruyama, Toshiki; Fukahori, Tokio; Takada, Hiroshi; Iwamoto, Akira
1995-01-01
The double-differential (p,xp') and (p,xn) reaction cross sections of 58 Ni and 90 Zr in the energy range from 120 to 200 MeV have been studied in terms of the Quantum Molecular Dynamics. It was found that the present calculation could give a quantitative explanation of experimentally observed values of both channels simultaneously without adjusting any parameter, showing the usefulness of the QMD approach to study the pre-equilibrium process in this energy region. Comparisons were also made with prediction of other theories such as Antisymmetrized Molecular Dynamics (AMD) and semiclassical distorted wave theory. Effect of the anti-symmetrization, which is in AMD but not in QMD, was found surprisingly small, being the result of QMD even slightly better. At the same time, it was found that the present calculation does not give the quasi-free peak of the 1-step cross sections similar to the semiclassical model, due probably to different treatment of the refraction and acceleration effects caused by the mean field. (author)
Beam and spin dynamics of hadron beams in intermediate-energy ring accelerators
International Nuclear Information System (INIS)
Lehrach, Andreas
2008-01-01
In this thesis beam and spin dynamics of ring accelerators are described. After a general theoretical treatment methods for the beam optimization and polarization conservation are discussed. Then experiments on spin manipulation at the COSY facility are considered. Finally the beam simulation and accelerator lay-out for the HESR with regards to the FAIR experiment are described. (HSI)
Molecular dynamics with deterministic and stochastic numerical methods
Leimkuhler, Ben
2015-01-01
This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...
Molecular ions, Rydberg spectroscopy and dynamics
International Nuclear Information System (INIS)
Jungen, Ch.
2015-01-01
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering
Molecular ions, Rydberg spectroscopy and dynamics
Energy Technology Data Exchange (ETDEWEB)
Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)
2015-01-22
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.
Analytical estimation of the dynamic apertures of circular accelerators
International Nuclear Information System (INIS)
Gao, J.
2000-02-01
By considering delta function sextupole, octupole, and deca-pole perturbations and using difference action-angle variable equations, we find some useful analytical formulae for the estimation of the dynamic apertures of circular accelerators due to single sextupole, single octupole, single deca-pole (single 2 m pole in general). Their combined effects are derived based on the Chirikov criterion of the onset of stochastic motions. Comparisons with numerical simulations are made, and the agreement is quite satisfactory. These formulae have been applied to determine the beam-beam limited dynamic aperture in a circular collider. (author)
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
Directory of Open Access Journals (Sweden)
Renata De Paris
2015-01-01
Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.
Model Independent Analysis of Beam Centroid Dynamics in Accelerators
International Nuclear Information System (INIS)
Wang, Chun-xi
2003-01-01
Fundamental issues in Beam-Position-Monitor (BPM)-based beam dynamics observations are studied in this dissertation. The major topic is the Model-Independent Analysis (MIA) of beam centroid dynamics. Conventional beam dynamics analysis requires a certain machine model, which itself of ten needs to be refined by beam measurements. Instead of using any particular machine model, MIA relies on a statistical analysis of the vast amount of BPM data that often can be collected non-invasively during normal machine operation. There are two major parts in MIA. One is noise reduction and degrees-of-freedom analysis using a singular value decomposition of a BPM-data matrix, which constitutes a principal component analysis of BPM data. The other is a physical base decomposition of the BPM-data matrix based on the time structure of pulse-by-pulse beam and/or machine parameters. The combination of these two methods allows one to break the resolution limit set by individual BPMs and observe beam dynamics at more accurate levels. A physical base decomposition is particularly useful for understanding various beam dynamics issues. MIA improves observation and analysis of beam dynamics and thus leads to better understanding and control of beams in both linacs and rings. The statistical nature of MIA makes it potentially useful in other fields. Another important topic discussed in this dissertation is the measurement of a nonlinear Poincare section (one-turn) map in circular accelerators. The beam dynamics in a ring is intrinsically nonlinear. In fact, nonlinearities are a major factor that limits stability and influences the dynamics of halos. The Poincare section map plays a basic role in characterizing and analyzing such a periodic nonlinear system. Although many kinds of nonlinear beam dynamics experiments have been conducted, no direct measurement of a nonlinear map has been reported for a ring in normal operation mode. This dissertation analyzes various issues concerning map
Model Independent Analysis of Beam Centroid Dynamics in Accelerators
Energy Technology Data Exchange (ETDEWEB)
Wang, Chun-xi
2003-04-21
Fundamental issues in Beam-Position-Monitor (BPM)-based beam dynamics observations are studied in this dissertation. The major topic is the Model-Independent Analysis (MIA) of beam centroid dynamics. Conventional beam dynamics analysis requires a certain machine model, which itself of ten needs to be refined by beam measurements. Instead of using any particular machine model, MIA relies on a statistical analysis of the vast amount of BPM data that often can be collected non-invasively during normal machine operation. There are two major parts in MIA. One is noise reduction and degrees-of-freedom analysis using a singular value decomposition of a BPM-data matrix, which constitutes a principal component analysis of BPM data. The other is a physical base decomposition of the BPM-data matrix based on the time structure of pulse-by-pulse beam and/or machine parameters. The combination of these two methods allows one to break the resolution limit set by individual BPMs and observe beam dynamics at more accurate levels. A physical base decomposition is particularly useful for understanding various beam dynamics issues. MIA improves observation and analysis of beam dynamics and thus leads to better understanding and control of beams in both linacs and rings. The statistical nature of MIA makes it potentially useful in other fields. Another important topic discussed in this dissertation is the measurement of a nonlinear Poincare section (one-turn) map in circular accelerators. The beam dynamics in a ring is intrinsically nonlinear. In fact, nonlinearities are a major factor that limits stability and influences the dynamics of halos. The Poincare section map plays a basic role in characterizing and analyzing such a periodic nonlinear system. Although many kinds of nonlinear beam dynamics experiments have been conducted, no direct measurement of a nonlinear map has been reported for a ring in normal operation mode. This dissertation analyzes various issues concerning map
A Framework for Dynamically-Loaded Hardware Library (HLL) in FPGA Acceleration
DEFF Research Database (Denmark)
Cardarilli, Gian Carlo; Di Carlo, Leonardo; Nannarelli, Alberto
2016-01-01
Hardware acceleration is often used to address the need for speed and computing power in embedded systems. FPGAs always represented a good solution for HW acceleration and, recently, new SoC platforms extended the flexibility of the FPGAs by combining on a single chip both high-performance CPUs...... and FPGA fabric. The aim of this work is the implementation of hardware accelerators for these new SoCs. The innovative feature of these accelerators is the on-the-fly reconfiguration of the hardware to dynamically adapt the accelerator’s functionalities to the current CPU workload. The realization...... of the accelerators preliminarily requires also the profiling of both the SW (ARM CPU + NEON Units) and HW (FPGA) performance, an evaluation of the partial reconfiguration times and the development of an applicationspecific IP-cores library. This paper focuses on the profiling aspect of both the SW and HW...
Babbitt, Gregory A; Coppola, Erin E; Mortensen, Jamie S; Ekeren, Patrick X; Viola, Cosmo; Goldblatt, Dallan; Hudson, André O
2018-02-01
Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of 'dual-use' codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA's helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties. How such structural optimization of the code within eukaryotic chromatin could have arisen from an RNA world is a mystery, but would imply some preadaptation in an RNA context. We analyzed synonymous (protein-silent) and nonsynonymous (protein-altering) mutational impacts on molecular dynamics in 13823 identically degenerate alternative codon reorganizations, defined by codon transitions in 7680 GPU-accelerated molecular dynamic simulations of implicitly and explicitly solvated double-stranded aRNA and bDNA structures. When compared to all possible alternative codon assignments, the standard genetic code minimized the impact of synonymous mutations on the random atomic fluctuations and correlations of carbon backbone vector trajectories while facilitating the specific movements that contribute to DNA polymer flexibility. This trend was notably stronger in the context of RNA supporting the idea that dual-use codon optimization and informational multiplexing in DNA resulted from the preadaptation of the RNA duplex to resist changes to thermostability. The nonrandom and divergent molecular dynamics of synonymous mutations also imply that the triplet-based code may have resulted from adaptive functional expansion enabling a primordial doublet code to multiplex gene regulatory information via the shape and charge of the minor groove.
How to combine binary collision approximation and multi-body potential for molecular dynamics
International Nuclear Information System (INIS)
Saito, Seiki; Nakamura, Hiroaki; Takayama, Arimichi; Ito, Atsushi M.; Kenmotsu, Takahiro
2010-01-01
Our group has been developing a hybrid simulation of the molecular dynamics (MD) and the binary collision approximation (BCA) simulation. One of the main problems of this hybridization model is that the multi-body potential suddenly appears at the moment when the simulation method switches from the BCA to the MD. This instantaneously emerged multi-body potential causes the acceleration or deceleration of atoms of the system. To solve this problem, the kinetic energy of atoms should be corrected to conserve the total energy in the system. This paper gives the solution. The hybrid simulation for hydrogen atom injection into a graphite material is executed in order to demonstrate the solution. (author)
A fermionic molecular dynamics technique to model nuclear matter
International Nuclear Information System (INIS)
Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.
2009-01-01
Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)
Dynamical photo-induced electronic properties of molecular junctions
Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.
2018-03-01
Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.
Dynamical processes in atomic and molecular physics
Ogurtsov, Gennadi
2012-01-01
Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece
Longitudinal and transverse dynamics of ions from residual gas in an electron accelerator
Gamelin, A.; Bruni, C.; Radevych, D.
2018-05-01
The ion cloud produced from residual gas in an electron accelerator can degrade machine performances and produce instabilities. The ion dynamics in an accelerator is governed by the beam-ion interaction, magnetic fields and eventual mitigation strategies. Due to the fact that the beam has a nonuniform transverse size along its orbit, the ions move longitudinally and accumulate naturally at some points in the accelerator. In order to design effective mitigation strategies it is necessary to understand the ion dynamics not only in the transverse plane but also in the longitudinal direction. After introducing the physics behind the beam-ion interaction, we show how to get accumulation points for a realistic electron storage ring lattice. Simulations of the ion cloud dynamics, including the effect of magnetic fields on the ions, clearing electrodes and clearing gaps are shown. Longitudinal ion trapping due to the magnetic mirror effect in the dipole fringe fields is also detailed. Finally, the effectiveness of clearing electrode using longitudinal clearing fields is discussed and compared to clearing electrodes producing transverse field only.
Theory and application of quantum molecular dynamics
Zeng Hui Zhang, John
1999-01-01
This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli
Dynamics and Thermodynamics of Molecular Machines
DEFF Research Database (Denmark)
Golubeva, Natalia
2014-01-01
to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...
Grandy, A Stuart; Neff, Jason C
2008-10-15
Advances in spectroscopic and other chemical methods have greatly enhanced our ability to characterize soil organic matter chemistry. As a result, the molecular characteristics of soil C are now known for a range of ecosystems, soil types, and management intensities. Placing this knowledge into a broader ecological and management context is difficult, however, and remains one of the fundamental challenges of soil organic matter research. Here we present a conceptual model of molecular soil C dynamics to stimulate inter-disciplinary research into the ecological implications of molecular C turnover and its management- and process-level controls. Our model describes three properties of soil C dynamics: 1) soil size fractions have unique molecular patterns that reflect varying degrees of biological and physical control over decomposition; 2) there is a common decomposition sequence independent of plant inputs or other ecosystem properties; and 3) molecular decomposition sequences, although consistent, are not uniform and can be altered by processes that accelerate or slow the microbial transformation of specific molecules. The consequences of this model include several key points. First, lignin presents a constraint to decomposition of plant litter and particulate C (>53 microm) but exerts little influence on more stable mineral-associated soil fractions stabilized onto mineral fractions has a distinct composition related more to microbially processed organic matter than to plant-related compounds. Third, disturbances, such as N fertilization and tillage, which alter decomposition rates, can have "downstream effects"; that is, a disturbance that directly alters the molecular dynamics of particulate C may have a series of indirect effects on C stabilization in silt and clay fractions.
Beam dynamics studies of the Heavy Ion Fusion Accelerator injector
International Nuclear Information System (INIS)
Henestroza, E.; Yu, S.S.; Eylon, S.
1995-04-01
A driver-scale injector for the Heavy Ion Fusion Accelerator project has been built at LBL. This machine has exceeded the design goals of high voltage (> 2 MV), high current (> 0.8 A of K + ) and low normalized emittance (< 1 π mm-mr). The injector consists of a 750 keV diode pre-injector followed by an electrostatic quadrupole accelerator (ESQ) which provides strong (alternating gradient) focusing for the space-charge dominated beam and simultaneously accelerates the ions to 2 MeV. The fully 3-D PIC code WARP together with EGUN and POISSON were used to design the machine and analyze measurements of voltage, current and phase space distributions. A comparison between beam dynamics characteristics as measured for the injector and corresponding computer calculations will be presented
International Nuclear Information System (INIS)
Ito, Yuki; Jung, Changho; Luo, Yi; Koyama, Michihisa; Endou, Akira; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira
2006-01-01
Recently, we have developed a new tight-binding quantum chemical molecular dynamics program 'Colors' for combinatorial computational chemistry approach. This methodology is based on our original tight-binding approximation and realized over 5000 times acceleration compared to the conventional first-principles molecular dynamics method. In the present study, we applied our new program to the simulations on various realistic large-scale models of the automotive three-way catalysts, ultrafine Pt particle/CeO 2 (111) support. Significant electron transfer from the Pt particle to the CeO 2 (111) surface was observed and it was found to strongly depend on the size of the Pt particle. Furthermore, our simulation results suggest that the reduction of the Ce atom due to the electron transfer from the Pt particle to the CeO 2 surface is a main reason for the strong interaction of the Pt particle and CeO 2 (111) support
Dynamic signature of molecular association in methanol
International Nuclear Information System (INIS)
Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.
2016-01-01
Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.
Molecular dynamics for fermions
International Nuclear Information System (INIS)
Feldmeier, H.; Schnack, J.
2000-02-01
The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)
Pattern recognition in molecular dynamics. [FORTRAN
Energy Technology Data Exchange (ETDEWEB)
Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)
1977-07-01
An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.
Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation
Institute of Scientific and Technical Information of China (English)
Chengzhen Sun; Bofeng Bai
2017-01-01
Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.
Classical and quantum molecular dynamics in NMR spectra
Szymański, Sławomir
2018-01-01
The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...
Multiscale equation-free algorithms for molecular dynamics
Abi Mansour, Andrew
Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.
Scalable Molecular Dynamics for Large Biomolecular Systems
Directory of Open Access Journals (Sweden)
Robert K. Brunner
2000-01-01
Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.
Podbielska, Halina; Kasprzak, Henryk T.; Voloshin, Arkady S.; Pennig, Dietmar; von Bally, Gert
1992-08-01
The unilateral axially dynamic fixator (Orthofix) was mounted on a sheep tibial shaft. Three fixation modes: static, dynamic controlled, and dynamic free were examined by means of double exposure holographic interferometry. Simultaneously, the acceleration was measured by an accelerometer and displayed on the monitor together with loading characteristics. The first exposure was made before the acting force was applied to the tibia plateau. The second one after the moment when the acceleration wave started to propagate through the specimen. We stated that in the case of dynamization less torsion occurs at the fracture site. So far, we have not been able to determine any correlation between results of holographic and accelerometric measurements.
Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors
Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery
2015-05-01
Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.
Molecular quantum dynamics. From theory to applications
International Nuclear Information System (INIS)
Gatti, Fabien
2014-01-01
An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the
Molecular quantum dynamics. From theory to applications
Energy Technology Data Exchange (ETDEWEB)
Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253
2014-09-01
An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible
Excited-state molecular photoionization dynamics
International Nuclear Information System (INIS)
Pratt, S.T.
1995-01-01
This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)
Symmetry of quantum molecular dynamics
International Nuclear Information System (INIS)
Burenin, A.V.
2002-01-01
The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru
Dynamic Monte Carlo simulations of radiatively accelerated GRB fireballs
Chhotray, Atul; Lazzati, Davide
2018-05-01
We present a novel Dynamic Monte Carlo code (DynaMo code) that self-consistently simulates the Compton-scattering-driven dynamic evolution of a plasma. We use the DynaMo code to investigate the time-dependent expansion and acceleration of dissipationless gamma-ray burst fireballs by varying their initial opacities and baryonic content. We study the opacity and energy density evolution of an initially optically thick, radiation-dominated fireball across its entire phase space - in particular during the Rph matter-dominated fireballs due to Thomson scattering. We quantify the new phases by providing analytical expressions of Lorentz factor evolution, which will be useful for deriving jet parameters.
Molecular dynamics modeling of polymer flammability
International Nuclear Information System (INIS)
Nyden, M.R.; Brown, J.E.; Lomakin, S.M.
1992-01-01
Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)
Institute of Scientific and Technical Information of China (English)
呼义翔; 雷天时; 吴撼宇; 郭宁; 韩娟娟; 邱爱慈; 王亮平; 黄涛; 丛培天; 张信军; 李岩; 曾正中; 孙铁平
2011-01-01
The transmission-line-circuit model of the Z accelerator, developed originally by W. A. STYGAR, P. A. CORCORAN, et al., is revised. The revised model uses different calculations for the electron loss and flow impedance in the magnetically insulated transmission line system of the Z accelerator before and after magnetic insulation is established. By including electron pressure and zero electric field at the cathode, a closed set of equations is obtained at each time step, and dynamic shunt resistance （used to represent any electron loss to the anode） and flow impedance are solved, which have been incorporated into the transmission line code for simulations of the vacuum section in the Z accelerator. Finally, the results are discussed in comparison with earlier findings to show the effectiveness and limitations of the model.
Electron-nuclear dynamics of molecular systems
International Nuclear Information System (INIS)
Diz, A.; Oehrn, Y.
1994-01-01
The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions
International Nuclear Information System (INIS)
Tygier, S.; Appleby, R.B.; Garland, J.M.; Hock, K.; Owen, H.; Kelliher, D.J.; Sheehy, S.L.
2015-01-01
We present PyZgoubi, a framework that has been developed based on the tracking engine Zgoubi to model, optimise and visualise the dynamics in particle accelerators, especially fixed-field alternating-gradient (FFAG) accelerators. We show that PyZgoubi abstracts Zgoubi by wrapping it in an easy-to-use Python framework in order to allow simple construction, parameterisation, visualisation and optimisation of FFAG accelerator lattices. Its object oriented design gives it the flexibility and extensibility required for current novel FFAG design. We apply PyZgoubi to two example FFAGs; this includes determining the dynamic aperture of the PAMELA medical FFAG in the presence of magnet misalignments, and illustrating how PyZgoubi may be used to optimise FFAGs. We also discuss a robust definition of dynamic aperture in an FFAG and show its implementation in PyZgoubi
Energy Technology Data Exchange (ETDEWEB)
Tygier, S., E-mail: sam.tygier@hep.manchester.ac.uk [Cockcroft Accelerator Group, The University of Manchester (United Kingdom); Appleby, R.B., E-mail: robert.appleby@manchester.ac.uk [Cockcroft Accelerator Group, The University of Manchester (United Kingdom); Garland, J.M. [Cockcroft Accelerator Group, The University of Manchester (United Kingdom); Hock, K. [University of Liverpool (United Kingdom); Owen, H. [Cockcroft Accelerator Group, The University of Manchester (United Kingdom); Kelliher, D.J.; Sheehy, S.L. [STFC Rutherford Appleton Laboratory (United Kingdom)
2015-03-01
We present PyZgoubi, a framework that has been developed based on the tracking engine Zgoubi to model, optimise and visualise the dynamics in particle accelerators, especially fixed-field alternating-gradient (FFAG) accelerators. We show that PyZgoubi abstracts Zgoubi by wrapping it in an easy-to-use Python framework in order to allow simple construction, parameterisation, visualisation and optimisation of FFAG accelerator lattices. Its object oriented design gives it the flexibility and extensibility required for current novel FFAG design. We apply PyZgoubi to two example FFAGs; this includes determining the dynamic aperture of the PAMELA medical FFAG in the presence of magnet misalignments, and illustrating how PyZgoubi may be used to optimise FFAGs. We also discuss a robust definition of dynamic aperture in an FFAG and show its implementation in PyZgoubi.
Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.
Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N
2015-04-21
Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.
Dynamics of molecular superrotors in an external magnetic field
Korobenko, Aleksey; Milner, Valery
2015-08-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.
Candidate molten salt investigation for an accelerator driven subcritical core
International Nuclear Information System (INIS)
Sooby, E.; Baty, A.; Beneš, O.; McIntyre, P.; Pogue, N.; Salanne, M.; Sattarov, A.
2013-01-01
Highlights: • Developing accelerator driven subcritical fission to destroy transuranics in SNF. • The core is a vessel containing a molten mixture of NaCl and transuranic chlorides. • Molecular dynamics used to calculate the thermophysical properties of the salt. • Density and molecular structure for actinide salts reported here. • The neutronics of ADS fission in molten salt are presented. -- Abstract: We report a design for accelerator-driven subcritical fission in a molten salt core (ADSMS) that utilizes a fuel salt composed of NaCl and transuranic (TRU) chlorides. The ADSMS core is designed for fast neutronics (28% of neutrons >1 MeV) to optimize TRU destruction. The choice of a NaCl-based salt offers benefits for corrosion, operating temperature, and actinide solubility as compared with LiF-based fuel salts. A molecular dynamics (MD) code has been used to estimate properties of the molten salt system which are important for ADSMS design but have never been measured experimentally. Results from the MD studies are reported. Experimental measurements of fuel salt properties and studies of corrosion and radiation damage on candidate metals for the core vessel are anticipated
Candidate molten salt investigation for an accelerator driven subcritical core
Energy Technology Data Exchange (ETDEWEB)
Sooby, E., E-mail: soobyes@tamu.edu [Texas A and M University, Accelerator Research Laboratory, 3380 University Dr. East, College Station, TX 77845 (United States); Baty, A. [Texas A and M University, Accelerator Research Laboratory, 3380 University Dr. East, College Station, TX 77845 (United States); Beneš, O. [European Commission, DG Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, 76125 Karlsruhe (Germany); McIntyre, P.; Pogue, N. [Texas A and M University, Accelerator Research Laboratory, 3380 University Dr. East, College Station, TX 77845 (United States); Salanne, M. [Université Pierre et Marie Curie, CNRS, Laboratoire PECSA, F-75005 Paris (France); Sattarov, A. [Texas A and M University, Accelerator Research Laboratory, 3380 University Dr. East, College Station, TX 77845 (United States)
2013-09-15
Highlights: • Developing accelerator driven subcritical fission to destroy transuranics in SNF. • The core is a vessel containing a molten mixture of NaCl and transuranic chlorides. • Molecular dynamics used to calculate the thermophysical properties of the salt. • Density and molecular structure for actinide salts reported here. • The neutronics of ADS fission in molten salt are presented. -- Abstract: We report a design for accelerator-driven subcritical fission in a molten salt core (ADSMS) that utilizes a fuel salt composed of NaCl and transuranic (TRU) chlorides. The ADSMS core is designed for fast neutronics (28% of neutrons >1 MeV) to optimize TRU destruction. The choice of a NaCl-based salt offers benefits for corrosion, operating temperature, and actinide solubility as compared with LiF-based fuel salts. A molecular dynamics (MD) code has been used to estimate properties of the molten salt system which are important for ADSMS design but have never been measured experimentally. Results from the MD studies are reported. Experimental measurements of fuel salt properties and studies of corrosion and radiation damage on candidate metals for the core vessel are anticipated.
Femtochemistry and femtobiology ultrafast dynamics in molecular science
Douhal, Abderrazzak
2002-01-01
This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol
Dynamic behavior of IREB in a collective ion acceleration experiment
International Nuclear Information System (INIS)
Fine, T.A.; Rhee, M.J.
1989-01-01
The authors report an experimental study of dynamic behavior of net current in conjunction with collective ion acceleration. In the presence of neutral gas, either puffed in or released from the anode foil, the IREB injected is subject to the charge and current neutralizations, resulting in a complicated time and space dependent beam distribution in the drift tube. To investigate the dynamic behavior of the current in the drift tube, typically a 0.5 MeV, 70 kA, 100 ns electron beam of 2.54 cm diam is injected through a foil anode into a drift tube of 15 cm diam. Reproducibility of experiment was improved by using a specially designed anode system with a foil changer which allowed the production of many shots of high current electron beam without disturbing the vacuum condition. The net currents were measured by a Rogowski coil built in the anode system, and a movable Faraday cup along the drift tube. The ions accelerated were diagnosed mainly by a Thomson spectrometer system placed at the end of the drift tube
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu
2011-01-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We
Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water
DEFF Research Database (Denmark)
Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore
2010-01-01
We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...
Dynamic analysis of an accelerator-based subcritical radioactive waste burning system
International Nuclear Information System (INIS)
Woosley, M.L. Jr.; Rydin, R.A.
1997-01-01
There has been a recent revival of interest in accelerator-driven subcritical fluid-fueled systems for radioactive waste management. This motivates the need for dynamic analysis of the nuclear kinetics of such systems. A physical description of the Los Alamos Accelerator-Based Conversion (ABC) concept is provided. This system is used as the basis for the kinetic study in this research. The current approach to the dynamic simulation of an accelerator-driven subcritical fluid-fueled system includes four functional blocks: A discrete ordinates model is used to calculate the flux distribution for the source-driven system (DORT); A nodal convection model is used to calculate time-dependent isotope and temperature distributions which impact reactivity (ABCcore); A nodal importance weighting model is used to calculate the reactivity impact of temperature and isotope distributions and to feed this information back to the time-dependent nodal convection model (ABCvip); A transient driver simulates system transients and records simulation data (ABCtrans). Specific transients which have been analyzed with the current modeling system are discussed. These transients include loss-of-flow and loss-of-cooling accidents, xenon and samarium transients, and cold-plug and overfueling events. The results of various transients have uncovered unpredictable behavior, unresolved design issues, and the need for active control. 11 refs., 6 figs., 1 tab
Gender differences in head-neck segment dynamic stabilization during head acceleration.
Tierney, Ryan T; Sitler, Michael R; Swanik, C Buz; Swanik, Kathleen A; Higgins, Michael; Torg, Joseph
2005-02-01
Recent epidemiological research has revealed that gender differences exist in concussion incidence but no study has investigated why females may be at greater risk of concussion. Our purpose was to determine whether gender differences existed in head-neck segment kinematic and neuromuscular control variables responses to an external force application with and without neck muscle preactivation. Forty (20 females and 20 males) physically active volunteers participated in the study. The independent variables were gender, force application (known vs unknown), and force direction (forced flexion vs forced extension). The dependent variables were kinematic and EMG variables, head-neck segment stiffness, and head-neck segment flexor and extensor isometric strength. Statistical analyses consisted of multiple multivariate and univariate analyses of variance, follow-up univariate analyses of variance, and t-tests (P Gender differences existed in head-neck segment dynamic stabilization during head angular acceleration. Females exhibited significantly greater head-neck segment peak angular acceleration (50%) and displacement (39%) than males despite initiating muscle activity significantly earlier (SCM only) and using a greater percentage of their maximum head-neck segment muscle activity (79% peak activity and 117% muscle activity area). The head-neck segment angular acceleration differences may be because females exhibited significantly less isometric strength (49%), neck girth (30%), and head mass (43%), resulting in lower levels of head-neck segment stiffness (29%). For our subject demographic, the results revealed gender differences in head-neck segment dynamic stabilization during head acceleration in response to an external force application. Females exhibited significantly greater head-neck segment peak angular acceleration and displacement than males despite initiating muscle activity earlier (SCM only) and using a greater percentage of their maximum head-neck segment
Dynamics of molecular superrotors in an external magnetic field
International Nuclear Information System (INIS)
Korobenko, Aleksey; Milner, Valery
2015-01-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)
The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation
Chen, Jundong
2018-03-01
Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.
Kinetics from Replica Exchange Molecular Dynamics Simulations.
Stelzl, Lukas S; Hummer, Gerhard
2017-08-08
Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.
DEFF Research Database (Denmark)
Papaleo, Elena
2015-01-01
that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....
AceCloud: Molecular Dynamics Simulations in the Cloud.
Harvey, M J; De Fabritiis, G
2015-05-26
We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.
Molecular dynamics simulations of RNA motifs
Czech Academy of Sciences Publication Activity Database
Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.
2002-01-01
Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics
ACCELERATORS: Nonlinear dynamics in Sardinia
International Nuclear Information System (INIS)
Anon.
1985-01-01
In the last few years, two schools devoted to accelerator physics have been set up, one on either side of the Atlantic. The US School on High Energy Particle Accelerators has organized Summer Schools on the physics of particle accelerators, hosted by the major American Laboratories, each year since 1981
ACCELERATORS: Nonlinear dynamics in Sardinia
Energy Technology Data Exchange (ETDEWEB)
Anon.
1985-05-15
In the last few years, two schools devoted to accelerator physics have been set up, one on either side of the Atlantic. The US School on High Energy Particle Accelerators has organized Summer Schools on the physics of particle accelerators, hosted by the major American Laboratories, each year since 1981.
Monte Carlo-molecular dynamics simulations for two-dimensional magnets
International Nuclear Information System (INIS)
Kawabata, C.; takeuchi, M.; Bishop, A.R.
1985-01-01
A combined Monte Carlo-molecular dynamics simulation technique is used to study the dynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians
Molecular dynamics and Monte Carlo calculations in statistical mechanics
International Nuclear Information System (INIS)
Wood, W.W.; Erpenbeck, J.J.
1976-01-01
Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references
International Nuclear Information System (INIS)
Jing Yuhang; Meng Qingyuan; Zhao Wei
2009-01-01
Molecular dynamics simulations are performed to investigate the interaction between 60 deg. shuffle dislocation and tetrainterstitial (I 4 ) cluster in silicon, using Stillinger-Weber (SW) potential to calculate the interatomic forces. Based on Parrinello-Rahman method, shear stress is exerted on the model to move the dislocation. Simulation results show that the I 4 cluster can bend the dislocation line and delay the dislocation movement. During the course of intersection the dislocation line sections relatively far away from the I 4 cluster accelerate first, and then decelerate. The critical shear stress unpinning the 60 deg. dislocation from the I 4 cluster decreases as the temperature increases in the models.
Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties
Czech Academy of Sciences Publication Activity Database
Fojtíková, J.; Kalvoda, L.; Sedlák, Petr
2015-01-01
Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf
Nanotribology investigations with classical molecular dynamics
Solhjoo, Soheil
2017-01-01
This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:
Klvana, Martin; Pavlova, Martina; Koudelakova, Tana; Chaloupkova, Radka; Dvorak, Pavel; Prokop, Zbynek; Stsiapanava, Alena; Kuty, Michal; Kuta-Smatanova, Ivana; Dohnalek, Jan; Kulhanek, Petr; Wade, Rebecca C; Damborsky, Jiri
2009-10-09
Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein X-ray crystallography, were constructed and biochemically characterized. The mutants showed distinct catalytic efficiencies with the halogenated substrate 1,2,3-trichloropropane. Release pathways for the two dehalogenation products, 2,3-dichloropropane-1-ol and the chloride ion, and exchange pathways for water molecules, were studied using classical and random acceleration molecular dynamics simulations. Five different pathways, denoted p1, p2a, p2b, p2c, and p3, were identified. The individual pathways showed differing selectivity for the products: the chloride ion releases solely through p1, whereas the alcohol releases through all five pathways. Water molecules play a crucial role for release of both products by breakage of their hydrogen-bonding interactions with the active-site residues and shielding the charged chloride ion during its passage through a hydrophobic tunnel. Exchange of the chloride ions, the alcohol product, and the waters between the buried active site and the bulk solvent can be realized by three different mechanisms: (i) passage through a permanent tunnel, (ii) passage through a transient tunnel, and (iii) migration through a protein matrix. We demonstrate that the accessibility of the pathways and the mechanisms of ligand exchange were modified by mutations. Insertion of bulky aromatic residues in the tunnel corresponding to pathway p1 leads to reduced accessibility to the ligands and a change in mechanism of opening from permanent to transient. We propose that engineering the accessibility of tunnels and the mechanisms of ligand exchange is a powerful strategy for modification of the functional properties of enzymes with buried active sites.
International Nuclear Information System (INIS)
Levine, Benjamin G.; Stone, John E.; Kohlmeyer, Axel
2011-01-01
The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.
Electron-beam dynamics for an advanced flash-radiography accelerator
Energy Technology Data Exchange (ETDEWEB)
Ekdahl, Carl August Jr. [Los Alamos National Laboratory
2015-06-22
Beam dynamics issues were assessed for a new linear induction electron accelerator. Special attention was paid to equilibrium beam transport, possible emittance growth, and beam stability. Especially problematic would be high-frequency beam instabilities that could blur individual radiographic source spots, low-frequency beam motion that could cause pulse-to-pulse spot displacement, and emittance growth that could enlarge the source spots. Beam physics issues were examined through theoretical analysis and computer simulations, including particle-in cell (PIC) codes. Beam instabilities investigated included beam breakup (BBU), image displacement, diocotron, parametric envelope, ion hose, and the resistive wall instability. Beam corkscrew motion and emittance growth from beam mismatch were also studied. It was concluded that a beam with radiographic quality equivalent to the present accelerators at Los Alamos will result if the same engineering standards and construction details are upheld.
Tissue compensation using dynamic collimation on a linear accelerator
International Nuclear Information System (INIS)
Gaballa, Hani E.; Mitev, George; Zwicker, Robert D.; Ting, Joseph Y.; Tercilla, Oscar F.
1995-01-01
Purpose: The availability of computer-controlled collimators on some accelerators has led to techniques for dynamic beam modification, mainly to simulate beam wedge filters. This work addresses the practical aspects of dynamic tissue compensation in one dimension using available treatment-planning software. Methods and Materials: Data derived from the treatment-planning program is used with an iterative calculational routine to determine the monitor unit settings needed for the collimator-controlling computer. The method was first tested by simulating a 60 deg. physical wedge. Further studies were carried out on a specially fabricated plastic phantom that modeled the sagittal contour of the upper torso, neck, and lower head regions. Results: Dynamic wedge point doses generated by the planning program agreed within 1% with the values directly measured in a polystyrene phantom. In the patient phantom, dynamic collimation achieved calculated dose uniformity within 0.5% in a reference plane near the phantom midline. A comparison of computer-generated and measured point doses in this case showed agreement within 3%. Conclusions: Dynamic collimation can provide effective compensation for contours that vary primarily along one direction. A conventional treatment-planning program can be used to plan dynamic collimation and deliver a prescribed dose with reliable accuracy
Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics
Energy Technology Data Exchange (ETDEWEB)
Yu, H.G.; Muckerman, J.T.
2010-06-01
The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.
A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein
Directory of Open Access Journals (Sweden)
Mingyuan Xu
2018-05-01
Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.
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.
Modeling ramp compression experiments using large-scale molecular dynamics simulation.
Energy Technology Data Exchange (ETDEWEB)
Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)
2011-10-01
Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp; Tchipev, Nikola
2012-01-01
We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm
Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite
Yoon, Seyoon; Monteiro, Paulo J.M.
2013-01-01
The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current
Electron beam dynamics in the long-pulse, high-current DARHT-II linear induction accelerator
International Nuclear Information System (INIS)
Ekdahl, Carl A.; Abeyta, Epifanio O.; Aragon, Paul; Archuleta, Rita; Cook, Gerald; Dalmas, Dale; Esquibel, Kevin; Gallegos, Robert A.; Garnett, Robert; Harrison, James F.; Johnson, Jeffrey B.; Jacquez, Edward B.; Mccuistian, Brian T.; Montoya, Nicholas A.; Nath, Subrato; Nielsen, Kurt; Oro, David; Prichard, Benjamin; Rowton, Lawrence; Sanchez, Manolito; Scarpetti, Raymond; Schauer, Martin M.; Seitz, Gerald; Schulze, Martin; Bender, Howard A.; Broste, William B.; Carlson, Carl A.; Frayer, Daniel K.; Johnson, Douglas E.; Tom, C.Y.; Williams, John; Hughes, Thomas; Anaya, Richard; Caporaso, George; Chambers, Frank; Chen, Yu-Jiuan; Falabella, Steve; Guethlein, Gary; Raymond, Brett; Richardson, Roger; Trainham, C.; Watson, Jim; Weir, John; Genoni, Thomas; Toma, Carsten
2009-01-01
The DARHT-II linear induction accelerator (LIA) now accelerates 2-kA electron beams to more than 17 MeV. This LIA is unique in that the accelerated current pulse width is greater than 2 microseconds. This pulse has a flat-top region where the final electron kinetic energy varies by less than 1% for more than 1.5 microseconds. The long risetime of the 6-cell injector current pulse is 0.5 (micro)s, which can be scraped off in a beam-head cleanup zone before entering the 68-cell main accelerator. We discuss our experience with tuning this novel accelerator; and present data for the resulting beam transport and dynamics. We also present beam stability data, and relate these to previous stability experiments at lower current and energy.
Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter
DEFF Research Database (Denmark)
Toxvaerd, Søren
2001-01-01
Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...
Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations
International Nuclear Information System (INIS)
Kumar, Amit; Hajjar, Eric; Ruggerone, Paolo; Ceccarelli, Matteo
2010-01-01
In this paper we investigate the structural and dynamical properties of the two major porins (OmpF and OmpC) in Escherichia coli, using molecular dynamics (MD) simulations. In particular we characterized the atomic fluctuations, correlated motions, temperature dependence, solvent-accessible cross-sectional area and water dynamics in the key regions of the two channels. Our in-depth analysis allows us to highlight the importance of both the key conserved and substituted residues between OmpF and OmpC. The latter is characterized by a narrower and longer constriction region with respect to OmpF. OmpC also showed a higher stability upon increasing temperature. We then present the results of transport properties by using accelerated MD simulations to probe the diffusion of norfloxacin (a fluoroquinolone antibiotic) through the two porins OmpF/OmpC. Our study constitutes a step forward towards understanding the structure-function relationship of the two porins' channels. This will benefit the research of antibacterials with improved permeation properties and nanopores that aim to use these porins as sensing systems.
molecular dynamics simulations and quantum chemical calculations
African Journals Online (AJOL)
ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.
Invariant molecular-dynamics approach to structural phase transitions
International Nuclear Information System (INIS)
Wentzcovitch, R.M.
1991-01-01
Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics
Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids
International Nuclear Information System (INIS)
Aradi, Balint; Frauenheim, Thomas
2015-01-01
A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology
Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package
Dizkirici, Ayten; Tekpinar, Mustafa
2015-03-01
GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.
Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.
Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas
2015-07-14
A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.
NMR investigations of molecular dynamics
Palmer, Arthur
2011-03-01
NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.
Spin dynamics of electron beams in circular accelerators
International Nuclear Information System (INIS)
Boldt, Oliver
2014-04-01
Experiments using high energy beams of spin polarized, charged particles still prove to be very helpful in disclosing a deeper understanding of the fundamental structure of matter. An important aspect is to control the beam properties, such as brilliance, intensity, energy, and degree of spin polarization. In this context, the present studies show various numerical calculations of the spin dynamics of high energy electron beams in circular accelerators. Special attention has to be paid to the emission of synchrotron radiation, that occurs when deflecting charged particles on circular orbits. In the presence of the fluctuation of the kinetic energy due to the photon emission, each electron spin moves non-deterministically. This stochastic effect commonly slows down the speed of all numeric estimations. However, the shown simulations cover - using appropriate approximations - trackings for the motion of thousands of electron spins for up to thousands of turns. Those calculations are validated and complemented by empirical investigations at the electron stretcher facility ELSA of the University of Bonn. They can largely be extended to other boundary conditions and thus, can be consulted for new accelerator layouts.
Excitation dynamics and relaxation in a molecular heterodimer
International Nuclear Information System (INIS)
Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.
2012-01-01
Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.
The nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
Hoover, W.G.
1992-03-01
MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments
Reaction dynamics of molecular hydrogen on silicon surfaces
DEFF Research Database (Denmark)
Bratu, P.; Brenig, W.; Gross, A.
1996-01-01
of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...
State-to-state dynamics of molecular energy transfer
Energy Technology Data Exchange (ETDEWEB)
Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)
1993-12-01
The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.
Line-shape theory and molecular dynamics in collision-induced light scattering
International Nuclear Information System (INIS)
Balucani, U.; Tognetti, V.; Vallauri, R.
1979-01-01
Molecular-dynamics studies in argon at 148 amagats are presented for gaining information on the dynamical properties responsible for the depolarized light scattering from simple fluids. The total and pair-correlation functions are computed within the simple dipole--induced-dipole model of polarizability anisotropy. The pair spectral shape is derived. These results are compared with a theoretical analysis based on a continued-fraction approach. The necessary frequency moments are calculated both in the low-density limit and taking into account first-order density corrections, and compared with the molecular-dynamics data. The agreement between the theoretical spectra and molecular-dynamics data shows the validity of the memory-function approach. The comparison with the real experimental results allows one to test the relevant physical contributions to the polarizability anisotropy
Coulomb interactions via local dynamics: a molecular-dynamics algorithm
International Nuclear Information System (INIS)
Pasichnyk, Igor; Duenweg, Burkhard
2004-01-01
We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.
2012-01-01
In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...
Hu, Hao; Liu, Haiyan
2013-05-30
Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.
Soil dynamics and accelerated erosion: a sensitivity analysis of the LPJ Dynamic vegetation model
Bouchoms, Samuel; Van Oost, Kristof; Vanacker, Veerle; Kaplan, Jed O.; Vanwalleghem, Tom
2013-04-01
It is widely accepted that humans have become a major geomorphic force by disturbing natural vegetation patterns. Land conversion for agriculture purposes removes the protection of soils by the natural vegetation and leads to increased soil erosion by one to two orders of magnitude, breaking the balance that exists between the loss of soils and its production. Accelerated erosion and deposition have a strong influence on evolution and heterogeneity of basic soil characteristics (soil thickness, hydrology, horizon development,…) as well as on organic matter storage and cycling. Yet, since they are operating at a long time scale, those processes are not represented in state-of-art Dynamic Global Vegetation Models, which is a clear lack when exploring vegetation dynamics over past centuries. The main objectives of this paper are (i) to test the sensitivity of a Dynamic Global Vegetation Model, in terms of NPP and organic matter turnover, variations in state variables in response to accelerated erosion and (ii) to assess the performance of the model under the impact of erosion for a case-study in Central Spain. We evaluated the Lund-Postdam-Jena Dynamic Vegetation Model (LPJ DVGM) (Sitch et al, 2003) which simulates vegetation growth and carbon pools at the surface and in the soil based on climatic, pedologic and topographic variables. We assessed its reactions to changes in key soil properties that are affected by erosion such as texture and soil depth. We present the results of where we manipulated soil texture and bulk density while keeping the environmental drivers of climate, slope and altitude constant. For parameters exhibiting a strong control on NPP or SOM, a factorial analysis was conducted to test for interaction effects. The simulations show an important dependence on the clay content, especially for the slow cycling carbon pools and the biomass production, though the underground litter seems to be mostly influenced by the silt content. The fast cycling C
Ab initio molecular dynamics in a finite homogeneous electric field.
Umari, P; Pasquarello, Alfredo
2002-10-07
We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.
International Nuclear Information System (INIS)
Bresme, F.; Armstrong, J.
2014-01-01
We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation
A Study of diffusion and grain boundaries in ionic compounds by the molecular dynamic method
International Nuclear Information System (INIS)
Karakasidis, Theodoros
1995-01-01
In the first part, we present a model of variable cationic charges based on a rigid ion potential. In order to implement the model we performed static and dynamic simulations in calcium fluoride. The structural properties do not depend on the way the model is adjusted but the anion diffusion and the high frequency dielectric constant do. These results allowed to specify the criteria to adjust the variable charge model. As indicated by the behaviour of optical phonons this model introduced a supplementary polarisation mechanism to the rigid ion model. In the second part of this work, we studied the structural and diffusional behaviour of a high angle tilt grain boundary in NiO by molecular dynamics, using a usual rigid ion model. We examined structures with and without point defects between 0 K and 2500 K. The structure without defects presents always the lowest potential energy. In the others structures the defects can cluster and sometimes cause local changes in the boundary. Computer simulated images of high resolution electron microscopy, produced using these structures, present a similarity with the experimental ones. We calculated in the same boundary the diffusion coefficient of a doubly charged nickel vacancy between 2250 K and 2650 K. The atomic trajectories reveal the existence of preferential migration paths for the vacancy. The grain boundary diffusion is slightly anisotropic which is in agreement with an extrapolation of experimental results. A similar study in the volume reveals a migration energy higher than in the grain boundary. The calculated quantities allow for an estimation of the nickel diffusion acceleration due to the boundary. This acceleration is significant, but lower than the one measured by certain authors in polycrystalline, NiO; other authors studying bicrystals have not observed any acceleration. (author) [fr
Fermionic molecular dynamics for colliding and decaying nuclei
International Nuclear Information System (INIS)
Feldmeier, H.; Schnack, J.
1993-11-01
Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)
Optical spectra and lattice dynamics of molecular crystals
Zhizhin, GN
1995-01-01
The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.
Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids
International Nuclear Information System (INIS)
De Leeuw, S.W.; Brakkee, M.J.D.
1990-01-01
Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs
Orbital free molecular dynamics; Approche sans orbitale des plasmas denses
Energy Technology Data Exchange (ETDEWEB)
Lambert, F
2007-08-15
The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)
Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.
Cooke, Ben; Schmidler, Scott C
2008-10-28
We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.
International Nuclear Information System (INIS)
Vretenar, M
2014-01-01
The main features of radio-frequency linear accelerators are introduced, reviewing the different types of accelerating structures and presenting the main characteristics aspects of linac beam dynamics
Orthonormal Wavelet Bases for Quantum Molecular Dynamics
International Nuclear Information System (INIS)
Tymczak, C.; Wang, X.
1997-01-01
We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society
Non-Adiabatic Molecular Dynamics Methods for Materials Discovery
Energy Technology Data Exchange (ETDEWEB)
Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)
2017-04-04
The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.
International Nuclear Information System (INIS)
Erokhin, N.S.; Zol'nikova, N.N.; Kuznetsov, E.A.; Mikhajlovskaya, L.A.
2010-01-01
Based on numerical calculations considered the relativistic acceleration of charged particles in space plasma when surfing on the spatially localized package of electromagnetic waves. The problem is reduced to the study of unsteady, nonlinear equation for the wave phase at the carrier frequency at the location of the accelerated charge, which is solved numerically. We study the temporal dynamics of the relativistic factor, the component of momentum and velocity of the particle, its trajectory is given gyro-rotation in an external magnetic field after the departure of the effective potential well. Dependence of the dynamics of a particle interacting with the wave of the sign of the velocity of the charge along the wave front. We formulate the optimal conditions of the relativistic particle acceleration wave packet, indicate the possibility of again (after a number gyro-turnover) charge trapping wave with an additional relativistic acceleration.
Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes
Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes
2007-01-01
This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the
Molecular dynamics for reactions of heterogeneous catalysis
Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.
1991-01-01
An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.
Optimal Acceleration-Velocity-Bounded Trajectory Planning in Dynamic Crowd Simulation
Directory of Open Access Journals (Sweden)
Fu Yue-wen
2014-01-01
Full Text Available Creating complex and realistic crowd behaviors, such as pedestrian navigation behavior with dynamic obstacles, is a difficult and time consuming task. In this paper, we study one special type of crowd which is composed of urgent individuals, normal individuals, and normal groups. We use three steps to construct the crowd simulation in dynamic environment. The first one is that the urgent individuals move forward along a given path around dynamic obstacles and other crowd members. An optimal acceleration-velocity-bounded trajectory planning method is utilized to model their behaviors, which ensures that the durations of the generated trajectories are minimal and the urgent individuals are collision-free with dynamic obstacles (e.g., dynamic vehicles. In the second step, a pushing model is adopted to simulate the interactions between urgent members and normal ones, which ensures that the computational cost of the optimal trajectory planning is acceptable. The third step is obligated to imitate the interactions among normal members using collision avoidance behavior and flocking behavior. Various simulation results demonstrate that these three steps give realistic crowd phenomenon just like the real world.
Molecular dynamics simulations on PGLa using NMR orientational constraints
Energy Technology Data Exchange (ETDEWEB)
Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)
2015-11-15
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
Molecular dynamics simulations
International Nuclear Information System (INIS)
Alder, B.J.
1985-07-01
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs
A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow
Hunt, T.A.; Hunt, Thomas A.; Bernardi, Stefano; Todd, B.D.
2010-01-01
In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose
A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations
van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J
2012-01-01
Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,
A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations
van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.
2012-01-01
Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,
Accelerated Testing of Polymeric Composites Using the Dynamic Mechanical Analyzer
Abdel-Magid, Becky M.; Gates, Thomas S.
2000-01-01
Creep properties of IM7/K3B composite material were obtained using three accelerated test methods at elevated temperatures. Results of flexural creep tests using the dynamic mechanical analyzer (DMA) were compared with results of conventional tensile and compression creep tests. The procedures of the three test methods are described and the results are presented. Despite minor differences in the time shift factor of the creep compliance curves, the DMA results compared favorably with the results from the tensile and compressive creep tests. Some insight is given into establishing correlations between creep compliance in flexure and creep compliance in tension and compression. It is shown that with careful consideration of the limitations of flexure creep, a viable and reliable accelerated test procedure can be developed using the DMA to obtain the viscoelastic properties of composites in extreme environments.
International Nuclear Information System (INIS)
Omelyan, Igor; Kovalenko, Andriy
2013-01-01
We develop efficient handling of solvation forces in the multiscale method of multiple time step molecular dynamics (MTS-MD) of a biomolecule steered by the solvation free energy (effective solvation forces) obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model complemented with the Kovalenko-Hirata closure approximation). To reduce the computational expenses, we calculate the effective solvation forces acting on the biomolecule by using advanced solvation force extrapolation (ASFE) at inner time steps while converging the 3D-RISM-KH integral equations only at large outer time steps. The idea of ASFE consists in developing a discrete non-Eckart rotational transformation of atomic coordinates that minimizes the distances between the atomic positions of the biomolecule at different time moments. The effective solvation forces for the biomolecule in a current conformation at an inner time step are then extrapolated in the transformed subspace of those at outer time steps by using a modified least square fit approach applied to a relatively small number of the best force-coordinate pairs. The latter are selected from an extended set collecting the effective solvation forces obtained from 3D-RISM-KH at outer time steps over a broad time interval. The MTS-MD integration with effective solvation forces obtained by converging 3D-RISM-KH at outer time steps and applying ASFE at inner time steps is stabilized by employing the optimized isokinetic Nosé-Hoover chain (OIN) ensemble. Compared to the previous extrapolation schemes used in combination with the Langevin thermostat, the ASFE approach substantially improves the accuracy of evaluation of effective solvation forces and in combination with the OIN thermostat enables a dramatic increase of outer time steps. We demonstrate on a fully flexible model of alanine dipeptide in aqueous solution that the MTS-MD/OIN/ASFE/3D-RISM-KH multiscale method of molecular dynamics
Two-phase flow dynamics in a model steam generator under vertical acceleration oscillation field
International Nuclear Information System (INIS)
Ishida, T.; Teshima, N.; Sakurai, S.
1992-01-01
The influence of periodically varying acceleration on hydrodynamic response has been studied experimentally using an experimental rig which models a marine reactor subject to vertical motion. The effect on the primary loop is small, but the effect on the secondary loop is large. The variables of the secondary loop, such as circulation flow rate and water level, oscillate with acceleration. The variation of gains in frequency response is analysed. The variations of flow in the secondary loop and in the downcome water level, increase in proportion to the acceleration. The effect of the flow resistance in the secondary loop on the two-phase flow dynamics is clarified. (7 figures) (Author)
Reaction dynamics in polyatomic molecular systems
Energy Technology Data Exchange (ETDEWEB)
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
Energy conservation in molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren; Heilmann, Ole; Dyre, J. C.
2012-01-01
Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...
Implementation of surface hopping molecular dynamics using semiempirical methods
International Nuclear Information System (INIS)
Fabiano, E.; Keal, T.W.; Thiel, W.
2008-01-01
A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained
Ab Initio molecular dynamics with excited electrons
Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.
1994-01-01
A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.
Molecular dynamics coupled with a virtual system for effective conformational sampling.
Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi
2018-07-15
An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation
DEFF Research Database (Denmark)
Pedersen, U.R.; Peters, Günther H.j.; Westh, P.
2007-01-01
The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...
An Evaluation of Molecular Dynamics Performance on the Hybrid Cray XK6 Supercomputer
International Nuclear Information System (INIS)
Brown, W. Michael; Nguyen, Trung D.; Fuentes-Cabrera, Miguel A.; Fowlkes, Jason Davidson; Rack, Philip D.; Berger, Mark
2012-01-01
For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little modification to existing codes. Engineering and electrical power constraints have disrupted this trend, requiring more drastic changes to both hardware and software solutions. Here, we present details of the Cray XK6 architecture that achieves increased performance with the use of GPU accelerators. We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers. We present benchmark results for solid-state, biological, and mesoscopic systems and discuss some challenges for utilizing hybrid systems. We present some early work in improving application performance on the XK6 and performance results for the simulation of liquid copper nanostructures with the embedded atom method.
Swinburne, Thomas D.; Perez, Danny
2018-05-01
A massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.
Shekhar, Adarsh
Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in
Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics
Energy Technology Data Exchange (ETDEWEB)
Yu H. G.; Muckerman, J.T.
2012-05-29
The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.
Molecular dynamics simulation of self-diffusion coefficients for liquid metals
International Nuclear Information System (INIS)
Ju Yuan-Yuan; Zhang Qing-Ming; Gong Zi-Zheng; Ji Guang-Fu
2013-01-01
The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. (atomic and molecular physics)
Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.
Directory of Open Access Journals (Sweden)
Federica Chiappori
Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.
Catalysis and communication in dynamic molecular networks
Fanlo Virgos, Hugo
2015-01-01
The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity
Molecular dynamics study of atomic displacements in disordered solid alloys
Puzyrev, Yevgeniy S.
The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.
Graphics processing units accelerated semiclassical initial value representation molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Tamascelli, Dario; Dambrosio, Francesco Saverio [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy); Conte, Riccardo [Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States); Ceotto, Michele, E-mail: michele.ceotto@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano (Italy)
2014-05-07
This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the benchmark values. The computational time scaling of two GPUs (NVIDIA Tesla C2075 and Kepler K20), respectively, versus two CPUs (Intel Core i5 and Intel Xeon E5-2687W) and the critical issues related to the GPU implementation are discussed. The resulting reduction in computational time and power consumption is significant and semiclassical GPU calculations are shown to be environment friendly.
International Nuclear Information System (INIS)
Danilov, Denis; Nestler, Britta; Guerdane, Mohammed; Teichler, Helmar
2009-01-01
Results are presented from phase-field modelling and molecular dynamics simulations concerning the relaxation dynamics in a finite-temperature two-phase crystal-liquid sample subjected to an abrupt temperature drop. Relaxation takes place by propagation of the solidification front under formation of a spatially varying concentration profile in the melt. The molecular dynamics simulations are carried out with an interatomic model appropriate for the NiZr alloy system and provide the thermophysical data required for setting up the phase-field simulations. Regarding the concentration profile and velocity of the solidification front, best agreement between the phase-field model and molecular dynamics simulation is obtained when increasing the apparent diffusion coefficients in the phase-field treatment by a factor of four against their molecular dynamics estimates.
Visualizing functional motions of membrane transporters with molecular dynamics simulations.
Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad
2013-01-29
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.
Marshall Mccall, Patrick
Living cells are hierarchically self-organized forms of active soft matter: molecules on the nanometer scale form functional structures and organelles on the micron scale, which then compose cells on the scale of 10s of microns. While the biological functions of intracellular organelles are defined by the composition and properties of the structures themselves, how those bulk properties emerge from the properties and interactions of individual molecules remains poorly understood. Actin, a globular protein which self-assembles into dynamic semi-flexible polymers, is the basic structural material of cells and the major component of many functional organelles. In this thesis, I have used purified actin as a model system to explore the interplay between molecular-scale dynamics and organelle-scale functionality, with particular focus on the role of molecular-scale non-equilibrium activity. One of the most canonical forms of molecular-scale non-equilibrium activity is that of mechanoenzymes, also called motor proteins. These proteins utilized the free energy liberated by hydrolysis of ATP to perform mechanical work, thereby introducing non-equilibrium "active" stresses on the molecular scale. Combining experiments with mathematical modeling, we demonstrate in this thesis that non-equilibrium motor activity is sufficient to drive self-organization and pattern formation of the multimeric actin-binding motor protein Myosin II on 1D reconstituted actomyosin bundles. Like myosin, actin is itself an ATPase. However, nono-equilibrium ATP hydrolysis on actin is known to regulate the stability and assembly kinetics of actin filaments rather than generate active stresses per se. At the level of single actin filaments, the inhomogeneous nucleotide composition generated along the filament length by hydrolysis directs binding of regulatory proteins like cofilin, which mediate filament disassembly and thereby accelerate actin filament turnover. The concequences of this non
Laser Controlled Molecular Orientation Dynamics
International Nuclear Information System (INIS)
Atabek, O.
2004-01-01
Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation
Molecular potentials and relaxation dynamics
International Nuclear Information System (INIS)
Karo, A.M.
1981-01-01
The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy
Molecular dynamics simulations of solutions at constant chemical potential
Perego, C.; Salvalaglio, M.; Parrinello, M.
2015-04-01
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.
The 2011 Dynamics of Molecular Collisions Conference
Energy Technology Data Exchange (ETDEWEB)
Nesbitt, David J. [JILA, NIST
2011-07-11
The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor
Can Accelerators Accelerate Learning?
International Nuclear Information System (INIS)
Santos, A. C. F.; Fonseca, P.; Coelho, L. F. S.
2009-01-01
The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ)[1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.
Can Accelerators Accelerate Learning?
Santos, A. C. F.; Fonseca, P.; Coelho, L. F. S.
2009-03-01
The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ) [1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.
Towards the molecular bases of polymerase dynamics
International Nuclear Information System (INIS)
Chela Flores, J.
1991-03-01
One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs
Dynamical quenching of tunneling in molecular magnets
International Nuclear Information System (INIS)
José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.
2015-01-01
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation
Dynamical quenching of tunneling in molecular magnets
Energy Technology Data Exchange (ETDEWEB)
José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)
2015-12-15
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik
2010-03-17
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik; Szepessy, Anders
2010-01-01
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
J. Rodnizki, D. Berkovits, K. Lavie, I. Mardor, A. Shor and Y. Yanay (Soreq NRC, Yavne), K. Dunkel, C. Piel (ACCEL, Bergisch Gladbach), A. Facco (INFN/LNL, Legnaro, Padova), V. Zviagintsev (TRIUMF, Vancouver)
AbstractBeam dynamics simulations of SARAF (Soreq Applied Research Accelerator Facility) superconducting RF linear accelerator have been performed in order to establish the accelerator design. The multi-particle simulation includes 3D realistic electromagnetic field distributions, space charge forces and fabrication, misalignment and operation errors. A 4 mA proton or deuteron beam is accelerated up to 40 MeV with a moderated rms emittance growth and a high real-estate gradient of 2 MeV/m. An envelope of 40,000 macro-particles is kept under a radius of 1.1 cm, well below the beam pipe bore radius. The accelerator design of SARAF is proposed as an injector for the EURISOL driver accelerator. The Accel 176 MHZ β0=0.09 and β0=0.15 HWR lattice was extended to 90 MeV based on the LNL 352 MHZ β0=0.31 HWR. The matching between both lattices ensures smooth transition and the possibility to extend the accelerator to the required EURISOL ion energy.
Nanopore wall-liquid interaction under scope of molecular dynamics study: Review
Tsukanov, A. A.; Psakhie, S. G.
2017-12-01
The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.
Hong, Bingbing
2012-03-01
A molecular model of silica nanoparticles grafted with poly(ethylene oxide) oligomers has been developed for predicting the transport properties of nanoparticle organic-hybrid materials (NOHMs). Ungrafted silica nanoparticles in a medium of poly(ethylene oxide) oligomers were also simulated to clarify the effect of grafting on the dynamics of nanoparticles and chains. The model approximates nanoparticles as solid spheres and uses a united-atom representation for chains, including torsional and bond-bending interactions. The calculated viscosities from Green-Kubo relationships and temperature extrapolation are of the same order of magnitude as experimental data but show a smaller activation energy relative to real NOHMs systems. Grafted systems have higher viscosities, smaller diffusion coefficients, and slower chain dynamics than the ungrafted ones at high temperatures. At lower temperatures, grafted systems exhibit faster dynamics for both nanoparticles and chains relative to ungrafted systems, because of lower aggregation of particles and enhanced correlations between nanoparticles and chains. This agrees with the experimental observation that NOHMs have liquidlike behavior in the absence of a solvent. For both grafted and ungrafted systems at low temperatures, increasing chain length reduces the volume fraction of nanoparticles and accelerates the dynamics. However, at high temperatures, longer chains slow down nanoparticle diffusion. From the Stokes-Einstein relationship, it was determined that the coarse-grained treatment of nanoparticles leads to slip on the nanoparticle surfaces. Grafted systems obey the Stokes-Einstein relationship over the temperature range simulated, but ungrafted systems display deviations from it. © 2012 American Chemical Society.
Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics
International Nuclear Information System (INIS)
Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.
2004-01-01
Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches
International Nuclear Information System (INIS)
Gao, J.
1996-01-01
The research works presented in this memoir are oriented not only to the R and D programs towards future linear colliders, but also to the pedagogic purposes. The first part of this memoir (from Chapter 2 to Chapter 9) establishes an analytical framework of the disk-loaded slow wave accelerating structures with can be served as the advanced courses for the students who have got some basic trainings in the linear accelerator theories. The analytical formulae derived in this part describe clearly the properties of the disk-loaded accelerating structures, such as group velocity, shunt impedance, coupling coefficients κ and β, loss factors, and wake fields. The second part (from Chapter 11 to Chapter 13) gives the beam dynamics simulations and the final proposal of an S-Band Superconducting Linear Collider (SSLC) which is aimed to avoid the dark current problem in TESLA project. This memoir has not included all the works conducted since April 1992, such as beam dynamics simulations for CLIC Test Facility (CFT-2) and the design of High Charge Structures (HCS) (11π/12 mode) for CFT-2, in order to make this memoir more harmonious, coherent and continuous. (author)
The use of molecular dynamics for the thermodynamic properties of simple and transition metals
International Nuclear Information System (INIS)
Straub, G.K.
1987-04-01
The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated
Energy Technology Data Exchange (ETDEWEB)
Cawkwell, M. J., E-mail: cawkwell@lanl.gov; Niklasson, Anders M. N. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Dattelbaum, Dana M. [Weapons Experiments Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)
2015-02-14
The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.
Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M
2015-02-14
The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.
A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS
AHLSTROM, P; BERENDSEN, HJC
1993-01-01
Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)
Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators
International Nuclear Information System (INIS)
Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.
1999-01-01
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
Correlations and symmetry of interactions influence collective dynamics of molecular motors
International Nuclear Information System (INIS)
Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B
2015-01-01
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)
Molecular dynamics simulation of impact test
International Nuclear Information System (INIS)
Akahoshi, Y.; Schmauder, S.; Ludwig, M.
1998-01-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular dynamics simulation of impact test
Energy Technology Data Exchange (ETDEWEB)
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît
2018-01-01
Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield
Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins
Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru
2014-03-01
A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.
Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.
Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...
Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben
2017-08-22
A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.
Molecular dynamics simulation of a phospholipid membrane
Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.
We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in
Energy Technology Data Exchange (ETDEWEB)
Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)
2013-12-21
The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
International Nuclear Information System (INIS)
Ji, Pengfei; Zhang, Yuwen; Yang, Mo
2013-01-01
The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective
Ji, Pengfei; Zhang, Yuwen; Yang, Mo
2013-12-01
The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
International Nuclear Information System (INIS)
Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid
2015-01-01
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields
Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer
DEFF Research Database (Denmark)
Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.
-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...
Physics through the 1990s: Atomic, molecular, and optical physics
International Nuclear Information System (INIS)
1986-01-01
This report was prepared by the Panel on Atomic, Molecular, and Optical Physics of the Physics Survey Committee in response to its charge to describe the field, to characterize the recent advances, and to identify the current frontiers of research. Some of the areas discussed are: atomic structure, atomic dynamics, accelerator-based atomic physics, molecular photoionization and electron-molecule scattering, astrophysics, laser spectroscopy, atmospheric physics, plasma physics, and applications
Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.
Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N
2015-06-09
The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.
Electron-nuclear corellations for photoinduced dynamics in molecular dimers
Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.
2003-03-01
Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).
Vectorization, parallelization and implementation of Quantum molecular dynamics codes (QQQF, MONTEV)
Energy Technology Data Exchange (ETDEWEB)
Kato, Kaori [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan); Kunugi, Tomoaki; Kotake, Susumu; Shibahara, Masahiko
1998-03-01
This report describes parallelization, vectorization and implementation for two simulation codes, Quantum molecular dynamics simulation code QQQF and Photon montecalro molecular dynamics simulation code MONTEV, that have been developed for the analysis of the thermalization of photon energies in the molecule or materials. QQQF has been vectorized and parallelized on Fujitsu VPP and has been implemented from VPP to Intel Paragon XP/S and parallelized. MONTEV has been implemented from VPP to Paragon and parallelized. (author)
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS
JUFFER, AH; BERENDSEN, HJC
1993-01-01
A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the
International Nuclear Information System (INIS)
Li Changhu; Xu Liming; Teng Jianjian; Ge Wei; Zhang Jun; Ma Guangdong
2010-01-01
Objective: To explorer the application in detection the position accuracy of the multileaf collimator of Varian accelerator with dynamic therapy log files. Methods: A pre-designed MLC format files named PMLC for two Varian accelerators, the dynamic treatment log files were recorded 10 times on a different date, and be converted into the MLC format files named DMLC, compared with the original plan PMLC, so we can analysis two files for each leaf position deviation. In addition, we analysis the repeatability of MLC leaves position accuracy between 10 dynalog files of two accelerators. Results: No statistically significant difference between the average position of the 10 times leaf position of the two accelerators,their were 0.29 -0.29 and 0.29 -0.30 (z = -0.77, P=0.442). About 40%, 30%, 20% and 10% of the leaf position deviation was at ≤0.2 mm, 0.3 mm, 0.5 mm and 0.4 mm, respectively. the maximum value was 0.5 mm. More than 86% of the leaf position are completely coincident between 10 dynamic treatment files of two accelerators. The rate of position deviation no more 0. 05 mm was 96. 6% and 97.3%, respectively. And the maximum value was 0.09 mm. Conclusions: Dynamic treatment log file is a splendid tool in testing the actual position of multi-leaf collimator. The multi-leaf collimator of two accelerators be detected are precise and stabilized. (authors)
Molecular dynamics simulations and quantum chemical calculations ...
African Journals Online (AJOL)
Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...
Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain
Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.
2007-01-01
A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which
High efficiency RF amplifier development over wide dynamic range for accelerator application
Mishra, Jitendra Kumar; Ramarao, B. V.; Pande, Manjiri M.; Joshi, Gopal; Sharma, Archana; Singh, Pitamber
2017-10-01
Superconducting (SC) cavities in an accelerating section are designed to have the same geometrical velocity factor (βg). For these cavities, Radio Frequency (RF) power needed to accelerate charged particles varies with the particle velocity factor (β). RF power requirement from one cavity to other can vary by 2-5 dB within the accelerating section depending on the energy gain in the cavity and beam current. In this paper, we have presented an idea to improve operating efficiency of the SC RF accelerators using envelope tracking technique. A study on envelope tracking technique without feedback is carried out on a 1 kW, 325 MHz, class B (conduction angle of 180 degrees) tuned load power amplifier (PA). We have derived expressions for the efficiency and power output for tuned load amplifier operating on the envelope tracking technique. From the derived expressions, it is observed that under constant load resistance to the device (MOSFET), optimum amplifier efficiency is invariant whereas output power varies with the square of drain bias voltage. Experimental results on 1 kW PA module show that its optimum efficiency is always greater than 62% with variation less than 5% from mean value over 7 dB dynamic range. Low power amplifier modules are the basic building block for the high power amplifiers. Therefore, results for 1 kW PA modules remain valid for the high power solid state amplifiers built using these PA modules. The SC RF accelerators using these constant efficiency power amplifiers can improve overall accelerator efficiency.
Droplet spreading driven by van der Waals force: a molecular dynamics study
Wu, Congmin
2010-07-07
The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.
Molecular dynamics simulations of melting behavior of alkane as phase change materials slurry
International Nuclear Information System (INIS)
Rao Zhonghao; Wang Shuangfeng; Wu Maochun; Zhang Yanlai; Li Fuhuo
2012-01-01
Highlights: ► The melting behavior of phase change materials slurry was investigated by molecular dynamics simulation method. ► Four different PCM slurry systems including pure water and water/n-nonadecane composite were constructed. ► Amorphous structure and periodic boundary conditions were used in the molecular dynamics simulations. ► The simulated melting temperatures are very close to the published experimental values. - Abstract: The alkane based phase change materials slurry, with high latent heat storage capacity, is effective to enhance the heat transfer rate of traditional fluid. In this paper, the melting behavior of composite phase change materials slurry which consists of n-nonadecane and water was investigated by using molecular dynamics simulation. Four different systems including pure water and water/n-nonadecane composite were constructed with amorphous structure and periodic boundary conditions. The results showed that the simulated density and melting temperature were very close to the published experimental values. Mixing the n-nonadecane into water decreased the mobility but increased the energy storage capacity of composite systems. To describe the melting behavior of alkane based phase change materials slurry on molecular or atomic scale, molecular dynamics simulation is an effective method.
Ion beam dynamics in the acceleration region of the Vincy Cyclotron
International Nuclear Information System (INIS)
Tomic, S.; Samsonov, E.
1998-01-01
Modern concept of heavy ion cyclotrons assumes a tendency of decreasing the gaps between magnet poles, enabling better efficiency of the magnetic field circuit. This restricts possible solutions of acceleration structure and imposes the necessity of installing the dees in valleys of magnetic structures. This approach, which is accepted in the VINCY Cyclotron, requires a detailed study of the ion beam dynamics in the acceleration region. Consequently, we analyzed ion beams with eta = 1,05 and 0.25 in radial and axial phase space. Also, the energy spread in emittances and the influence of the first harmonic of the magnetic field on the radial betatron oscillations are discussed. The transformation of coherent into incoherent radial oscillations as well as the effect to radial off-centering on the beam vertical size at Walkinshaw resonance location, is pointed out (author)
Microsecond atomic-scale molecular dynamics simulations of polyimides
Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.
2013-01-01
We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long
Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms
Directory of Open Access Journals (Sweden)
Dirk-Sören Lühmann
2015-08-01
Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.
Moving contact lines: linking molecular dynamics and continuum-scale modelling.
Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K
2018-05-04
Despite decades of research, the modelling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily-life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide the link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which govern the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modelling, and highlight the opportunities for future developments in this area.
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.
Li, Jianwei; Nowak, Piotr; Otto, Sijbren
2013-06-26
Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.
International Nuclear Information System (INIS)
More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.
2012-01-01
Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)
Molecular dynamics studies of superionic conductors
International Nuclear Information System (INIS)
Rahman, A.; Vashishta, P.
1983-01-01
Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables
Nonequilibrium molecular dynamics theory, algorithms and applications
Todd, Billy D
2017-01-01
Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...
Marrink, SJ; Mark, AE
2003-01-01
Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at
Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations
Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter
2007-01-01
We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated
On higher ground: how well can dynamic body acceleration determine speed in variable terrain?
Directory of Open Access Journals (Sweden)
Owen R Bidder
Full Text Available INTRODUCTION: Animal travel speed is an ecologically significant parameter, with implications for the study of energetics and animal behaviour. It is also necessary for the calculation of animal paths by dead-reckoning. Dead-reckoning uses heading and speed to calculate an animal's path through its environment on a fine scale. It is often used in aquatic environments, where transmission telemetry is difficult. However, its adoption for tracking terrestrial animals is limited by our ability to measure speed accurately on a fine scale. Recently, tri-axial accelerometers have shown promise for estimating speed, but their accuracy appears affected by changes in substrate and surface gradients. The purpose of the present study was to evaluate four metrics of acceleration; Overall dynamic body acceleration (ODBA, vectorial dynamic body acceleration (VDBA, acceleration peak frequency and acceleration peak amplitude, as proxies for speed over hard, soft and inclined surfaces, using humans as a model species. RESULTS: A general linear model (GLM showed a significant difference in the relationships between the metrics and speed depending on substrate or surface gradient. When the data from all surface types were considered together, VeDBA had the highest coefficient of determination. CONCLUSIONS: All of the metrics showed some variation in their relationship with speed according to the surface type. This indicates that changes in the substrate or surface gradient during locomotion by animals would produce errors in speed estimates, and also in dead-reckoned tracks if they were calculated from speeds based entirely on a priori calibrations. However, we describe a method by which the relationship between acceleration metrics and speed can be corrected ad hoc, until tracks accord with periodic ground truthed positions, obtained via a secondary means (e.g. VHF or GPS telemetry. In this way, dead-reckoning provides a means to obtain fine scale movement data
Quantum molecular dynamics study of the Su-Schrieffer-Heeger model
Michielsen, Kristel; Raedt, Hans De
A quantum molecular dynamics technique is presented to compute the static and dynamic properties of a system of fermions coupled to classical degrees of freedom. The method is employed to investigate the properties of the Su-Schrieffer-Heeger model, an electron-phonon model which is often used to
A comparative molecular dynamics study of diffusion of n-decane ...
Indian Academy of Sciences (India)
Administrator
Abstract. Molecular dynamics simulations are reported on the structure and dynamics of n-decane and. 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We.
Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation
National Research Council Canada - National Science Library
Johnston, K
1998-01-01
.... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...
Czech Academy of Sciences Publication Activity Database
Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef
2012-01-01
Roč. 6, č. 3 (2012), s. 1901-1914 ISSN 1936-0851 R&D Projects: GA ČR GA203/09/1802; GA MŠk ME09020 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular rotors * molecular dynamics * potential energy barriers * friction * intramolecular vibrational redistribution Subject RIV: CC - Organic Chemistry Impact factor: 12.062, year: 2012
Mechanisms of Acceleration and Retardation of Water Dynamics by Ions
Czech Academy of Sciences Publication Activity Database
Stirnemann, G.; Wernersson, Erik; Jungwirth, Pavel; Laage, D.
2013-01-01
Roč. 135, č. 32 (2013), s. 11824-11831 ISSN 0002-7863 R&D Projects: GA ČR GBP208/12/G016 Grant - others:European Research Council(XE) FP7-279977 Institutional support: RVO:61388963 Keywords : ions * water * molecular dynamics * NMR * IR Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 11.444, year: 2013
International Nuclear Information System (INIS)
Verkhovtsev, A.; Korol, A.V.; Solovyov, A.V.
2017-01-01
We present the results of classical molecular dynamics simulations of collision-induced fusion and fragmentation of C 60 fullerenes, performed by means of the MBN Explorer software package. The simulations provide information on structural differences of the fused compound depending on kinematics of the collision process. The analysis of fragmentation dynamics at different initial conditions shows that the size distributions of produced molecular fragments are peaked for dimers, which is in agreement with a well-established mechanism of C 60 fragmentation via preferential C 2 emission. Atomic trajectories of the colliding particles are analyzed and different fragmentation patterns are observed and discussed. On the basis of the performed simulations, characteristic time of C 2 emission is estimated as a function of collision energy. The results are compared with experimental time-of-flight distributions of molecular fragments and with earlier theoretical studies. Considering the widely explored case study of C 60 -C 60 collisions, we demonstrate broad capabilities of the MBN Explorer software, which can be utilized for studying collisions of a broad variety of nano-scale and bio-molecular systems by means of classical molecular dynamics. (authors)
Czech Academy of Sciences Publication Activity Database
Chocholoušová, Jana; Feig, M.
2006-01-01
Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006
Cavalli, F.; Naimzada, A.; Pecora, N.
2017-10-01
In the present paper, we investigate the dynamics of a model in which the real part of the economy, described within a multiplier-accelerator framework, interacts with a financial market with heterogeneous speculators, in order to study the channels through which the two sectors influence each other. Employing analytical and numerical tools, we investigate stability conditions as well as bifurcations and possible periodic, quasi-periodic, and chaotic dynamics, enlightening how the degree of market interaction, together with the accelerator parameter and the intervention of the fiscal authority, may affect the business cycle and the course of the financial market. In particular, we show that even if the steady state is locally stable, multistability phenomena can occur, with several and complex dynamic structures coexisting with the steady state. Finally, simulations reveal that the proposed model is able to explain several statistical properties and stylized facts observed in real financial markets, including persistent high volatility, fat-tailed return distributions, volatility clustering, and positive autocorrelation of absolute returns.
Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets
Lehmann, Kevin K.
2003-03-01
Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.
Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...
Indian Academy of Sciences (India)
Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...
DyNet: visualization and analysis of dynamic molecular interaction networks.
Goenawan, Ivan H; Bryan, Kenneth; Lynn, David J
2016-09-01
: The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most 'rewired' nodes across many network states. DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). david.lynn@sahmri.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
Molecular dynamics for irradiation driven chemistry: application to the FEBID process*
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-10-01
A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp
2012-06-01
We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.
Molecular electron recollision dynamics in intense circularly polarized laser pulses
Bandrauk, André D.; Yuan, Kai-Jun
2018-04-01
Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.
Dynamic analysis of an accelerator-driven fluid-fueled subcritical radioactive waste burning system
International Nuclear Information System (INIS)
Woosley, M.L. Jr.; Rydin, R.A.
1998-01-01
The recent revival of interest in accelerator-driven subcritical fluid-fueled systems is documented. Several important applications of these systems are mentioned, and this is used to motivate the need for dynamic analysis of the nuclear kinetics of such systems. A physical description of the Los alamos National Laboratory accelerator-based conversion (ABC) concept is provided. This system is used as the basis for the kinetics study in this research. The current approach to the dynamic simulation of an accelerator-driven subcritical fluid-fueled system includes four functional elements: a discrete ordinates model is used to calculate the flux distribution for the source-driven system; a nodal convection model is used to calculate time-dependent isotope and temperature distributions that impact reactivity; a nodal importance weighting model is used to calculate the reactivity impact of temperature and isotope distributions and to feed this information back to the time-dependent nodal convection model; and a transient driver is used to simulate transients, model the balance of plant, and record simulation data. Specific transients that have been analyzed with the current modeling system are discussed. These transients include loss-of-flow and loss-of-cooling accidents, xenon and samarium transients, and cold-plug and overfueling events. The results of various transients have uncovered unpredictable behavior, unresolved design issues, and the need for active control. The need for the development of a nodal-coupling spatial kinetics model is mentioned
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)
2015-12-07
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.
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
International Nuclear Information System (INIS)
Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter
2015-01-01
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
Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.
Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars
2018-04-24
In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.
Computational challenges of large-scale, long-time, first-principles molecular dynamics
International Nuclear Information System (INIS)
Kent, P R C
2008-01-01
Plane wave density functional calculations have traditionally been able to use the largest available supercomputing resources. We analyze the scalability of modern projector-augmented wave implementations to identify the challenges in performing molecular dynamics calculations of large systems containing many thousands of electrons. Benchmark calculations on the Cray XT4 demonstrate that global linear-algebra operations are the primary reason for limited parallel scalability. Plane-wave related operations can be made sufficiently scalable. Improving parallel linear-algebra performance is an essential step to reaching longer timescales in future large-scale molecular dynamics calculations
Molecular dynamics study of silver
International Nuclear Information System (INIS)
Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.
1995-03-01
We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs
Nonlinear dynamics of zigzag molecular chains (in Russian)
DEFF Research Database (Denmark)
Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth
1999-01-01
models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...
Dynamics of particles accelerated by head-on collisions of two magnetized plasma shocks
Takeuchi, Satoshi
2018-02-01
A kinetic model of the head-on collision of two magnetized plasma shocks is analyzed theoretically and in numerical calculations. When two plasmas with anti-parallel magnetic fields collide, they generate magnetic reconnection and form a motional electric field at the front of the collision region. This field accelerates the particles sandwiched between both shock fronts to extremely high energy. As they accelerate, the particles are bent by the transverse magnetic field crossing the magnetic neutral sheet, and their energy gains are reduced. In the numerical calculations, the dynamics of many test particles were modeled through the relativistic equations of motion. The attainable energy gain was obtained by multiplying three parameters: the propagation speed of the shock, the magnitude of the magnetic field, and the acceleration time of the test particle. This mechanism for generating high-energy particles is applicable over a wide range of spatial scales, from laboratory to interstellar plasmas.
Crystal structure and pair potentials: A molecular-dynamics study
Energy Technology Data Exchange (ETDEWEB)
Parrinello, M.; Rahman, A.
1980-10-06
With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.
Molecular dynamics simulations and free energy profile of ...
Indian Academy of Sciences (India)
aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.
DEFF Research Database (Denmark)
Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P
2008-01-01
. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...
Plastic dislocation motion via nonequilibrium molecular and continuum dynamics
International Nuclear Information System (INIS)
Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.
1980-01-01
The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition
Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ
DEFF Research Database (Denmark)
Euro, Liliya; Haapanen, Outi; Róg, Tomasz
2017-01-01
of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...
Molecular Dynamics: New Frontier in Personalized Medicine.
Sneha, P; Doss, C George Priya
2016-01-01
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.
Single-particle dynamics - RF acceleration
International Nuclear Information System (INIS)
Montague, B.W.
1977-01-01
In this paper the rf acceleration of both synchronous and non-synchronous particles is discussed and a simple linearized equation of small amplitude synchrotron oscillations is derived. Phase stability, the hamiltonian for synchrotron oscillations, oscillation amplitudes and adiabatic damping are then briefly discussed. The final sections of the paper contain a description of the basic principles of rf beam stacking in the longitudinal phase space of intersecting Storage Rings and a description of phase displacement acceleration which inspite of certain disadvantages, remains an attractive technique for proton storage rings. (B.D.)
NGLview-interactive molecular graphics for Jupyter notebooks.
Nguyen, Hai; Case, David A; Rose, Alexander S
2018-04-01
NGLview is a Jupyter/IPython widget to interactively view molecular structures as well as trajectories from molecular dynamics simulations. Fast and scalable molecular graphics are provided through the NGL Viewer. The widget supports showing data from the file-system, online data bases and from objects of many popular analysis libraries including mdanalysis, mdtraj, pytraj, rdkit and more. The source code is freely available under the MIT license at https://github.com/arose/nglview. Python packages are available from PyPI and bioconda. NGLview uses Python on the server-side and JavaScript on the client. The integration with Jupyter is done through the ipywidgets package. The NGL Viewer is embedded client-side to provide WebGL accelerated molecular graphics. asr.moin@gmail.com.
International Nuclear Information System (INIS)
Washizu, Hitoshi; Sanda, Shuzo; Hyodo, Shi-aki; Ohmori, Toshihide; Nishino, Noriaki; Suzuki, Atsushi
2007-01-01
Friction control of machine elements on a molecular level is a challenging subject in vehicle technology. We describe the molecular dynamics studies of friction in two significant lubrication regimes. As a case of elastohydrodynamic lubrication, we introduce the mechanism of momentum transfer related to the molecular structure of the hydrocarbon fluids, phase transition of the fluids under high pressure, and a submicron thickness simulation of the oil film using a tera-flops computer. For boundary lubrication, the dynamic behavior of water molecules on hydrophilic and hydrophobic silicon surfaces under a shear condition is studied. The dynamic structure of the hydrogen bond network on the hydrophilic surface is related to the low friction of the diamond-like carbon containing silicon (DLC-Si) coating
Dynamic analysis of electron density in the course of the internal motion of molecular system
International Nuclear Information System (INIS)
Tachibana, A.; Hori, K.; Asai, Y.; Yamabe, T.
1984-01-01
The general dynamic aspect of electron density of a molecular system is studied on the basis of the general equation of the electron orbital which is formulated for the dynamic study of electronic motion. The newly defined electron orbital incorporates the dynamics of molecular vibration into the electronic structures. In this scheme, the change of electron distribution caused by excitation of vibrational state is defined as the ''dynamic electron transfer.'' The dynamic electron density is found to have the remarkable ''additive'' property. The time-dependent aspect of the dynamic electron redistribution is also analyzed on the basis of the ''coherent state.'' The new method relates the classical vibrational amplitude to the quantum number of the vibrational state. As a preliminary application of the present treatment, the dynamic electron densities of H 2 , HD, HT, HF, and HCl molecules are calculated by use of ab initio molecular orbital method
Molecular dynamic analysis of the structure of dendrimers
Energy Technology Data Exchange (ETDEWEB)
Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it
2004-01-01
We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.
Molecular dynamic analysis of the structure of dendrimers
International Nuclear Information System (INIS)
Canetta, E.; Maino, G.
2004-01-01
We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques
Free energy from molecular dynamics with multiple constraints
den Otter, Wouter K.; Briels, Willem J.
2000-01-01
In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to
Molecular Dynamics and Bioactivity of a Novel Mutated Human ...
African Journals Online (AJOL)
Keywords: Parathyroid hormone, Mutation prediction, Molecular dynamics, RANKL/OPG, UAMS-32P cell. Tropical .... PTH1R were used as MD simulation starting points. A full-atom ... Values of RMSD, Rg, and potential energy evaluation ...
Classical molecular dynamics simulation of nuclear fuels
International Nuclear Information System (INIS)
Devanathan, R.; Krack, M.; Bertolus, M.
2015-01-01
Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)
Development of an automated system for the operation of an electron beam accelerator
International Nuclear Information System (INIS)
Somessari, Samir L.; Moura, João A.; Calvo, Wilson Ap. Parejo
2017-01-01
Electron beam accelerators are used in many applications, such as basic physical research, chemistry, medicine, molecular biology, microelectronics, agriculture and industry, among others. The majority of the accelerators have electrons from a hot tungsten filament and their energy is increased as it passes through an electric field in the vacuum chamber. For industrial purposes, the most common model is Dynamitrons®. At IPEN-CNEN/SP, there is an electron beam accelerator Dynamitron® Type (Manufactured by RDI- Radiation Dynamics Inc., 1978) model DC1500/25/4. The technology applied was available in the 60's and 70's, but, nowadays is obsolete. Moreover, there are not original spare parts for this equipment any longer. The aim of this work is to develop a nationalized automated operation system for the accelerator, to replace the old equipment. (author)
Development of an automated system for the operation of an electron beam accelerator
Energy Technology Data Exchange (ETDEWEB)
Somessari, Samir L.; Moura, João A.; Calvo, Wilson Ap. Parejo, E-mail: somessar@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)
2017-11-01
Electron beam accelerators are used in many applications, such as basic physical research, chemistry, medicine, molecular biology, microelectronics, agriculture and industry, among others. The majority of the accelerators have electrons from a hot tungsten filament and their energy is increased as it passes through an electric field in the vacuum chamber. For industrial purposes, the most common model is Dynamitrons®. At IPEN-CNEN/SP, there is an electron beam accelerator Dynamitron® Type (Manufactured by RDI- Radiation Dynamics Inc., 1978) model DC1500/25/4. The technology applied was available in the 60's and 70's, but, nowadays is obsolete. Moreover, there are not original spare parts for this equipment any longer. The aim of this work is to develop a nationalized automated operation system for the accelerator, to replace the old equipment. (author)
Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Cedrix J. Dongmo Foumthuim
2018-01-01
Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
The chaos and order in nuclear molecular dynamics
International Nuclear Information System (INIS)
Srokowski, T.
1995-01-01
The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or 12 C, 16 O and 20 Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs
Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen
1999-06-01
Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.
Directory of Open Access Journals (Sweden)
Elena ePapaleo
2015-05-01
Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
Energy Technology Data Exchange (ETDEWEB)
Antipov, S. A.; Nagaitsev, S.; Valishev, A.
2017-04-01
Fermilab is constructing the Integrable Optics Test Accelerator (IOTA) as the centerpiece of the Accelerator R&D Program towards high-intensity circular machines. One of the factors limiting the beam intensity in present circular accelerators is collective instabilities, which can be suppressed by a spread of betatron frequencies (tunes) through the Landau damping mechanism or by an external damper, if the instability is slow enough. The spread is usually created by octupole magnets, which introduce the tune dependence on the amplitude and, in some cases, by a chromatic spread (tune dependence on particle's momentum). The introduction of octupoles usually lead to a resonant behavior and a reduction of the dynamic aperture. One of the goals of the IOTA research program is to achieve a high betatron tune spread, while retaining a large dynamic aperture using conventional octupole magnets in a special but realistic accelerator configuration. In this report, we present results of computer simulations of an electron beam in the IOTA by particle tracking and the Frequency Map Analysis. The results show that the ring's octupole magnets can be configured to provide a betatron tune shift of 0.08 (for particles at large amplitudes) with the dynamical aperture of over 20 beam sigma for a 150-MeV electron beam. The influence of the synchrotron motion, lattice errors, and magnet imperfections is insignificant for the parameters and levels of tolerances set by the design of the ring. The described octupole insert could be beneficial for suppression of space-charge induced instabilities in high intensity machines.
Fermionic molecular dynamics for ground states and collisions of nuclei
International Nuclear Information System (INIS)
Feldmeier, H.; Bieler, K.; Schnack, J.
1994-08-01
The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)
CERN. Geneva HR-RFA; Métral, E
2006-01-01
1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges
UCLA accelerator research ampersand development. Progress report
International Nuclear Information System (INIS)
1997-01-01
This report discusses work on advanced accelerators and beam dynamics at ANL, BNL, SLAC, UCLA and Pulse Sciences Incorporated. Discussed in this report are the following concepts: Wakefield acceleration studies; plasma lens research; high gradient rf cavities and beam dynamics studies at the Brookhaven accelerator test facility; rf pulse compression development; and buncher systems for high gradient accelerator and relativistic klystron applications
International Nuclear Information System (INIS)
Ogawa, Teiichiro
1986-01-01
Emission spectrum by controlled electron impact has been a successful technique for the investigation of molecular dynamics. (1) Molecular excitation. Aromatic molecules give an optical emission similar to fluorescence. However, as is shown by the vibrational structure and the electron energy dependence of benzene emission, its excitation process is not necessarily optical. Some aliphatic molecules also exhibit an emission band at the ultraviolet region. (2) Molecular dissociation. Analysis of the Doppler profile, the threshold energy, the excitation function and the isotope effect of the atomic emission produced in electron-molecule collisions has clarified the dynamics of the molecular dissociation. Especially the Doppler profile has given the translational energy distribution of the fragment atom, which is very useful to disclose the potential energy curve. Its angular dependence has recently found to allow determination of the symmetry of the intermediate excited state and the magnetic sublevel distribution of the fragment atom. These finding has revealed detailed state-to-state dynamics of the molecular dissociation. (author)
International Nuclear Information System (INIS)
Minoshima, Yusuke; Seki, Yusuke; Takayanagi, Toshiyuki; Shiga, Motoyuki
2016-01-01
Highlights: • Dynamics of excess electron attachment to guanine–cytosine base pair. • Ring-polymer and classical molecular dynamics simulations are performed. • Temperature and isotope substitution effects are investigated. - Abstract: The dynamical process of electron attachment to a guanine–cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.
Energy Technology Data Exchange (ETDEWEB)
Minoshima, Yusuke; Seki, Yusuke [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Takayanagi, Toshiyuki, E-mail: tako@mail.saitama-u.ac.jp [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Shiga, Motoyuki [Center for Computational Science and E-Systems, Japan Atomic Energy Agency, 148-4, Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba 277-0871 (Japan)
2016-06-15
Highlights: • Dynamics of excess electron attachment to guanine–cytosine base pair. • Ring-polymer and classical molecular dynamics simulations are performed. • Temperature and isotope substitution effects are investigated. - Abstract: The dynamical process of electron attachment to a guanine–cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.
Molecular dynamics simulation of a chemical reaction
International Nuclear Information System (INIS)
Gorecki, J.; Gryko, J.
1988-06-01
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
International Nuclear Information System (INIS)
Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira
2005-01-01
The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed
International Nuclear Information System (INIS)
Dzhilavyan, L.Z.; Karev, A.I.
1981-01-01
The results of experimental and theoretical investigations of the dynamics of a positron beam produced in a tantalum converter of the 6 mm thickness in the process of beam reacceleration in an electron linac (ELA) are presented. The mean finite positron currents and their dependences on the accelerating electric field are measured. The energy spectra of accelerated positrons are given. A good agreement between the calculated and experimental data is shown. As a result of investigations some peculiarities of positron production on the ELA intersection targets, which are defined by both the initial positron beam parameters from the converter and the dynamics of positron reacceleration in the ELA [ru
Wu, Bin
Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and
International Nuclear Information System (INIS)
Hardy, David J.; Schulten, Klaus; Wolff, Matthew A.; Skeel, Robert D.; Xia, Jianlin
2016-01-01
The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short.
Zhao, Lei; Cheng, Jiangtao
2017-09-07
In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.
Stereochemical errors and their implications for molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Freddolino Peter L
2011-05-01
Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.
In situ diffraction profile analysis during tensile deformation motivated by molecular dynamics
International Nuclear Information System (INIS)
Van Swygenhoven, H.; Budrovic, Z.; Derlet, P.M.; Froseth, A.G.; Van Petegem, S.
2005-01-01
Molecular dynamics simulations can provide insight into the slip mechanism at the atomic scale and suggest that in nanocrystalline metals dislocations are nucleated and absorbed by the grain boundaries. However, this technique is limited by very short simulation times. Using suggestions from molecular dynamics, we have developed a new in situ X-ray diffraction technique wherein the profile analysis of several Bragg diffraction peaks during tensile deformation is possible. Combining experiment and careful structural analysis the results confirm the suggestions from atomistic simulations
Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.
2017-03-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.
A molecular dynamics algorithm for simulation of field theories in the canonical ensemble
International Nuclear Information System (INIS)
Kogut, J.B.; Sinclair, D.K.
1986-01-01
We add a single scalar degree of freedom (''demon'') to the microcanonical ensemble which converts its molecular dynamics into a simulation method for the canonical ensemble (euclidean path integral) of the underlying field theory. This generalization of the microcanonical molecular dynamics algorithm simulates the field theory at fixed coupling with a completely deterministic procedure. We discuss the finite size effects of the method, the equipartition theorem and ergodicity. The method is applied to the planar model in two dimensions and SU(3) lattice gauge theory with four species of light, dynamical quarks in four dimensions. The method is much less sensitive to its discrete time step than conventional Langevin equation simulations of the canonical ensemble. The method is a straightforward generalization of a procedure introduced by S. Nose for molecular physics. (orig.)
Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories
Directory of Open Access Journals (Sweden)
Jenny Farmer
2017-11-01
Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.
Liquid-vapor coexistence by molecular dynamics simulation
International Nuclear Information System (INIS)
Baranyai, Andras; Cummings, Peter T.
2000-01-01
We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics
Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein
International Nuclear Information System (INIS)
Asafi, M S; Tekpinar, M; Yildirim, A
2016-01-01
Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated. (paper)
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
International Nuclear Information System (INIS)
Dellerue, Serge
2000-01-01
Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr
BEAMPATH: a program library for beam dynamics simulation in linear accelerators
International Nuclear Information System (INIS)
Batygin, Y.K.
1992-01-01
A structured programming technique was used to develop software for space charge dominated beams investigation in linear accelerators. The method includes hierarchical program design using program independent modules and a flexible combination of modules to provide a most effective version of structure for every specific case of simulation. A modular program BEAMPATH was developed for 2D and 3D particle-in-cell simulation of beam dynamics in a structure containing RF gaps, radio-frequency quadrupoles (RFQ), multipole lenses, waveguides, bending magnets and solenoids. (author) 5 refs.; 2 figs
Vogelsberg, Cortnie Sue
Amphidynamic crystals are an extremely promising platform for the development of artificial molecular machines and stimuli-responsive materials. In analogy to skeletal muscle, their function will rely upon the collective operation of many densely packed molecular machines (i.e. actin-bound myosin) that are self-assembled in a highly organized anisotropic medium. By choosing lattice-forming elements and moving "parts" with specific functionalities, individual molecular machines may be synthesized and self-assembled in order to carry out desirable functions. In recent years, efforts in the design of amphidynamic materials based on molecular gyroscopes and compasses have shown that a certain amount of free volume is essential to facilitate internal rotation and reorientation within a crystal. In order to further establish structure/function relationships to advance the development of increasingly complex molecular machinery, molecular rotors and a molecular "spinning" top were synthesized and incorporated into a variety of solid-state architectures with different degrees of periodicity, dimensionality, and free volume. Specifically, lamellar molecular crystals, hierarchically ordered periodic mesoporous organosilicas, and metal-organic frameworks were targeted for the development of solid-state molecular machines. Using an array of solid-state nuclear magnetic resonance spectroscopy techniques, the dynamic properties of these novel molecular machine assemblies were determined and correlated with their corresponding structural features. It was found that architecture type has a profound influence on functional dynamics. The study of layered molecular crystals, composed of either molecular rotors or "spinning" tops, probed functional dynamics within dense, highly organized environments. From their study, it was discovered that: 1) crystallographically distinct sites may be utilized to differentiate machine function, 2) halogen bonding interactions are sufficiently
Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios
2015-12-01
We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.
Molecular Dynamics with Helical Periodic Boundary Conditions
Czech Academy of Sciences Publication Activity Database
Kessler, Jiří; Bouř, Petr
2014-01-01
Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014
Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril
Energy Technology Data Exchange (ETDEWEB)
Okumura, Hisashi [Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585 (Japan); Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 (Japan)
2015-12-31
Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.
Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting
National Research Council Canada - National Science Library
Low, Tammy K
2006-01-01
.... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...
Using an electrostatic accelerator to determine the stereochemical structures of molecular ions
International Nuclear Information System (INIS)
Gemmell, D.S.
1980-01-01
Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the stereochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2 + , HeH + , CH + , NH + , OH + , N 2 + , O 2 + , etc.) with an accuracy of approx. 0.01 A. H 3 + has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2 + , N 2 O + , C 3 H 3 + , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2 + ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 +- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means
Directory of Open Access Journals (Sweden)
Usman Sumo Friend Tambunan
2017-04-01
Full Text Available Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world’s population in tropical and subtropical countries. Nonstructural protein 5 (NS5 methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S -adenosyl- l -methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2′OH, resulting in S -adenosyl- l -homocysteine (SAH. The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity test. The 2 simulations were performed using Molecular Operating Environment (MOE 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356 based on ΔG binding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.
GAMMA-RAY EMISSION OF ACCELERATED PARTICLES ESCAPING A SUPERNOVA REMNANT IN A MOLECULAR CLOUD
International Nuclear Information System (INIS)
Ellison, Donald C.; Bykov, Andrei M.
2011-01-01
We present a model of gamma-ray emission from core-collapse supernovae (SNe) originating from the explosions of massive young stars. The fast forward shock of the supernova remnant (SNR) can accelerate particles by diffusive shock acceleration (DSA) in a cavern blown by a strong, pre-SN stellar wind. As a fundamental part of nonlinear DSA, some fraction of the accelerated particles escape the shock and interact with a surrounding massive dense shell producing hard photon emission. To calculate this emission, we have developed a new Monte Carlo technique for propagating the cosmic rays (CRs) produced by the forward shock of the SNR, into the dense, external material. This technique is incorporated in a hydrodynamic model of an evolving SNR which includes the nonlinear feedback of CRs on the SNR evolution, the production of escaping CRs along with those that remain trapped within the remnant, and the broadband emission of radiation from trapped and escaping CRs. While our combined CR-hydro-escape model is quite general and applies to both core collapse and thermonuclear SNe, the parameters we choose for our discussion here are more typical of SNRs from very massive stars whose emission spectra differ somewhat from those produced by lower mass progenitors directly interacting with a molecular cloud.
Molecular dynamics in high electric fields
International Nuclear Information System (INIS)
Apostol, M.; Cune, L.C.
2016-01-01
Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.
Physical properties of Cu nanoparticles: A molecular dynamics study
International Nuclear Information System (INIS)
Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.
2014-01-01
Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index
Huge-scale molecular dynamics simulation of multibubble nuclei
Watanabe, Hiroshi
2013-12-01
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.
Molecular dynamics of the structure and thermodynamics of dusty ...
African Journals Online (AJOL)
The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...
Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems
Stanton, L. G.; Glosli, J. N.; Murillo, M. S.
2018-04-01
Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.
Antipov, S. A.; Nagaitsev, S.; Valishev, A.
2017-04-01
Fermilab is constructing the Integrable Optics Test Accelerator (IOTA) as the centerpiece of the Accelerator R&D Program towards high-intensity circular machines. One of the factors limiting the beam intensity in present circular accelerators is collective instabilities, which can be suppressed by a spread of betatron frequencies (tunes) through the Landau damping mechanism or by an external damper, if the instability is slow enough. The spread is usually created by octupole magnets, which introduce the tune dependence on the amplitude and, in some cases, by a chromatic spread (tune dependence on particle's momentum). The introduction of octupoles usually has both beneficial (improved Landau damping) and harmful properties, such as a resonant behavior and a reduction of the dynamic aperture. One of the research goals at the IOTA ring is to achieve a large betatron tune spread, while retaining a large dynamic aperture, using conventional octupole magnets in a special but realistic accelerator configuration. The configuration, although not integrable by design, approximates an autonomous 2D Hamiltonian system. In this paper, we present results of computer simulations of an electron beam in the IOTA by particle tracking and the Frequency Map Analysis. The results show that the ring's octupole magnets can be configured to provide a betatron tune shift of 0.08 (for particles at large amplitudes) with the dynamical aperture of over 20 beam sigma for a 150-MeV electron beam. The influence of the synchrotron motion, lattice errors, and magnet imperfections is insignificant for the parameters and levels of tolerances set by the design of the ring. The described octupole insert could be beneficial for enhancing Landau damping in high intensity machines.
Huang, Kun; García, Angel E
2014-10-14
The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl- sn -glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation.
Lipid Configurations from Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek
2018-01-01
of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...
Molecular dynamics studies of actinide nitrides
International Nuclear Information System (INIS)
Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo
2004-01-01
The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)
Molecular dynamics of surfactant protein C
DEFF Research Database (Denmark)
Ramírez, Eunice; Santana, Alberto; Cruz, Anthony
2006-01-01
Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...
Energy Technology Data Exchange (ETDEWEB)
Popp, Antonia
2011-12-16
The experiments presented in this thesis study several aspects of electron acceleration in a laser-driven plasma wave. High-intensity lasers can efficiently drive a plasma wave that sustains electric fields on the order of 100 GV/m. Electrons that are trapped in this plasma wave can be accelerated to GeV-scale energies. As the accelerating fields in this scheme are 3-4 orders of magnitude higher than in conventional radio-frequency accelerators, the necessary acceleration distance can be reduced by the same factor, turning laser-wakefield acceleration (LWFA) into a promising compact, and potentially cheaper, alternative. However, laser-accelerated electron bunches have not yet reached the parameter standards of conventional accelerators. This work will help to gain better insight into the acceleration process and to optimize the electron bunch properties. The 25 fs, 1.8 J-pulses of the ATLAS laser at the Max-Planck-Institute of Quantum Optics were focused into a steady-state flow gas cell. This very reproducible and turbulence-free gas target allows for stable acceleration of electron bunches. Thus the sensitivity of electron parameters to subtle changes of the experimental setup could be determined with meaningful statistics. At optimized experimental parameters, electron bunches of {approx}50 pC total charge were accelerated to energies up to 450 MeV with a divergence of {approx}2 mrad FWHM. As, in a new design of the gas cell, its length can be varied from 2 to 14 mm, the electron bunch energy could be evaluated after different acceleration distances, at two different electron densities. From this evolution important acceleration parameters could be extracted. At an electron density of 6.43. 10{sup 18} cm{sup -3} the maximum electric field strength in the plasma wave was determined to be {approx}160 GV/m. The length after which the relativistic electrons outrun the accelerating phase of the electric field and are decelerated again, the so-called dephasing length
International Nuclear Information System (INIS)
Popp, Antonia
2011-01-01
The experiments presented in this thesis study several aspects of electron acceleration in a laser-driven plasma wave. High-intensity lasers can efficiently drive a plasma wave that sustains electric fields on the order of 100 GV/m. Electrons that are trapped in this plasma wave can be accelerated to GeV-scale energies. As the accelerating fields in this scheme are 3-4 orders of magnitude higher than in conventional radio-frequency accelerators, the necessary acceleration distance can be reduced by the same factor, turning laser-wakefield acceleration (LWFA) into a promising compact, and potentially cheaper, alternative. However, laser-accelerated electron bunches have not yet reached the parameter standards of conventional accelerators. This work will help to gain better insight into the acceleration process and to optimize the electron bunch properties. The 25 fs, 1.8 J-pulses of the ATLAS laser at the Max-Planck-Institute of Quantum Optics were focused into a steady-state flow gas cell. This very reproducible and turbulence-free gas target allows for stable acceleration of electron bunches. Thus the sensitivity of electron parameters to subtle changes of the experimental setup could be determined with meaningful statistics. At optimized experimental parameters, electron bunches of ∼50 pC total charge were accelerated to energies up to 450 MeV with a divergence of ∼2 mrad FWHM. As, in a new design of the gas cell, its length can be varied from 2 to 14 mm, the electron bunch energy could be evaluated after different acceleration distances, at two different electron densities. From this evolution important acceleration parameters could be extracted. At an electron density of 6.43. 10 18 cm -3 the maximum electric field strength in the plasma wave was determined to be ∼160 GV/m. The length after which the relativistic electrons outrun the accelerating phase of the electric field and are decelerated again, the so-called dephasing length, was found to be 4.9 mm
Temperature dependent dynamics of DegP-trimer: A molecular dynamics study
Directory of Open Access Journals (Sweden)
Nivedita Rai
2015-01-01
Full Text Available DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46–80 of LA loop express a flip towards right (at 280 and left ( at 320 K with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.
The dance of molecules: new dynamical perspectives on highly excited molecular vibrations.
Kellman, Michael E; Tyng, Vivian
2007-04-01
At low energies, molecular vibrational motion is described by the normal modes model. This model breaks down at higher energy, with strong coupling between normal modes and onset of chaotic dynamics. New anharmonic modes are born in bifurcations, or branchings of the normal modes. Knowledge of these new modes is obtained through the window of frequency-domain spectroscopy, using techniques of nonlinear classical dynamics. It may soon be possible to "watch" molecular rearrangement reactions spectroscopically. Connections are being made with reaction rate theories, condensed phase systems, and motions of electrons in quantum dots.
Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.
Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro
2015-01-01
Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Energy Technology Data Exchange (ETDEWEB)
Car, R.; Parrinello, M.
1988-01-18
An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.
International Nuclear Information System (INIS)
Gupta, Moumita; Dastidar, Krishna Rai
2009-01-01
We study the dynamics of the atomic and molecular Bose-Einstein condensates (BECs) of 87 Rb in a spherically symmetric trap coupled by stimulated Raman photoassociation process. Considering the higher order nonlinearity in the atom-atom interaction we analyze the dynamics of the system using coupled modified Gross-Pitaevskii (MGP) equations and compare it with mean-field coupled Gross-Pitaevskii (GP) dynamics. Considerable differences in the dynamics are obtained in these two approaches at large scattering length, i.e., for large values of peak-gas parameter x pk ≥10 -3 . We show how the dynamics of the coupled system is affected when the atom-molecule and molecule-molecule interactions are considered together with the atom-atom interaction and also when the strengths of these three interactions are increased. The effect of detuning on the efficiency of conversion of atomic fractions into molecules is demonstrated and the feasibility of maximum molecular BEC formation by varying the Raman detuning parameter at different values of time is explored. Thus by varying the Raman detuning and the scattering length for atom-atom interaction one can control the dynamics of the coupled atomic-molecular BEC system. We have also solved coupled Gross-Pitaevskii equations for atomic to molecular condensate formation through magnetic Feshbach resonance in a BEC of 85 Rb. We found similar features for oscillations between atomic and molecular condensates noted in previous theoretical study and obtained fairly good agreement with the evolution of total atomic condensate observed experimentally.
Improved scaling of temperature-accelerated dynamics using localization
Energy Technology Data Exchange (ETDEWEB)
Shim, Yunsic; Amar, Jacques G. [Department of Physics and Astronomy, University of Toledo, Toledo, Ohio 43606 (United States)
2016-07-07
While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N{sup 3} where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scaling of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary “bottlenecks” to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N{sup 1/2}. Some additional possible methods to improve the scaling of TAD are also discussed.
Improved scaling of temperature-accelerated dynamics using localization
International Nuclear Information System (INIS)
Shim, Yunsic; Amar, Jacques G.
2016-01-01
While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N 3 where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scaling of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary “bottlenecks” to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N 1/2 . Some additional possible methods to improve the scaling of TAD are also discussed.
Molecular dynamics study of the silica-water-SDA interactions
Szyja, B.M.; Jansen, A.P.J.; Verstraelen, T.; Santen, van R.A.
2009-01-01
In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species
Dynamic High Pressure Study of Chemistry and Physics of Molecular Materials
Jezowski, Sebastian Ryszard
Both temperature and pressure control and influence the packing of molecules in crystalline phases. Our molecular simulations indicate that at ambient pressure, the cubic polymorph of tetracyanoethylene, TCNE, is the energetically stable form up to ˜ 160 K. The observed transition from the cubic to the monoclinic polymorph occurs however only at temperatures above ˜ 318 K due to the large transition barrier. The temperature-induced phase transition in TCNE studied with high-resolution IR spectroscopy is explained in terms of the increased vibrational entropy in the crystals of the monoclinic polymorph. Based upon the inverted design of the Merril-Bassett Diamond Anvil Cell, an improved, second generation dynamic Diamond Anvil Cell was developed. Based on the fluorescence of ruby crystals, we were able to demonstrate that the pressure variation range can be further increased at least up to 7 kbar and that the dynamic pressure compression of up to 1400 GPa/s can be achieved. A new class of mechanophoric system, bis-anthracene, BA, and its photoisomer, PI, is shown to respond reversibly to a mild, static pressure induced by a Diamond Anvil Cell as well as to shear deformation based on absorption spectroscopic measurements. The forward reaction occurs upon illumination with light while the back-reaction may be accelerated upon heating or mechanical stress, coupled to a rehybridization on four equivalent carbon atoms. It is an intriguing result as high pressure stabilizes the photodimerized species in related systems. Our molecular volume simulations ruled out significant differences in the volumes between bis-anthracene and its photoisomer. Kinetic absorption measurements at several different pressures reveal a negative volume of activation in the exothermic back-reaction at room temperature. Through a series of temperature-dependent kinetic measurements it is shown that the barrier of activation for the back-reaction is reduced by more than an order of magnitude at
MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation
International Nuclear Information System (INIS)
Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.
1991-01-01
We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus
Statistical ensembles and molecular dynamics studies of anisotropic solids. II
International Nuclear Information System (INIS)
Ray, J.R.; Rahman, A.
1985-01-01
We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities
Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy
Ocaya, R. O.; Terblans, J. J.
2017-10-01
Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.
Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics
Directory of Open Access Journals (Sweden)
Wei Zhang
2017-07-01
Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.
Molecular Dynamics Approach in Designing Thermostable Aspergillus niger Xylanase
Malau, N. D.; Sianturi, M.
2017-03-01
Molecular dynamics methods we have applied as a tool in designing thermostable Aspergillus niger Xylanase, by examining Root Mean Square Deviation (RMSD) and The Stability of the Secondary Structure of enzymes structure at its optimum temperature and compare with its high temperature behavior. As RMSD represents structural fluctuation at a particular temperature, a better understanding of this factor will suggest approaches to bioengineer these enzymes to enhance their thermostability. In this work molecular dynamic simulations of Aspergillus niger xylanase (ANX) have been carried at 400K (optimum catalytic temperature) for 2.5 ns and 500K (ANX reported inactive temperature) for 2.5 ns. Analysis have shown that the Root Mean Square Deviation (RMSD) significant increase at higher temperatures compared at optimum temperature and some of the secondary structures of ANX that have been damaged at high temperature. Structural analysis revealed that the fluctuations of the α-helix and β-sheet regions are larger at higher temperatures compared to the fluctuations at optimum temperature.
A new parallel molecular dynamics algorithm for organic systems
International Nuclear Information System (INIS)
Plimpton, S.; Hendrickson, B.; Heffelfinger, G.
1993-01-01
A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed
Molecular Dynamics Simulations of displacement cascades in metallic systems
International Nuclear Information System (INIS)
Doan, N.V.; Tietze, H.
1995-01-01
We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)
Ultrafast dissociation: An unexpected tool for probing molecular dynamics
International Nuclear Information System (INIS)
Morin, Paul; Miron, Catalin
2012-01-01
Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.
Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C
2013-11-07
Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.
Creer, Brent Y.; Smedal, Harald A.; Wingrove, Rodney C.
1960-01-01
A research program the general objective of which was to measure the effects of various sustained accelerations on the control performance of pilots, was carried out on the Aviation Medical Acceleration Laboratory centrifuge, U.S. Naval Air Development Center, Johnsville, PA. The experimental setup consisted of a flight simulator with the centrifuge in the control loop. The pilot performed his control tasks while being subjected to acceleration fields such as might be encountered by a forward-facing pilot flying an atmosphere entry vehicle. The study was divided into three phases. In one phase of the program, the pilots were subjected to a variety of sustained linear acceleration forces while controlling vehicles with several different sets of longitudinal dynamics. Here, a randomly moving target was displayed to the pilot on a cathode-ray tube. For each combination of acceleration field and vehicle dynamics, pilot tracking accuracy was measured and pilot opinion of the stability and control characteristics was recorded. Thus, information was obtained on the combined effects of complexity of control task and magnitude and direction of acceleration forces on pilot performance. These tests showed that the pilot's tracking performance deteriorated markedly at accelerations greater than about 4g when controlling a lightly damped vehicle. The tentative conclusion was also reached that regardless of the airframe dynamics involved, the pilot feels that in order to have the same level of control over the vehicle, an increase in the vehicle dynamic stability was required with increases in the magnitudes of the acceleration impressed upon the pilot. In another phase, boundaries of human tolerance of acceleration were established for acceleration fields such as might be encountered by a pilot flying an orbital vehicle. A special pilot restraint system was developed to increase human tolerance to longitudinal decelerations. The results of the tests showed that human tolerance
The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations
International Nuclear Information System (INIS)
Bianchi, L.
2000-05-01
Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial
Molecular beam studies of reaction dynamics
International Nuclear Information System (INIS)
Lee, Yuan T.
1991-03-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation
Molecular beam studies of reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
A molecular dynamics calculation of solid phase of malonic acid ...
Indian Academy of Sciences (India)
Sathya S R R Perumal
Keywords. Hydrogen bond chain; elastic constants; molecular dynamics. 1. Introduction ... theory - a probabilistic model to determine the hydro- gen bonds within the .... compares poorly with the experimental value of 108.5. Similarly β and γ ...
On the molecular dynamics in the hurricane interactions with its environment
Meyer, Gabriel; Vitiello, Giuseppe
2018-06-01
By resorting to the Burgers model for hurricanes, we study the molecular motion involved in the hurricane dynamics. We show that the Lagrangian canonical formalism requires the inclusion of the environment degrees of freedom. This also allows the description of the motion of charged particles. In view of the role played by moist convection, cumulus and cloud water droplets in the hurricane dynamics, we discuss on the basis of symmetry considerations the role played by the molecular electrical dipoles and the formation of topologically non-trivial structures. The mechanism of energy storage and dissipation, the non-stationary time dependent Ginzburg-Landau equation and the vortex equation are studied. Finally, we discuss the fractal self-similarity properties of hurricanes.
International Nuclear Information System (INIS)
Antipov, S.A.; Nagaitsev, S.; Valishev, A.
2017-01-01
Fermilab is constructing the Integrable Optics Test Accelerator (IOTA) as the centerpiece of the Accelerator R and D Program towards high-intensity circular machines. One of the factors limiting the beam intensity in present circular accelerators is collective instabilities, which can be suppressed by a spread of betatron frequencies (tunes) through the Landau damping mechanism or by an external damper, if the instability is slow enough. The spread is usually created by octupole magnets, which introduce the tune dependence on the amplitude and, in some cases, by a chromatic spread (tune dependence on particle's momentum). The introduction of octupoles usually has both beneficial (improved Landau damping) and harmful properties, such as a resonant behavior and a reduction of the dynamic aperture. One of the research goals at the IOTA ring is to achieve a large betatron tune spread, while retaining a large dynamic aperture, using conventional octupole magnets in a special but realistic accelerator configuration. The configuration, although not integrable by design, approximates an autonomous 2D Hamiltonian system. In this paper, we present results of computer simulations of an electron beam in the IOTA by particle tracking and the Frequency Map Analysis. The results show that the ring's octupole magnets can be configured to provide a betatron tune shift of 0.08 (for particles at large amplitudes) with the dynamical aperture of over 20 beam sigma for a 150-MeV electron beam. The influence of the synchrotron motion, lattice errors, and magnet imperfections is insignificant for the parameters and levels of tolerances set by the design of the ring. The described octupole insert could be beneficial for enhancing Landau damping in high intensity machines.
Aono, T.; Kazama, A.; Okada, R.; Iwasaki, T.; Isono, Y.
2018-03-01
We developed a eutectic-based wafer-level-packaging (WLP) technique for piezoresistive micro-electromechanical systems (MEMS) accelerometers on the basis of molecular dynamics analyses and shear tests of WLP accelerometers. The bonding conditions were experimentally and analytically determined to realize a high shear strength without solder material atoms diffusing to adhesion layers. Molecular dynamics (MD) simulations and energy dispersive x-ray (EDX) spectrometry done after the shear tests clarified the eutectic reaction of the solder materials used in this research. Energy relaxation calculations in MD showed that the diffusion of solder material atoms into the adhesive layer was promoted at a higher temperature. Tensile creep MD simulations also suggested that the local potential energy in a solder material model determined the fracture points of the model. These numerical results were supported by the shear tests and EDX analyses for WLP accelerometers. Consequently, a bonding load of 9.8 kN and temperature of 300 °C were found to be rational conditions because the shear strength was sufficient to endure the polishing process after the WLP process and there was little diffusion of solder material atoms to the adhesion layer. Also, eutectic-bonding-based WLP was effective for controlling the attenuation of the accelerometers by determining the thickness of electroplated solder materials that played the role of a cavity between the accelerometers and lids. If the gap distance between the two was less than 6.2 µm, the signal gains for x- and z-axis acceleration were less than 20 dB even at the resonance frequency due to air-damping.
Energy Technology Data Exchange (ETDEWEB)
Spentzouris, P.; /Fermilab; Cary, J.; /Tech-X, Boulder; McInnes, L.C.; /Argonne; Mori, W.; /UCLA; Ng, C.; /SLAC; Ng, E.; Ryne, R.; /LBL, Berkeley
2011-11-14
The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors. ComPASS is in the first year of executing its plan to develop the next-generation HPC accelerator modeling tools. ComPASS aims to develop an integrated simulation environment that will utilize existing and new accelerator physics modules with petascale capabilities, by employing modern computing and solver technologies. The ComPASS vision is to deliver to accelerator scientists a virtual accelerator and virtual prototyping modeling environment, with the necessary multiphysics, multiscale capabilities. The plan for this development includes delivering accelerator modeling applications appropriate for each stage of the ComPASS software evolution. Such applications are already being used to address challenging problems in accelerator design and optimization. The ComPASS organization
International Nuclear Information System (INIS)
Wang, J.; Gutierre, M.S.
2010-01-01
This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.
Wiedemann, Helmut
2015-01-01
This book by Helmut Wiedemann is a well-established, classic text, providing an in-depth and comprehensive introduction to the field of high-energy particle acceleration and beam dynamics. The present 4th edition has been significantly revised, updated and expanded. The newly conceived Part I is an elementary introduction to the subject matter for undergraduate students. Part II gathers the basic tools in preparation of a more advanced treatment, summarizing the essentials of electrostatics and electrodynamics as well as of particle dynamics in electromagnetic fields. Part III is an extensive primer in beam dynamics, followed, in Part IV, by an introduction and description of the main beam parameters and including a new chapter on beam emittance and lattice design. Part V is devoted to the treatment of perturbations in beam dynamics. Part VI then discusses the details of charged particle acceleration. Parts VII and VIII introduce the more advanced topics of coupled beam dynamics and describe very intense bea...
International Nuclear Information System (INIS)
Morini, Filippo; Deleuze, Michael S.; Watanabe, Noboru; Takahashi, Masahiko
2015-01-01
The influence of thermally induced nuclear dynamics (molecular vibrations) in the initial electronic ground state on the valence orbital momentum profiles of furan has been theoretically investigated using two different approaches. The first of these approaches employs the principles of Born-Oppenheimer molecular dynamics, whereas the so-called harmonic analytical quantum mechanical approach resorts to an analytical decomposition of contributions arising from quantized harmonic vibrational eigenstates. In spite of their intrinsic differences, the two approaches enable consistent insights into the electron momentum distributions inferred from new measurements employing electron momentum spectroscopy and an electron impact energy of 1.2 keV. Both approaches point out in particular an appreciable influence of a few specific molecular vibrations of A 1 symmetry on the 9a 1 momentum profile, which can be unravelled from considerations on the symmetry characteristics of orbitals and their energy spacing
Metal cluster fission: jellium model and Molecular dynamics simulations
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia
2004-01-01
Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...
Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica
2012-10-09
NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.
Beam Dynamics Design Studies of a Superconducting Radioactive Ion Beam Post-accelerator
Fraser, MA; Pasini, M
2011-01-01
The HIE-ISOLDE project at CERN proposes a superconducting upgrade to increase the energy range and quality of the radioactive ion beams produced at ISOLDE, which are currently post- accelerated by the normal conducting REX linac. The specification and design choices for the HIE-ISOLDE linac are outlined along with a comprehensive beam dynamics study undertaken to understand and mitigate the sources of beam emittance dilution. The dominant cause of transverse emittance growth was attributed to the coupling between the transverse and longitudinal motions through the phase dependence of the rf defocusing force in the accelerating cavities. A parametric resonance induced by the coupling was observed and its excitation surveyed as a function of trans- verse phase advance using numerical simulations and analytic models to understand and avoid the regions of transverse beam instability. Other sources of emittance growth were studied and where necessary ameliorated, including the beam steering force in the quarter-wa...
An improved cellular automata model for train operation simulation with dynamic acceleration
Li, Wen-Jun; Nie, Lei
2018-03-01
Urban rail transit plays an important role in the urban public traffic because of its advantages of fast speed, large transport capacity, high safety, reliability and low pollution. This study proposes an improved cellular automaton (CA) model by considering the dynamic characteristic of the train acceleration to analyze the energy consumption and train running time. Constructing an effective model for calculating energy consumption to aid train operation improvement is the basis for studying and analyzing energy-saving measures for urban rail transit system operation.
General accelerator physics. Proceedings. Vol. 2
International Nuclear Information System (INIS)
Bryant, P.; Turner, S.
1985-01-01
This course on accelerator physics is the first in a series of two, which is planned by the CERN Accelerator School. Starting at the level of a science graduate, this course covers mainly linear theory. The topics include: transverse and longitudinal beam dynamics, insertions, coupling, transition, dynamics of radiating particles, space-charge forces, neutralization, beam profiles, luminosity calculations in colliders, longitudinal phase-space stacking, phase-displacement acceleration, transfer lines, injection and extraction. Some more advanced topics are also introduced: coherent instabilities in coasting beams, general collective phenomena, quantum lifetime, and intra-beam scattering. The seminar programme is based on two themes: firstly, the sub-systems of an accelerator and, secondly, the uses to which accelerators are put. (orig.)
Rheology of liquid n-triacontane: Molecular dynamics simulation
International Nuclear Information System (INIS)
Kondratyuk, N D; Norman, G E; Stegailov, V V
2016-01-01
Molecular dynamics is applied to calculate diffusion coefficients of n-triacontane C 30 H 62 using Einstein-Smoluchowski and Green-Kubo relations. The displacement 〈Δr 2 〉( t ) has a subdiffusive part 〈Δr 2 〉 ∼ t α , caused by molecular crowding at low temperatures. Longtime asymptotes of 〈v(0)v(t)〉 are collated with the hydrodynamic tail t -3/2 demonstrated for atomic liquids. The influence of these asymptotes on the compliance of Einstein-Smoluchowski and Green-Kubo methods is analyzed. The effects of the force field parameters on the diffusion process are treated. The results are compared with experimental data. (paper)
Energy Technology Data Exchange (ETDEWEB)
Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)
2014-12-09
The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.
Viscosity calculations at molecular dynamics simulations
International Nuclear Information System (INIS)
Kirova, E M; Norman, G E
2015-01-01
Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)
Radiative damping in plasma-based accelerators
Directory of Open Access Journals (Sweden)
I. Yu. Kostyukov
2012-11-01
Full Text Available The electrons accelerated in a plasma-based accelerator undergo betatron oscillations and emit synchrotron radiation. The energy loss to synchrotron radiation may seriously affect electron acceleration. The electron dynamics under combined influence of the constant accelerating force and the classical radiation reaction force is studied. It is shown that electron acceleration cannot be limited by radiation reaction. If initially the accelerating force was stronger than the radiation reaction force, then the electron acceleration is unlimited. Otherwise the electron is decelerated by radiative damping up to a certain instant of time and then accelerated without limits. It is shown that regardless of the initial conditions the infinite-time asymptotic behavior of an electron is governed by a self-similar solution providing that the radiative damping becomes exactly equal to 2/3 of the accelerating force. The relative energy spread induced by the radiative damping decreases with time in the infinite-time limit. The multistage schemes operating in the asymptotic acceleration regime when electron dynamics is determined by the radiation reaction are discussed.
Three-stage classical molecular dynamics model for simulation of heavy-ion fusion
Directory of Open Access Journals (Sweden)
Godre Subodh S.
2015-01-01
Full Text Available A three-stage Classical Molecular Dynamics (3S-CMD approach for heavy-ion fusion is developed. In this approach the Classical Rigid-Body Dynamics simulation for heavy-ion collision involving light deformed nucleus is initiated on their Rutherford trajectories at very large initial separation. Collision simulation is then followed by relaxation of the rigid-body constrains for one or both the colliding nuclei at distances close to the barrier when the trajectories of all the nucleons are obtained in a Classical Molecular Dynamics approach. This 3S-CMD approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but also the internal vibrational excitations of one or both the nuclei at distances close to the barrier. The results of the dynamical simulation for 24Mg+208Pb collision show significant modification of the fusion barrier and calculated fusion cross sections due to internal excitations.
Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations
International Nuclear Information System (INIS)
Kim, Woongkee; Kaviany, Massoud; Shim, J. H.
2014-01-01
It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments
Charge Carrier Dynamics at Silver Nanocluster-Molecular Acceptor Interfaces
Almansaf, Abdulkhaleq
2017-07-01
A fundamental understanding of interfacial charge transfer at donor-acceptor interfaces is very crucial as it is considered among the most important dynamical processes for optimizing performance in many light harvesting systems, including photovoltaics and photo-catalysis. In general, the photo-generated singlet excitons in photoactive materials exhibit very short lifetimes because of their dipole-allowed spin radiative decay and short diffusion lengths. In contrast, the radiative decay of triplet excitons is dipole forbidden; therefore, their lifetimes are considerably longer. The discussion in this thesis primarily focuses on the relevant parameters that are involved in charge separation (CS), charge transfer (CT), intersystem crossing (ISC) rate, triplet state lifetime, and carrier recombination (CR) at silver nanocluster (NCs) molecular-acceptors interfaces. A combination of steady-state and femto- and nanosecond broadband transient absorption spectroscopies were used to investigate the charge carrier dynamics in various donor-acceptor systems. Additionally, this thesis was prolonged to investigate some important factors that influence the charge carrier dynamics in Ag29 silver NCs donor-acceptor systems, such as the metal doping and chemical structure of the nanocluster and molecular acceptors. Interestingly, clear correlations between the steady-state measurements and timeresolved spectroscopy results are found. In the first study, we have investigated the interfacial charge transfer dynamics in positively charged meso units of 5, 10, 15, 20-tetra (1- methyl-4-pyridino)-porphyrin tetra (p-toluene sulfonate) (TMPyP) and neutral charged 5, 10, 15, 20-tetra (4-pyridyl)-porphyrin (TPyP), with negatively charged undoped and gold (Au)- doped silver Ag29 NCs. Moreover, this study showed the impact of Au doping on the charge carrier dynamics of the system. In the second study, we have investigated the interfacial charge transfer dynamics in [Pt2 Ag23 Cl7 (PPh3
Petascale molecular dynamics simulation using the fast multipole method on K computer
Ohno, Yousuke; Yokota, Rio; Koyama, Hiroshi; Morimoto, Gentaro; Hasegawa, Aki; Masumoto, Gen; Okimoto, Noriaki; Hirano, Yoshinori; Ibeid, Huda; Narumi, Tetsu; Taiji, Makoto
2014-01-01
In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
Petascale molecular dynamics simulation using the fast multipole method on K computer
Ohno, Yousuke
2014-10-01
In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.
Yoo, Jejoong; Aksimentiev, Aleksei
2013-12-10
The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.
Molecular dynamics of interfacial water and cations associated with clay minerals
International Nuclear Information System (INIS)
Cygan, Randall T.; Greathouse, Jeffery A.; Teich-McGoldrick, Stephanie L.; Nenoff, Tina M.; Daemen, Luke L.
2012-01-01
Document available in extended abstract form only. Clay mineral interfaces, including interlayer and external surfaces, play an essential role in many geochemical processes. Adsorption, dissolution, precipitation, nucleation, and growth mechanisms, in particular, are controlled by the interplay of structure, thermodynamics, kinetics, and transport at clay mineral-water interfaces. Molecular details of these geochemical processes are especially important in evaluating the fate of radionuclide waste in the environment. Such details are typically beyond the sensitivity of experimental and analytical methods and therefore require accurate models and simulations. Also, the basal surfaces and interlayers of clay minerals offer structurally constrained interfacial environments to better evaluate the local molecular chemistry. We have developed and used classical and quantum methods to examine the complex behavior of clay mineral-water interfaces and dynamics of interlayer species. Bulk structures, swelling behavior, diffusion, and adsorption processes are evaluated and compared to experimental and spectroscopic findings. In particular, inelastic neutron scattering methods provide a successful probe of vibrational behavior of interlayer species to help guide the simulations. Librations involving rock, wag, and twist motions of water molecules are particularly sensitive to the interlayer environment of smectite minerals such as montmorillonite and beidellite. Trends in librational modes for interlayer water as a function of clay structure and cation hydration energy are readily explained using structural and vibrational analysis derived from molecular simulation. Molecular dynamics simulations of virtual phases, including hydrated pyrophyllite, help to explain the behavior of interlayer water that is not associated with cation species. Additionally, we use large-scale molecular dynamics simulations of other layered minerals, such as muscovite, to evaluate adsorption
Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates
Energy Technology Data Exchange (ETDEWEB)
Zhang Junfang [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia); Rivero, Mayela [CSIRO Petroleum, PO Box 1130, Bentley, Western Australia, 6102 (Australia); Choi, S K [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia)
2007-02-14
We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 A. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.
FPGA Acceleration by Dynamically-Loaded Hardware Libraries
DEFF Research Database (Denmark)
Lomuscio, Andrea; Nannarelli, Alberto; Re, Marco
-the-y the speciffic processor in the FPGA, and we transfer the execution from the CPU to the FPGA-based accelerator. Results show that significant speed-up and energy efficiency can be obtained by HLL acceleration on system-on-chips where reconfigurable fabric is placed next to the CPUs....
Molecular dynamics study on the relaxation properties of bilayered ...
Indian Academy of Sciences (India)
2017-08-31
Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...
Molecular dynamics studies of crystalline nucleation in one-component Yukawa plasmas
International Nuclear Information System (INIS)
Ravelo, R.; Hammerberg, J.E.; Holian, B.L.
1992-01-01
We report on molecular dynamics studies of one-component Yukawa plasmas undergoing rapid quenches from a fluid state with a Coulomb parameter Γ = 40 to solid states in the range 350 < Γ < 800. The detailed dynamical structure of ordering appears more complicated than results from classical theories of nucleation, with planar formation being observed before fully 3-dimensional ordering appears
Particle-in-Cell Code BEAMPATH for Beam Dynamics Simulations in Linear Accelerators and Beamlines
International Nuclear Information System (INIS)
Batygin, Y.
2004-01-01
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
Particle-in-Cell Code BEAMPATH for Beam Dynamics Simulations in Linear Accelerators and Beamlines
Energy Technology Data Exchange (ETDEWEB)
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.
Molecular dynamics simulation of a DNA containing a single strand break
Energy Technology Data Exchange (ETDEWEB)
Yamaguchi, H.; Siebers, G.; Furukawa, A.; Otagiri, N.; Osman, R
2002-07-01
Molecular dynamics simulations were performed for a dodecamer DNA containing a single strand break (SSB), which has been represented by a 3'-OH deoxyribose and 5'-OH phosphate in the middle of the strand. Molecular force field parameters of the 5'-OH phosphate region were determined from an ab initio calculation at the HF/6-31G level using the program package GAMESS. The DNA was placed in a periodic boundary box with water molecules and Na+ counter-ions to produce a neutralised system. After minimisation, the system was heated to 300 K, equilibrated and a production run at constant NTP was executed for 1 ns using AMBER 4.1. Snapshots of the SSB-containing DNA and a detailed analysis of the equilibriated average structure revealed surprisingly small conformational changes compared to normal DNA. However, dynamic properties calculated using the essential dynamics method showed some features that may be important for the recognition of this damage by repair enzymes. (author)
Molecular structures and intramolecular dynamics of pentahalides
Ischenko, A. A.
2017-03-01
This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.
Bolhuis, Peter
Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.
International Nuclear Information System (INIS)
Bhowmik, Rahul; Katti, Kalpana S.; Verma, Devendra; Katti, Dinesh R.
2007-01-01
Polymer-hydroxyapatite (HAP) composites are widely investigated for their potential use as bone replacement materials. The molecular interactions at mineral polymer interface are known to have significant role of mechanical response of the composite system. Modeling interactions between such dissimilar molecules using molecular dynamics (MD) is an area of current interest. Molecular dynamics studies require potential function or force field parameters. Some force fields are described in literature that represents the structure of hydroxyapatite reasonably well. Yet, the applicability of these force fields for studying the interaction between dissimilar materials (such as mineral and polymer) is limited, as there is no accurate representation of polymer in these force fields. We have obtained the parameters of consistent valence force field (CVFF) for monoclinic hydroxyapatite. Validation of parameters was done by comparing the computationally obtained unit cell parameters, vibrational spectra and atomic distances with XRD and FTIR experiments. Using the obtained parameters of HAP, and available parameters of polymer (polyacrylic acid), interaction study was performed with MD simulations. The MD simulations showed that several hydrogen bonds may form between HAP and polyacrylic acid depending upon the exposed surface of HAP. Also there are some favourable planes of HAP where polyacrylic acid is most likely to attach. We have also simulated the mineralization of HAP using a 'synthetic biomineralization'. These modeling studies are supported by photoacoustic spectroscopy experiments on both porous and non porous composite samples for potential joint replacement and bone tissue engineering applications
A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon
International Nuclear Information System (INIS)
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
International Nuclear Information System (INIS)
Koszykowski, M.L.; Pfeffer, G.A.; Noid, D.W.
1987-01-01
Nonlinear dynamics plays a dominant role in a variety of important problems in chemical physics. Examples are unimolecular reactions, infrared multiphoton decomposition of molecules, the pumping process of the gamma ray laser, dissociation of vibrationally excited state-selected van der Waals's complexes, and many other chemical and atomic processes. The present article discusses recent theoretical studies on the quasi-periodic and chaotic dynamic aspects of vibrational-rotational states of atomic, nuclear, and molecular systems using the semiclassical spectral method (SSM). The authors note that the coordinates, momenta, and so on, are found using classical mechanics in the studies included in this review. They outline the semiclassical spectral method and a wide variety of applications. Although this technique was first developed ten years ago, it has proved to be tremendously successful as a tool used in dynamics problems. Applications include problems in nonlinear dynamics, molecular and atomic spectra, surface science, astronomy and stellar dynamics, nuclear physics, and polymer physics
International Nuclear Information System (INIS)
Spentzouris, P.; Cary, J.; McInnes, L.C.; Mori, W.; Ng, C.; Ng, E.; Ryne, R.
2008-01-01
The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R and D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors.
Rayleigh-Taylor mixing with time-dependent acceleration
Abarzhi, Snezhana
2016-10-01
We extend the momentum model to describe Rayleigh-Taylor (RT) mixing driven by a time-dependent acceleration. The acceleration is a power-law function of time, similarly to astrophysical and plasma fusion applications. In RT flow the dynamics of a fluid parcel is driven by a balance per unit mass of the rates of momentum gain and loss. We find analytical solutions in the cases of balanced and imbalanced gains and losses, and identify their dependence on the acceleration exponent. The existence is shown of two typical regimes of self-similar RT mixing-acceleration-driven Rayleigh-Taylor-type and dissipation-driven Richtymer-Meshkov-type with the latter being in general non-universal. Possible scenarios are proposed for transitions from the balanced dynamics to the imbalanced self-similar dynamics. Scaling and correlations properties of RT mixing are studied on the basis of dimensional analysis. Departures are outlined of RT dynamics with time-dependent acceleration from canonical cases of homogeneous turbulence as well as blast waves with first and second kind self-similarity. The work is supported by the US National Science Foundation.
Skorov, Yu; Reshetnyk, V.; Rezac, L.; Zhao, Y.; Marschall, R.; Blum, J.; Hartogh, P.
2018-04-01
A significant fraction of cometary dust grains leaving the nucleus surface are extremely porous and fluffy particles as recent observation from the Rosetta mission revealed. In this paper our aim is to investigate the dynamics of such grains when subjected to a gas flow, representing the cometary outgassing. We perform numerical experiments to quantify how the internal porous texture is reflected in quantities such as: effective cross-section, gas drag coefficient, and light scattering efficiency. We also derive particle speeds for the different types of aggregates as a function of radial distance and compare them to the observations by the GIADA instrument. Using our original method for constructing hierarchical aggregates we increase the level of aggregation to reach particle sizes up to few millimeters, consistent with the observations. In addition, a non-constant gas velocity is now considered in the framework of free molecular as well as fully collisional flow models, and radiation pressure calculations use the effective medium theory appropriate for such particles. These improvements lead us to conclude that dynamical models should account for accelerating gas flow, which leads to a smaller terminal speed of fluffy dust grains. Second, solar radiation pressure calculated based on the Mie theory approximation can lead to orders of magnitude error for the very porous particles, instead the effective medium theory should be used. Finally, although numerical simulations can reproduce the GIADA measurements of dust speeds, we cannot conclude that there exists a preferred model of porous particles build as a ballistic cluster aggregate.
Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study
DEFF Research Database (Denmark)
Laradji, Mohamed; Mouritsen, Ole G.
2000-01-01
Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface, corres...
Vision-Augmented Molecular Dynamics Simulation of Nanoindentation
Directory of Open Access Journals (Sweden)
Rajab Al-Sayegh
2015-01-01
Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.
Coupled electron-phonon transport from molecular dynamics with quantum baths
DEFF Research Database (Denmark)
Lu, Jing Tao; Wang, J. S.
2009-01-01
Based on generalized quantum Langevin equations for the tight-binding wavefunction amplitudes and lattice displacements, electron and phonon quantum transport are obtained exactly using molecular dynamics (MD) in the ballistic regime. The electron-phonon interactions can be handled with a quasi...
A resource letter CSSMD-1: computer simulation studies by the method of molecular dynamics
International Nuclear Information System (INIS)
Goel, S.P.; Hockney, R.W.
1974-01-01
A comprehensive bibliography on computer simulation studies by the method of Molecular Dynamics is presented. The bibliography includes references to relevant literature published up to mid 1973, starting from the first paper of Alder and Wainwright, published in 1957. The procedure of the method of Molecular Dynamics, the main fields of study in which it has been used, its limitations and how these have been overcome in some cases are also discussed [pt
Large-scale molecular dynamics simulations of self-assembling systems.
Klein, Michael L; Shinoda, Wataru
2008-08-08
Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.
International Nuclear Information System (INIS)
Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M
2010-01-01
Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives
Classical molecular dynamics simulation of weakly-bound projectile heavy-ion reactions
Directory of Open Access Journals (Sweden)
Morker Mitul R.
2015-01-01
Full Text Available A 3-body classical molecular dynamics approach for heavy-ion reactions involving weakly bound projectiles is developed. In this approach a weakly bound projectile is constructed as a two-body cluster of the constituent tightly bound nuclei in a configuration corresponding to the observed breakup energy. This 3-body system with their individual nucleon configuration in their ground state is dynamically evolved for given initial conditions using the three-stage classical molecular dynamics approach (3S-CMD. Various levels of rigidbody constraints on the projectile constituents and the target are considered at appropriate stages. This 3-dimensional approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but internal excitations and breakup probabilities at distances close to the barrier also. Dynamical simulations of 6Li+209Bi show all the possible reaction mechanism like complete fusion, incomplete fusion, scattering and breakup scattering. Complete fusion cross sections of 6Li+209Bi and 7Li+209Bi reactions are calculated in this approach with systematic relaxations of the rigid-body constraints on one or more constituent nuclei.
Molecular dynamics of bacteriorhodopsin.
Lupo, J A; Pachter, R
1997-02-01
A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.
Magnetic effects on the solvent properties investigated by molecular dynamics simulation
Energy Technology Data Exchange (ETDEWEB)
Moosavi, Fatemeh, E-mail: moosavibaigi@um.ac.ir; Gholizadeh, Mostafa
2014-03-15
This paper investigates how an external constant magnetic field in the Z-direction affects the performance of a solvent. The molecular dynamics simulation comprised common inorganic and organic solvents including water, acetone, acetonitrile, toluene, and n-hexane at the ambient temperature and pressure. A static magnetic field applied in the simulation process is able to reduce the solvent mobility in the solution in order to enhance the solvent–solute reaction. Simulation results show that the diffusivity decreases because of increasing the effective interactions. Besides, magnetic field reduces the volume of the solvent and increases the strength of the hydrogen bonds by maximizing attractive electrostatic and vdW interactions caused by changes in the radial distribution function of the solvents. Hydrogen-bonding characteristics of solvents investigated by molecular dynamics simulations were evidence for the hydrogen bonding strength of O···H that is a more efficient intermolecular hydrogen-bonding in comparison with N···H. - Highlights: • Molecular dynamics simulation technique investigates the effect of magnetic field on transport dynamics inside the solvent bulk. • External constant magnetic field influences on intermolecular interactions, thermophysics, and transport properties of the solvents. • Applying magnetic field strengthened hydrogen bond maximizes attractive electrostatic interactions, charge distribution becomes stronger, and the molecule mobility is demoted. • The low diffusivity of the solvents in the solutions increases the performance of the interactions and promotes the interactions. • On introducing a magnetic field of flux density parallel to the Z-direction, solvent acts as an obstacle to diffusion of solutes.
Directory of Open Access Journals (Sweden)
Trullàs J.
2011-05-01
Full Text Available Molecular dynamics simulations of molten NaI at 995 K have been carried out using polarizable ion models based on rigid ion pair potentials to which the anion induced dipole polarization is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and deformation short-range damping interactions that oppose the electrically induced dipole moments. The structure and self-diffusion results are compared with those obtained by Galamba and Costa Cabral using first principles Hellmann-Feynman molecular dynamics simulations and using classical molecular dynamics of a shell model which allows only the iodide polarization
Thermal conductivity of water: Molecular dynamics and generalized hydrodynamics results
Bertolini, Davide; Tani, Alessandro
1997-10-01
Equilibrium molecular dynamics simulations have been carried out in the microcanonical ensemble at 300 and 255 K on the extended simple point charge (SPC/E) model of water [Berendsen et al., J. Phys. Chem. 91, 6269 (1987)]. In addition to a number of static and dynamic properties, thermal conductivity λ has been calculated via Green-Kubo integration of the heat current time correlation functions (CF's) in the atomic and molecular formalism, at wave number k=0. The calculated values (0.67+/-0.04 W/mK at 300 K and 0.52+/-0.03 W/mK at 255 K) are in good agreement with the experimental data (0.61 W/mK at 300 K and 0.49 W/mK at 255 K). A negative long-time tail of the heat current CF, more apparent at 255 K, is responsible for the anomalous decrease of λ with temperature. An analysis of the dynamical modes contributing to λ has shown that its value is due to two low-frequency exponential-like modes, a faster collisional mode, with positive contribution, and a slower one, which determines the negative long-time tail. A comparison of the molecular and atomic spectra of the heat current CF has suggested that higher-frequency modes should not contribute to λ in this temperature range. Generalized thermal diffusivity DT(k) decreases as a function of k, after an initial minor increase at k=kmin. The k dependence of the generalized thermodynamic properties has been calculated in the atomic and molecular formalisms. The observed differences have been traced back to intramolecular or intermolecular rotational effects and related to the partial structure functions. Finally, from the results we calculated it appears that the SPC/E model gives results in better agreement with experimental data than the transferable intermolecular potential with four points TIP4P water model [Jorgensen et al., J. Chem. Phys. 79, 926 (1983)], with a larger improvement for, e.g., diffusion, viscosities, and dielectric properties and a smaller one for thermal conductivity. The SPC/E model shares
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
International Nuclear Information System (INIS)
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-01-01
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Tambunan, Usman Sumo Friend; Nasution, Mochammad Arfin Fardiansyah; Azhima, Fauziah; Parikesit, Arli Aditya; Toepak, Erwin Prasetya; Idrus, Syarifuddin; Kerami, Djati
2017-01-01
Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world's population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S -adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2'OH, resulting in S -adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔG binding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.
Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.
Yagasaki, Takuma; Saito, Shinji
2009-09-15
Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is
Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation
Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting
2017-07-01
To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project
Getting the ion-protein interactions right in molecular dynamics simulations
Czech Academy of Sciences Publication Activity Database
Duboué-Dijon, Elise; Mason, Philip E.; Jungwirth, Pavel
2017-01-01
Roč. 46, Suppl 1 (2017), S66 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : ion-protein interaction * molecular dynamics simulations * neutron scattering * insulin Subject RIV: BO - Biophysics
Molecular dynamics simulations of lipid vesicle fusion in atomic detail
Knecht, Volker; Marrink, Siewert-Jan
The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic
Validating clustering of molecular dynamics simulations using polymer models
Directory of Open Access Journals (Sweden)
Phillips Joshua L
2011-11-01
Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our
Drenscko, Mihaela
Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of
Incorporation of quantum statistical features in molecular dynamics
International Nuclear Information System (INIS)
Ohnishi, Akira; Randrup, J.
1995-01-01
We formulate a method for incorporating quantum fluctuations into molecular-dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous transitions to occur between the wave packets which are not energy eigenstates. The ensuing diffusive evolution in the space of the wave packet parameters exhibits appealing physical properties, including relaxation towards quantum-statistical equilibrium. (author)
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel
International Nuclear Information System (INIS)
Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.
2011-01-01
This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12σ, 14σ and 16σ and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.
Kurbatov, A. O.; Balabaev, N. K.; Mazo, M. A.; Kramarenko, E. Yu.
2018-01-01
Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics.
Usui, Kota; Hunger, Johannes; Bonn, Mischa; Sulpizi, Marialore
2018-05-01
Room temperature ionic liquids (RTILs) have been shown to exhibit spatial heterogeneity or structural heterogeneity in the sense that they form hydrophobic and ionic domains. Yet studies of the relationship between this structural heterogeneity and the ˜picosecond motion of the molecular constituents remain limited. In order to obtain insight into the time scales relevant to this structural heterogeneity, we perform molecular dynamics simulations of a series of RTILs. To investigate the relationship between the structures, i.e., the presence of hydrophobic and ionic domains, and the dynamics, we gradually increase the size of the hydrophobic part of the cation from ethylammonium nitrate (EAN), via propylammonium nitrate (PAN), to butylammonium nitrate (BAN). The two ends of the organic cation, namely, the charged Nhead-H group and the hydrophobic Ctail-H group, exhibit rotational dynamics on different time scales, evidencing dynamical heterogeneity. The dynamics of the Nhead-H group is slower because of the strong coulombic interaction with the nitrate counter-ionic anions, while the dynamics of the Ctail-H group is faster because of the weaker van der Waals interaction with the surrounding atoms. In particular, the rotation of the Nhead-H group slows down with increasing cationic chain length, while the rotation of the Ctail-H group shows little dependence on the cationic chain length, manifesting that the dynamical heterogeneity is enhanced with a longer cationic chain. The slowdown of the Nhead-H group with increasing cationic chain length is associated with a lower number of nitrate anions near the Nhead-H group, which presumably results in the increase of the energy barrier for the rotation. The sensitivity of the Nhead-H rotation to the number of surrounding nitrate anions, in conjunction with the varying number of nitrate anions, gives rise to a broad distribution of Nhead-H reorientation times. Our results suggest that the asymmetry of the cations and the
Molecular dynamics simulation of carbon molecular sieve preparation for air separation
International Nuclear Information System (INIS)
Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh; Shariaty-Niassar, Mojtaba
2015-01-01
Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments
Molecular dynamics simulation of carbon molecular sieve preparation for air separation
Energy Technology Data Exchange (ETDEWEB)
Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh [Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of); Shariaty-Niassar, Mojtaba [University of Tehran, Tehran(Iran, Islamic Republic of)
2015-03-15
Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments.
Molecular dynamics simulation of bubble nucleation in explosive boiling
International Nuclear Information System (INIS)
Zou Yu; Chinese Academy of Sciences, Beijing; Huai Xiulan; Liang Shiqiang
2009-01-01
Molecular dynamics (MD) simulation is carried out for the bubble nucleation of liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. The results indicate that the initial equilibrium temperature of liquid and molecular cluster size affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of bubble nucleation, the potential energy of the system slowly increases. In the bubble nucleation of explosive boiling, the lower the initial equilibrium temperature, the larger the size of the molecular cluster, and the more the heat transferred into the system of the simulation cell, causing the increase potential energy in a larger range. (authors)
Hydration dynamics in water clusters via quantum molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of
Molecular dynamics of liquid crystals
Sarman, Sten
1997-02-01
We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.
Moffett, Alexander S; Bender, Kyle W; Huber, Steven C; Shukla, Diwakar
2017-07-28
The structural motifs responsible for activation and regulation of eukaryotic protein kinases in animals have been studied extensively in recent years, and a coherent picture of their activation mechanisms has begun to emerge. In contrast, non-animal eukaryotic protein kinases are not as well understood from a structural perspective, representing a large knowledge gap. To this end, we investigated the conformational dynamics of two key Arabidopsis thaliana receptor-like kinases, brassinosteroid-insensitive 1 (BRI1) and BRI1-associated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphorylated kinase domains. Molecular dynamics simulations calculate the motion of each atom in a protein based on classical approximations of interatomic forces, giving researchers insight into protein function at unparalleled spatial and temporal resolutions. We found that in an otherwise "active" BAK1 the αC helix is highly disordered, a hallmark of deactivation, whereas the BRI1 αC helix is moderately disordered and displays swinging behavior similar to numerous animal kinases. An analysis of all known sequences in the A. thaliana kinome found that αC helix disorder may be a common feature of plant kinases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
A molecular dynamics approach to barrodiffusion
Cooley, James; Marciante, Mathieu; Murillo, Michael
2016-10-01
Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin
CAS CERN Accelerator School. 5. Advanced accelerator physics course. Proceedings. Vol. 2
International Nuclear Information System (INIS)
Turner, S.
1995-01-01
The fifth CERN Accelerator School (CAS) advanced course on Accelerator Physics was given at the Paradise Hotel, Rhodes, Greece from 20 September to 1 October 1993. Its syllabus was based on the previous similar courses held at Oxford 1985, Berlin 1987, Uppsala 1989 and Noordwijkerhout 1991, and whose proceedings were published as CERN Reports 97-03, 89-01, 90-04 and 92-01, respectively. The present volumes are intended to replace and to bring up to date all the material in earlier publications. They contain not only all the lectures given in the Rhodes course but a number of important contributions to previous courses which are thought to be essential for a complete understanding of all aspects of the design and construction of particle accelerators at an advanced level. They include sections on Hamiltonian equations and accelerator optics, chromaticity and dynamic beam aperture, particle tracking, the kinetic theory, longitudinal beam optics, coherent instabilities, beam-beam dynamics, intra-beam scattering, beam cooling, Schottky noise, beam radiation, neutralisation, beam polarisation, radio-frequency quadrupoles, as well as chapters on space charge, superconducting magnets, crystal bending, beam-beam measurement and accelerator medical applications. (orig.)
CAS CERN Accelerator School. 5. Advanced accelerator physics course. Proceedings. Vol. 1
Energy Technology Data Exchange (ETDEWEB)
Turner, S [ed.
1995-11-22
The fifth CERN Accelerator School (CAS) advanced course on Accelerator Physics was given at the Paradise Hotel, Rhodes, Greece from 20 September to 1 October 1993. Its syllabus was based on the previous similar courses held at Oxford 1985, Berlin 1987, Uppsala 1989 and Noordwijkerhout 1991, and whose proceedings were published as CERN Reports 87-03, 89-01, 90-04 and 92-01, respectively. The present volumes are intended to replace and to bring up to date all the material in earlier publications. They contain not only all the lectures given in the Rhodes course but a number of important contributions to previous courses which are thought to be essential for a complete understanding of all aspects of the design and construction of particle accelerators at an advanced level. They include sections on Hamiltonian equations and accelerator optics, chromaticity and dynamic beam aperture, particle tracking, the kinetic theory, longitudinal beam optics, coherent instabilities, beam-beam dynamics, intra-beam scattering, beam cooling, Schottky noise, beam radiation, neutralisation, beam polarisation, radio-frequency quadrupoles, as well as chapters on space charge, superconducting magnets, crystal bending, beam-beam measurement and accelerator medical applications. (orig.).
CAS CERN Accelerator School. 5. Advanced accelerator physics course. Proceedings. Vol. 1
International Nuclear Information System (INIS)
Turner, S.
1995-01-01
The fifth CERN Accelerator School (CAS) advanced course on Accelerator Physics was given at the Paradise Hotel, Rhodes, Greece from 20 September to 1 October 1993. Its syllabus was based on the previous similar courses held at Oxford 1985, Berlin 1987, Uppsala 1989 and Noordwijkerhout 1991, and whose proceedings were published as CERN Reports 87-03, 89-01, 90-04 and 92-01, respectively. The present volumes are intended to replace and to bring up to date all the material in earlier publications. They contain not only all the lectures given in the Rhodes course but a number of important contributions to previous courses which are thought to be essential for a complete understanding of all aspects of the design and construction of particle accelerators at an advanced level. They include sections on Hamiltonian equations and accelerator optics, chromaticity and dynamic beam aperture, particle tracking, the kinetic theory, longitudinal beam optics, coherent instabilities, beam-beam dynamics, intra-beam scattering, beam cooling, Schottky noise, beam radiation, neutralisation, beam polarisation, radio-frequency quadrupoles, as well as chapters on space charge, superconducting magnets, crystal bending, beam-beam measurement and accelerator medical applications. (orig.)
CAS CERN Accelerator School. 5. Advanced accelerator physics course. Proceedings. Vol. 2
Energy Technology Data Exchange (ETDEWEB)
Turner, S [ed.
1995-11-22
The fifth CERN Accelerator School (CAS) advanced course on Accelerator Physics was given at the Paradise Hotel, Rhodes, Greece from 20 September to 1 October 1993. Its syllabus was based on the previous similar courses held at Oxford 1985, Berlin 1987, Uppsala 1989 and Noordwijkerhout 1991, and whose proceedings were published as CERN Reports 97-03, 89-01, 90-04 and 92-01, respectively. The present volumes are intended to replace and to bring up to date all the material in earlier publications. They contain not only all the lectures given in the Rhodes course but a number of important contributions to previous courses which are thought to be essential for a complete understanding of all aspects of the design and construction of particle accelerators at an advanced level. They include sections on Hamiltonian equations and accelerator optics, chromaticity and dynamic beam aperture, particle tracking, the kinetic theory, longitudinal beam optics, coherent instabilities, beam-beam dynamics, intra-beam scattering, beam cooling, Schottky noise, beam radiation, neutralisation, beam polarisation, radio-frequency quadrupoles, as well as chapters on space charge, superconducting magnets, crystal bending, beam-beam measurement and accelerator medical applications. (orig.).
A molecular dynamics study of the effects of fast molecular motions on solid-state NMR parameters
Czech Academy of Sciences Publication Activity Database
Dračínský, Martin; Hodgkinson, P.
2013-01-01
Roč. 15, č. 43 (2013), s. 8705-8712 ISSN 1466-8033 Grant - others:Seventh Framework Programme of the European Union(XE) FP7-299242 People Institutional support: RVO:61388963 Keywords : molecular dynamics * DFT calculations * NMR spectroscopy Subject RIV: CC - Organic Chemistry Impact factor: 3.858, year: 2013
Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo
2016-01-21
Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.
Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.
2006-01-01
A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation
Directory of Open Access Journals (Sweden)
G.M. Bhuiyan
2012-10-01
Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.
Directory of Open Access Journals (Sweden)
Yesylevskyy S. O.
2010-04-01
Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed
Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations
DEFF Research Database (Denmark)
Jensen, Morten Østergaard; Jensen, T.R.; Kjær, Kristian
2002-01-01
Electron density profiles calculated from molecular dynamics trajectories are used to deduce the orientation and conformation of Thermomyces lanuginosa lipase and a mutant adsorbed at an air-water interface. It is demonstrated that the profiles display distinct fine structures, which uniquely...... characterize enzyme orientation and conformation. The density profiles are, on the nanosecond timescale, determined by the average enzyme conformation. We outline a Computational scheme that from a single molecular dynamics trajectory allows for extraction of electron density profiles referring to different...
Rayleigh-Taylor mixing with space-dependent acceleration
Abarzhi, Snezhana
2016-11-01
We extend the momentum model to describe Rayleigh-Taylor (RT) mixing driven by a space-dependent acceleration. The acceleration is a power-law function of space coordinate, similarly to astrophysical and plasma fusion applications. In RT flow the dynamics of a fluid parcel is driven by a balance per unit mass of the rates of momentum gain and loss. We find analytical solutions in the cases of balanced and imbalanced gains and losses, and identify their dependence on the acceleration exponent. The existence is shown of two typical sub-regimes of self-similar RT mixing - the acceleration-driven Rayleigh-Taylor-type mixing and dissipation-driven Richtymer-Meshkov-type mixing with the latter being in general non-universal. Possible scenarios are proposed for transitions from the balanced dynamics to the imbalanced self-similar dynamics. Scaling and correlations properties of RT mixing are studied on the basis of dimensional analysis. Departures are outlined of RT dynamics with space-dependent acceleration from canonical cases of homogeneous turbulence as well as blast waves with first and second kind self-similarity. The work is supported by the US National Science Foundation.
Molecular dynamics modeling and simulation of void growth in two dimensions
Chang, H.-J.; Segurado, J.; Rodríguez de la Fuente, O.; Pabón, B. M.; LLorca, J.
2013-10-01
The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.