Accelerating Fermionic Molecular Dynamics
Clark, M. A.; Kennedy, A. D.
2004-01-01
We consider how to accelerate fermionic molecular dynamics algorithms by introducing n pseudofermion fields coupled with the nth root of the fermionic kernel. This reduces the maximum pseudofermionic force, and thus allows a larger molecular dynamics integration step size without hitting an instability in the integrator.
Introduction to Accelerated Molecular Dynamics
Perez, Danny [Los Alamos National Laboratory
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
Accelerated molecular dynamics simulations of protein folding
Miao, Y.; Feixas, F; Eun, C; McCammon, JA
2015-01-01
© 2015 Wiley Periodicals, Inc. Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native ...
Implementation of Accelerated Molecular Dynamics in NAMD
Wang, Yi; Harrison, Christopher B.; Schulten, Klaus; McCammon, J. Andrew
2011-01-01
Accelerated molecular dynamics (aMD) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Here we present the implementation of aMD in the parallel simulation program NAMD. We show that aMD simulations performed with NAMD have only a small overhead compared with classical MD simulations. Through example applications to the alanine dipeptide, we discuss the choice of acceleration parameters, the inte...
Accelerating convergence of molecular dynamics-based structural relaxation
Christensen, Asbjørn
2005-01-01
We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to...
Accelerated Molecular Dynamics Simulations of Reactive Hydrocarbon Systems
Stuart, Steven J.
2014-02-25
The research activities in this project consisted of four different sub-projects. Three different accelerated dynamics techniques (parallel replica dynamics, hyperdynamics, and temperature-accelerated dynamics) were applied to the modeling of pyrolysis of hydrocarbons. In addition, parallel replica dynamics was applied to modeling of polymerization.
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics
Wang, Yi; Markwick, Phineus R.L.; de Oliveira, César Augusto F.; McCammon, J. Andrew
2011-01-01
Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ∼1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC bilayer. Overall, the aMD simulations are found to produce significant speedup in trans–gauche isome...
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In most cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems
Accelerated molecular dynamics methods: introduction and recent developments
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.
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
Wereszczynski, Jeff; McCammon, J. Andrew
2010-01-01
Accelerated molecular dynamics (aMD) has been shown to enhance conformational space sampling relative to classical molecular dynamics; however, the exponential reweighting of aMD trajectories, which is necessary for the calculation of free energies relating to the classical system, is oftentimes problematic, especially for systems larger than small poly peptides. Here, we propose a method of accelerating only the degrees of freedom most pertinent to sampling, thereby reducing the total accele...
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.
Graphics processing units accelerated semiclassical initial value representation molecular dynamics
Tamascelli, Dario; Dambrosio, Francesco S.; Conte, Riccardo; Ceotto, Michele
2013-01-01
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 bench...
GPU Accelerated Semiclassical Initial Value Representation Molecular Dynamics
Tamascelli, Dario; Conte, Riccardo; Ceotto, Michele
2013-01-01
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 CUDA implementation of the semiclassical code are provided. 4 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 (C2075 and K20) versus two CPUs (intel core i5 and Intel Xeon E5-2687W) shows that the CPU code scales linearly, whereas the GPU CUDA code roughly constantly for most of the trajectory range considered. 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.
Graphics processing units accelerated semiclassical initial value representation molecular dynamics
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
Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J. Andrew
2013-01-01
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale eve...
Lindert, S; Bucher, D; Eastman, P; Pande, V.; McCammon, JA
2013-01-01
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale eve...
Cameron Abrams; Giovanni Bussi
2013-01-01
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 u...
Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.
Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (Oak Ridge National Laboratories, Oak Ridge, TN); Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl
2011-09-01
Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.
Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew
2013-11-12
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling. PMID:24634618
Sorella, Sandro
2016-01-01
We propose an ab-initio molecular dynamics method, capable to reduce dramatically the autocorrelation time required for the simulation of classical and quantum particles at finite temperature. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix $S$. Here we apply this technique, within a Quantum Monte Carlo (QMC) based wavefuntion approach and within the Born-Oppheneimer approximation, for determining the phase diagram of high-pressure Hydrogen with simulations much longer than the autocorrelation time. With the proposed method, we are able to equilibrate in few hundreds steps even close to the liquid-liquid phase transition (LLT). Within our approach we find that the LLT transition is consistent with recent density functionals predicting a much larger transition pressures when the long range dispersive forces are taken into account.
Glowacki, David R; O'Connor, Michael; Calabró, Gaetano; Price, James; Tew, Philip; Mitchell, Thomas; Hyde, Joseph; Tew, David P; Coughtrie, David J; McIntosh-Smith, Simon
2014-01-01
With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude. PMID:25340458
Geng, Hua Y
2014-01-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibration...
Hybrid Acceleration of a Molecular DynamicsSimulation Using Short-Ranged Potentials
Hornich, Julian
2013-01-01
Molecular dynamics simulations are a very usefultool to study the behavior and interaction of atoms and molecules in chemicaland bio-molecular systems. With the fast rising complexity of such simulationshybrid systems with both, multi-core processors (CPUs) and multiple graphics processingunits (GPUs), become more and more popular. To obtain an optimal performance thisthesis presents and evaluates two different hybrid algorithms, employing allavailable compute capacity from CPUs and GPUs. The...
Deciphering mechanism of the 'myristoyl switch' with classical and accelerated molecular dynamics
Magarkar, Aniket; Kohagen, Miriam; Jungwirth, Pavel
2015-01-01
Roč. 44, Suppl 1 (2015), S169. ISSN 0175-7571. [EBSA European Biophysics Congress /10./. 18.07.2015-22.07.2015, Dresden] Institutional support: RVO:61388963 Keywords : molecular dynamics * myristoyl switch * calcium ion binding Subject RIV: CF - Physical ; Theoretical Chemistry
ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale
Harvey, M J; De Fabritiis, G
2009-01-01
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23,000 atoms. We illustrate the characteristics of the code, its validation and performance. We also run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.
Fan, Zheyong; Siro, Topi; harju, Ari
2012-01-01
In this paper, we develop a highly efficient molecular dynamics code fully implemented on graphics processing units for thermal conductivity calculations using the Green-Kubo formula. We compare two different schemes for force evaluation, a previously used thread-scheme where a single thread is used for one particle and each thread calculates the total force for the corresponding particle, and a new block-scheme where a whole block is used for one particle and each thread in the block calcula...
Spellings, Matthew; Anderson, Joshua A; Glotzer, Sharon C
2016-01-01
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.
Molecular dynamics study of accelerated ion-induced shock waves in biological media
de Vera, Pablo; Currell, Fred J; Solov'yov, Andrey V
2016-01-01
We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which lies beyond the possibilities of the analytical model.
GPU accelerated dislocation dynamics
Ferroni, Francesco; Tarleton, Edmund; Fitzgerald, Steven
2014-09-01
In this paper we analyze the computational bottlenecks in discrete dislocation dynamics modeling (associated with segment-segment interactions as well as the treatment of free surfaces), discuss the parallelization and optimization strategies, and demonstrate the effectiveness of Graphical Processing Unit (GPU) computation in accelerating dislocation dynamics simulations and expanding their scope. Individual algorithmic benchmark tests as well as an example large simulation of a thin film are presented.
Acceleration Schemes for Ab-Initio Molecular Dynamics and Electronic Structure Calculations
Tassone, Francesco; Mauri, Francesco; Car, Roberto
1994-01-01
We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest descent algorithms while retaining their numerical cost per time step. Our damped dynamics has efficiency comparable to that of conjugate gradient methods in typical electronic minimization problems. Then, we analyse the factors that limit the size of the integ...
Substructured multibody molecular dynamics.
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
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
Object-Oriented Programming has been used extensively to model the LBL Advanced Light Source 1.5 GeV electron storage ring. This paper is on the present status of the class library construction with emphasis on a dynamic modeling
The Modern Temperature-Accelerated Dynamics Approach.
Zamora, Richard J; Uberuaga, Blas P; Perez, Danny; Voter, Arthur F
2016-06-01
Accelerated molecular dynamics (AMD) is a class of MD-based methods used to simulate atomistic systems in which the metastable state-to-state evolution is slow compared with thermal vibrations. Temperature-accelerated dynamics (TAD) is a particularly efficient AMD procedure in which the predicted evolution is hastened by elevating the temperature of the system and then recovering the correct state-to-state dynamics at the temperature of interest. TAD has been used to study various materials applications, often revealing surprising behavior beyond the reach of direct MD. This success has inspired several algorithmic performance enhancements, as well as the analysis of its mathematical framework. Recently, these enhancements have leveraged parallel programming techniques to enhance both the spatial and temporal scaling of the traditional approach. We review the ongoing evolution of the modern TAD method and introduce the latest development: speculatively parallel TAD. PMID:26979413
GPU-Accelerated Molecular Modeling Coming Of Age
Stone, John E.; Hardy, David J.; Ivan S. Ufimtsev; Schulten, Klaus
2010-01-01
Graphics processing units (GPUs) have traditionally been used in molecular modeling solely for visualization of molecular structures and animation of trajectories resulting from molecular dynamics simulations. Modern GPUs have evolved into fully programmable, massively parallel co-processors that can now be exploited to accelerate many scientific computations, typically providing about one order of magnitude speedup over CPU code and in special cases providing speedups of two orders of magnit...
Polymer friction Molecular Dynamics
Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.
2010-01-01
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 dynamic mechanical properties and molecular weight distribution of two experimental polymer bonded explosives, X-0287 and X-0298, maintained at 23, 60, and 740C 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% B2 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 -590C and in the aged explosive at 500C. 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 650C. 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
Nonequilibrium molecular dynamics
Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Polymer friction Molecular Dynamics
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....
BÄRBEL M. R. STADLER; Stadler, Peter F
2003-01-01
Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability...
Molecular dynamics for fermions
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.)
ACCELERATORS: Nonlinear dynamics in Sardinia
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
Orbital free molecular dynamics
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)
Open boundary molecular dynamics
Delgado-Buscalioni, R.; Sablić, J.; Praprotnik, M.
2015-09-01
This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.
Molecular Dynamics of Acetylcholinesterase
Shen, T Y.; Tai, Kaihsu; Henchman, Richard H.; Mccammon, Andy
2002-06-01
Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.
From Molecular Dynamics to Dissipative Particle Dynamics
Flekkoy, Eirik G.; Coveney, Peter V.
1999-01-01
A procedure is introduced for deriving a coarse-grained dissipative particle dynamics from molecular dynamics. The rules of the dissipative particle dynamics are derived from the underlying molecular interactions, and a Langevin equation is obtained that describes the forces experienced by the dissipative particles and specifies the associated canonical Gibbs distribution for the system.
Parallel beam dynamics simulation of linear accelerators
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 b...
Modified Newtonian dynamics from acceleration fluctuations
Jordan, Thomas F.
2004-01-01
A speculative mathematical model is used to generate the modified Newtonian dynamics called MOND from fluctuations of the number of quanta of quantized acceleration. The one new parameter can be chosen either to make the transition to modification comparable to that obtained from the functions used to fit data with MOND, or to make the modification at larger accelerations comparable in magnitude to the unexplained accelerations of Pioneer 10 and 11.
Ion dynamics and acceleration in relativistic shocks
Martins, S. F.; Fonseca, R. A.; Silva, L. O.; Mori, W. B.
2009-01-01
Ab-initio numerical study of collisionless shocks in electron-ion unmagnetized plasmas is performed with fully relativistic particle in cell simulations. The main properties of the shock are shown, focusing on the implications for particle acceleration. Results from previous works with a distinct numerical framework are recovered, including the shock structure and the overall acceleration features. Particle tracking is then used to analyze in detail the particle dynamics and the acceleration ...
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
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
Notes on beam dynamics in linear accelerators
Gluckstern, R.L.
1980-09-01
A collection of notes, on various aspects of beam dynamics in linear accelerators, which were produced by the author during five years (1975 to 1980) of consultation for the LASL Accelerator Technology (AT) Division and Medium-Energy Physics (MP) Division is presented.
The nonequilibrium molecular dynamics
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
Single particle dynamics in circular accelerators
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)
Beam dynamics in high energy particle accelerators
Wolski, Andrzej
2014-01-01
Particle accelerators are essential tools for scientific research in fields as diverse as high energy physics, materials science and structural biology. They are also widely used in industry and medicine. Producing the optimum design and achieving the best performance for an accelerator depends on a detailed understanding of many (often complex and sometimes subtle) effects that determine the properties and behavior of the particle beam. Beam Dynamics in High Energy Particle Accelerators provides an introduction to the concepts underlying accelerator beam line design and analysis, taking an approach that emphasizes the elegance of the subject and leads into the development of a range of powerful techniques for understanding and modeling charged particle beams.
Pulse Power Supply for Plasma Dynamic Accelerator
YANG Xuanzong; LIU Jian; FENG Chunhua; WANG Long
2008-01-01
A new concept of a coaxial plasma dynamic accelerator with a self-energized mag-netic compressor coil to simulate the effects of space debris impact is demonstrated. A brief description is presented about the pulse power supply system including the charging circuit, start switch and current transfer system along with some of the key techniques for this kind of acceler-ator. Using this accelerator configuration, ceramic beads of 100 μm in diameter were accelerated to a speed as high as 18 km/sec. The facility can be used in a laboratory setting to study impact phenomena on solar array materials, potential structural materials for use in space.
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Molecular dynamics simulations
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
Niu, Yuzhen; Li, Shuyan; Pan, Dabo; Liu, Huanxiang; Yao, Xiaojun
2016-02-21
B-RAF kinase is a clinically validated target implicated in melanoma and advanced renal cell carcinoma (RCC). PLX4720 and TAK-632 are promising inhibitors against B-RAF with different dissociation rate constants (koff), but the specific mechanism that determines the difference of their dissociation rates remains unclear. In order to understand the kinetically different behaviors of these two inhibitors, their unbinding pathways were explored by random acceleration and steered molecular dynamics simulations. The random acceleration molecular dynamics (RAMD) simulations show that PLX4720 dissociates along the ATP-channel, while TAK-632 dissociates along either the ATP-channel or the allosteric-channel. The steered molecular dynamics (SMD) simulations reveal that TAK-632 is more favorable to escape from the binding pocket through the ATP-channel rather than the allosteric-channel. The PMF calculations suggest that TAK-632 presents longer residence time, which is in qualitative agreement with the experimental koff(koff = 3.3 × 10(-2) s(-1) and ΔGoff = -82.17 ± 0.29 kcal mol(-1) for PLX4720; koff = 1.9 × 10(-5) s(-1) and ΔGoff = -39.73 ± 0.79 kcal mol(-1) for PLX4720). Furthermore, the binding free decomposition by MM/GBSA illustrates that the residues K36, E54, V57, L58, L120, I125, H127, G146 and D147 located around the allosteric binding pocket play important roles in determining the longer residence time of TAK-632 by forming stronger hydrogen bond and hydrophobic interactions. Our simulations provide valuable information to design selective B-RAF inhibitors with long residence time in the future. PMID:26862741
Jacobi equations and particle accelerator beam dynamics
Torrome, Ricardo Gallego
2012-01-01
A geometric formulation of the linear beam dynamics in accelerator physics is presented. In particular, it is proved that the linear transverse and longitudinal dynamics can be interpret geometrically as an approximation to the Jacobi equation of an affine averaged Lorentz connection. We introduce a specific notion reference trajectory as integral curves of the main velocity vector field. A perturbation caused by the statistical nature of the bunch of particles is considered.
Yang, Zhongyue; Doubleday, Charles; Houk, K N
2015-12-01
We describe a solvent-perturbed transition state (SPTS) sampling scheme for simulating chemical reaction dynamics in condensed phase. The method, adapted from Truhlar and Gao's ensemble-averaged variational transition state theory, includes the effect of instantaneous solvent configuration on the potential energy surface of the reacting system (RS) and allows initial conditions for the RS to be sampled quasiclassically by TS normal mode sampling. We use a QM/MM model with direct dynamics, in which QM forces of the RS are computed at each trajectory point. The SPTS scheme is applied to the acceleration of the Diels-Alder reaction of cyclopentadiene (CP) + methyl vinyl ketone (MVK) in water. We explored the effect of the number of SPTS and of solvent box size on the distribution of bond lengths in the TS. Statistical sampling of the sampling was achieved when distribution of forming bond lengths converged. We describe the region enclosing the partial bond lengths as the transition zone. Transition zones in the gas phase, SMD implicit solvent, QM/MM, and QM/MM+QM (3 water molecules treated by QM) vary according to the ability of the medium to stabilize zwitterionic structures. Mean time gaps between formation of C-C bonds vary from 11 fs for gas phase to 25 fs for QM/MM+QM. Mean H-bond lengths to O(carbonyl) in QM/MM+QM are 0.14 Å smaller at the TS than in MVK reactant, and the mean O(carbonyl)-H(water)-O(water) angle of H-bonds at the TS is 10° larger than in MVK reactant. PMID:26588803
Physical adsorption and molecular dynamics
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.)
Galilei invariant molecular dynamics
We construct a C*-dynamical model for a chemical reaction. Galilei invariance of our nonrelativistic model is demonstrated by defining it directly on a Galilean space-time fibrebundle with C*-algebra valued fibre, i.e. without reference to any coordinate system. The existence of equilibrium states in this model is established and some of their properties are discussed. (orig.)
Molecular confinement accelerates deformation of entangled polymers during squeeze flow.
Rowland, Harry D; King, William P; Pethica, John B; Cross, Graham L W
2008-10-31
The squeezing of polymers in narrow gaps is important for the dynamics of nanostructure fabrication by nanoimprint embossing and the operation of polymer boundary lubricants. We measured stress versus strain behavior while squeezing entangled polystyrene films to large strains. In confined conditions where films were prepared to a thickness less than the size of the bulk macromolecule, resistance to deformation was markedly reduced for both solid-glass forging and liquid-melt molding. For melt flow, we further observed a complete inversion of conventional polymer viscosity scaling with molecular weight. Our results show that squeeze flow is accelerated at small scales by an unexpected influence of film thickness in polymer materials. PMID:18832609
Kühne, Thomas D
2012-01-01
Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.
State-Dependent Molecular Dynamics
Ciann-Dong Yang
2014-10-01
Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
Dynamic hierarchical algorithm for accelerated microfossil identification
Wong, Cindy M.; Joseph, Dileepan
2015-02-01
Marine microfossils provide a useful record of the Earth's resources and prehistory via biostratigraphy. To study Hydrocarbon reservoirs and prehistoric climate, geoscientists visually identify the species of microfossils found in core samples. Because microfossil identification is labour intensive, automation has been investigated since the 1980s. With the initial rule-based systems, users still had to examine each specimen under a microscope. While artificial neural network systems showed more promise for reducing expert labour, they also did not displace manual identification for a variety of reasons, which we aim to overcome. In our human-based computation approach, the most difficult step, namely taxon identification is outsourced via a frontend website to human volunteers. A backend algorithm, called dynamic hierarchical identification, uses unsupervised, supervised, and dynamic learning to accelerate microfossil identification. Unsupervised learning clusters specimens so that volunteers need not identify every specimen during supervised learning. Dynamic learning means interim computation outputs prioritize subsequent human inputs. Using a dataset of microfossils identified by an expert, we evaluated correct and incorrect genus and species rates versus simulated time, where each specimen identification defines a moment. The proposed algorithm accelerated microfossil identification effectively, especially compared to benchmark results obtained using a k-nearest neighbour method.
A sampling of molecular dynamics
Sindhikara, Daniel Jon
The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: increasing efficiency, measuring convergence, avoiding pitfalls, and an application and analysis of a biological system. Chapters 3 and 4 deal with an enhanced sampling algorithm called "replica exchange molecular dynamics" which is designed to speed-up molecular dynamics simulations. The optimization of a key parameter of these simulations is analyzed. In these successive projects, it was found conclusively that maximizing "exchange attempt frequency" is the most efficient way to run a replica exchange molecular dynamics simulation. Chapter 5 describes an enhanced metric for convergence in parallel simulations called the normalized ergodic measure. The metric is applied to several properties for several replica exchange simulations. Advantages of this metric over other methods are described. Chapter 6 describes the implementation and optimization of an enhanced sampling algorithm similar to replica exchange molecular dynamics called multicanonical algorithm replica exchange molecular dynamics. The algorithm was implemented into a biomolecular simulation suite called AMBER. Additionally several parameters were analyzed and optimized. In Chapter 7, a pitfall in molecular dynamics is observed in biological systems that is caused by negligent use of a simulation's "thermostat". It was found that if the same pseudorandom number seed were used for multiple systems, they eventually synchronize. In this project, synchronization was observed in biological molecules. Various negative effects including corruption of data are pointed out. Chapter 8 describes molecular dynamics simulation of NikR, a homotetrameric nickel
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.
Acceleration-induced nonlocality: kinetic memory versus dynamic memory
Chicone, C.; Mashhoon, B.
2001-01-01
The characteristics of the memory of accelerated motion in Minkowski spacetime are discussed within the framework of the nonlocal theory of accelerated observers. Two types of memory are distinguished: kinetic and dynamic. We show that only kinetic memory is acceptable, since dynamic memory leads to divergences for nonuniform accelerated motion.
Molecular dynamics simulation of diffusivity
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Progress in quantum molecular dynamics
In this paper a microscopic simulation method of the quantum molecular dynamics (QMD) and its extensions to high- and low-energy regions are reported. Combined with the statistical decay calculation, QMD can reproduce experimental data with fixed and very few parameters. (J.P.N.)
Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.
2015-01-01
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the `Classical Wigner' approximation. Here, we show that the further approximation of this `Matsubara dynamics' gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by disc...
Gravitational acceleration and edge effects in molecular clouds
Li, Guang-Xing; Megeath, Tom; Wyrowski, Friedrich
2016-01-01
Gravity plays important roles in the evolution of molecular clouds. We present an acceleration mapping method to estimate the acceleration induced by gravitational interactions in molecular clouds based on observational data. We find that the geometry of a region has a significant impact on the behavior of gravity. In the Pipe nebula which can be approximated as a gas filament, we find that gravitational acceleration can effectively compress the end of this filament, which may have triggered star formation. We identify this as the "gravitational focusing" effect proposed by Burkert & Hartman (2004). In the sheet-like IC348-B3 region, gravity can lead to collapse at its edge, while in the centrally condensed NGC1333 cluster-forming region gravity can drive accretion towards the center. In general, gravitational acceleration tends to be enhanced in the localized regions around the ends of the filaments and the edges of sheet-like structures. Neglecting magnetic fields, these "gravitational focusing" and "ed...
From Molecular Dynamics to Brownian Dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
Molecular Dynamics for Dense Matter
Maruyama, Toshiki; Chiba, Satoshi
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions on the nuclear structure. First we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that the pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...
Accelerating glassy dynamics using graphics processing units
Colberg, Peter H
2009-01-01
Modern graphics hardware offers peak performances close to 1 Tflop/s, and NVIDIA's CUDA provides a flexible and convenient programming interface to exploit these immense computing resources. We demonstrate the ability of GPUs to perform high-precision molecular dynamics simulations for nearly a million particles running stably over many days. Particular emphasis is put on the numerical long-time stability in terms of energy and momentum conservation. Floating point precision is a crucial issue here, and sufficient precision is maintained by double-single emulation of the floating point arithmetic. As a demanding test case, we have reproduced the slow dynamics of a binary Lennard-Jones mixture close to the glass transition. The improved numerical accuracy permits us to follow the relaxation dynamics of a large system over 4 non-trivial decades in time. Further, our data provide evidence for a negative power-law decay of the velocity autocorrelation function with exponent 5/2 in the close vicinity of the transi...
Rheology via nonequilibrium molecular dynamics
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
Rheology via nonequilibrium molecular dynamics
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.
Laser Controlled Molecular Orientation Dynamics
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
Better, Cheaper, Faster Molecular Dynamics
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
Molecular dynamics investigation of dynamic crack stability
A series of molecular-dynamics simulations has been performed in order to evaluate the effects of several physical factors on dynamic crack stability. These factors are the crystalline structure and the interatomic interaction modeled by various empirical potentials. For brittle crack propagation at low temperature we find that steady-state crack velocities are limited to a band of accessible values. Increasing the overload beyond KIc, the crack can propagate with a steady-state velocity, which quickly reaches the terminal velocity of about 0.4 of the Rayleigh wave speed. The magnitude of the terminal velocity can be related to the nonlinearity of the interatomic interaction. Further increasing the overload does not change the steady-state velocity dramatically, but significantly increases the amplitude of acoustic emission from the crack tip. Loading the crack even further leads to instabilities which take the form of cleavage steps, dislocation emission, or branching. The instability is closely related to the buildup of a localized coherent, phononlike field generated by the bond-breaking events. The form of the instability depends critically on crystal structure and on the crystallographic orientation of the crack system but can also be correlated with the relative ease of dislocation generation (and motion). copyright 1997 The American Physical Society
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Molecular potentials and relaxation dynamics
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 X1Σ+ and a3Σ+ states of LiH, NaH, KH, RbH, and CsH and the X2Σ+ 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 5000K. 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
Driving ordering processes in molecular-dynamics simulations.
Dittmar, Harro; Kusalik, Peter G
2014-05-16
Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized. PMID:24877946
Molecular dynamics simulation of benzene
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Molecular dynamics studies of palladium
Equilibrium bulk properties of Pd are examined using molecular dynamics technique based on the embedded atom potential. We calculate the total energy and the lattice parameter as a function of temperature. Melting temperature is determined from the discontinuous transition in the energy and lattice parameter. Specific heat and linear coefficient of thermal expansion are calculated from the energy and lattice parameters respectively and results show good agreement with experimental values. Finally the mean square displacements of thermal expansion are calculated form the energy and lattice parameters respectively and results show good agreement with the experimental values. Finally the mean square displacements of the atoms in bulk Pd are compared with the mean square displacements on the three low-index faces (100), (110) and (III). (author)
Spectral Ewald Acceleration of Stokesian Dynamics for polydisperse suspensions
Wang, Mu; Brady, John F.
2016-02-01
In this work we develop the Spectral Ewald Accelerated Stokesian Dynamics (SEASD), a novel computational method for dynamic simulations of polydisperse colloidal suspensions with full hydrodynamic interactions. SEASD is based on the framework of Stokesian Dynamics (SD) with extension to compressible solvents, and uses the Spectral Ewald (SE) method [Lindbo and Tornberg (2010) [29
Theoretical Concepts in Molecular Photodissociation Dynamics
Henriksen, Niels Engholm
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 Mole...
Theoretical Concepts in Molecular Photodissociation Dynamics
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...
Accelerator dynamics of a fractional kicked rotor
Iomin, A.
2006-01-01
It is shown that the Weyl fractional derivative can quantize an open system. A fractional kicked rotor is studied in the framework of the fractional Schrodinger equation. The system is described by the non-Hermitian Hamiltonian by virtue of the Weyl fractional derivative. Violation of space symmetry leads to acceleration of the orbital momentum. Quantum localization saturates this acceleration, such that the average value of the orbital momentum can be a direct current and the system behaves ...
Evaluation of an Accelerated ELDRS Test Using Molecular Hydrogen
Pease, Ronald L.; Adell, Philippe C.; Rax, Bernard; McClure, Steven; Barnaby, Hugh J.; Kruckmeyer, Kirby; Triggs, B.
2011-01-01
An accelerated total ionizing dose (TID) hardness assurance test for enhanced low dose rate sensitive (ELDRS) bipolar linear circuits, using high dose rate tests on parts that have been exposed to molecular hydrogen, has been proposed and demonstrated on several ELDRS part types. In this study several radiation-hardened "ELDRS-free" part types have been tested using this same approach to see if the test is overly conservative.
Molecular dynamics of membrane proteins.
Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); Crozier, Paul Stewart; Stevens, Mark Jackson
2004-10-01
Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.
Symbolic mathematical computing: orbital dynamics and application to accelerators
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)
Dynamic Spectrum Sensing Through Accelerated Particle Swarm Optimization
Paschos, Alexandros E.; Kapinas, Vasileios M.; Hadjileontiadis, Leontios J.; Karagiannidis, George K.
2015-01-01
A novel optimization algorithm, called accelerated particle swarm optimization (APSO), is proposed for dynamic spectrum sensing in cognitive radio networks. While modified swarm-based optimization algorithms focus on slight variations of the standard mathematical formulas, in APSO, the acceleration variable of the particles in the swarm is also considered in the search space of the optimization problem. We show that the proposed APSO-based dynamic spectrum sensing technique is more efficient ...
Beam dynamics studies in a tesla positron pre-accelerator
Moiseev, V A; Flöttmann, K
2001-01-01
The TESLA linear collider is based on superconducting accelerating cavities.Behind the positron production target normal conducting cavities have to be used in order to cope with high particle losses and with focusing solenoid surrounding the cavities.The main purpose of this pre-accelerator is to provide maximum capture efficiency for the useful part of the totally acceptable positron beam with technically reasonable parameters of the linac.The coupled optimization of the capture optics behind the target and pre-accelerator rf-operation has been carried out.The beam dynamics simulation results as well as the pre-accelerator peculiarities are presented.
Molecular dynamics simulation by atomic mass weighting
Mao, Boryeu; Friedman, Alan R.
1990-01-01
A molecular dynamics-based simulation method in which atomic masses are weighted is described. Results from this method showed that the capability for conformation search in molecular dynamics simulation of a short peptide (FMRF-amide) is significantly increased by mass weighting.
The international entrepreneurial dynamics of accelerated internationalization
John A. Mathews; Zander, Ivo
2007-01-01
New forms of international business and multinational enterprises continue to be observed, and finding ways to account for their appearance constitutes a continuing challenge for IB scholars. In this paper we aim to delineate an emerging field of IB scholarship; we focus on the appearance of international new ventures, and the phenomenon of early and accelerated internationalization that they feature, as one that has slipped through the net of some of the existing IB frameworks. We propose th...
Thermally driven molecular linear motors - A molecular dynamics study
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...
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out
Quantum dynamics of complex molecular systems
Miller, William H.
2005-01-01
This Perspective presents a broad overview of the present status of theoretical capabilities for describing quantum dynamics in molecular systems with many degrees of freedom, e.g., chemical reactions in solution, clusters, solids, or biomolecular environments.
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
Ab initio mass tensor molecular dynamics
Tsuchida, Eiji
2010-01-01
Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal ato...
Molecular Dynamic Simulation on High Performance Infrastrucutres
Bergant, Anže
2016-01-01
This thesis covers comparison between different computer platforms of high performance computing while performing molecular dynamics simulations, which falls under very complex problems and needs lots of processing power. Our goal was to critically evaluate different platforms while solving molecular dynamics, so we used 1 to 16 processor cores on a computer cluster and one and two graphics processing units (GPU) for simulations. The results will be used while planning on buying new computer ...
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Jahn, S.; P. A. Madden
2008-01-01
The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q) from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω) from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the ...
Modeling the Hydrogen Bond within Molecular Dynamics
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
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)
Fermionic Molecular Dynamics for nuclear dynamics and thermodynamics
Hasnaoui, K H O; Gulminelli, F
2008-01-01
A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented
Laser fields in dynamically ionized plasma structures for coherent acceleration
Luu-Thanh, Ph.; Pukhov, A.; Kostyukov, I.
2015-01-01
With the emergence of the CAN (Coherent Amplification Network) laser technology, a new scheme for direct particle acceleration in periodic plasma structures has been proposed. By using our full electromagnetic relativistic particle-in-cell (PIC) simulation code equipped with ionisation module, we simulate the laser fields dynamics in the periodic structures of different materials. We study how the dynamic ionization influences the field structure.
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.
Spin dynamics in storage rings and linear accelerators
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
Polymer degradation and molecular relaxation during accelerated weathering of coatings
Fernando, B. Malcolm Dilhan
2011-12-01
A model polyester-urethane coating similar to those on USAF aircraft was the focus in this research. It was studied for physical property changes during accelerated weathering. Isothermal aging and natural weathering were utilized as control studies. Coatings subjected to accelerated weathering had an increase in tensile modulus, glass transition temperature and surface stiffness. DSC analysis of these coatings clearly showed evidence for 'physical aging'. This phenomenon was pursued further to find out the impact of macromolecular relaxation on the polymer physical properties. The unique feature of this research is the investigation of kinetics of macromolecular relaxation whilst a polymer undergoes simultaneous degradation. Assessment was done for some material parameters as found in theoretical models. Fictive temperature (Tf), apparent activation energy (Deltah*/R) and non linearity parameter ( x) found in Tool-Narayanswamy-Moyniham (TNM) model were explored. Tf was found to be decreasing with weathering and explained the increasingly aged 'state' of the structure. Deltah*/R was found to be increasing and explains an increased energy barrier to overcome to attain relaxation. DSC peak-shift method was used to characterize x. At early stages there is a stronger non linearity of relaxation (lower x) with a stronger structure dependence and later the relaxation kinetics seems more temperature dependent (higher x). MDSC was done to characterize the non exponentiality parameter (beta) as found in the Kohlrauch-Williams-Watts (KWW) equation. Decreasing beta value with exposure implies an increasingly broad distribution of relaxation times. The Cooperatively Rearranging Regions (CRR) concept of Adams and Gibbs was also examined. Molecular weight (Ma) of the volume (Va) represented by a CRR was compared with Mc, the molecular weight between crosslinks. Nanoindentation was done to explore the coatings' surface mechanical properties. During accelerated weathering the
Accelerating Dynamic Cardiac MR Imaging Using Structured Sparse Representation
Nian Cai
2013-01-01
Full Text Available Compressed sensing (CS has produced promising results on dynamic cardiac MR imaging by exploiting the sparsity in image series. In this paper, we propose a new method to improve the CS reconstruction for dynamic cardiac MRI based on the theory of structured sparse representation. The proposed method user the PCA subdictionaries for adaptive sparse representation and suppresses the sparse coding noise to obtain good reconstructions. An accelerated iterative shrinkage algorithm is used to solve the optimization problem and achieve a fast convergence rate. Experimental results demonstrate that the proposed method improves the reconstruction quality of dynamic cardiac cine MRI over the state-of-the-art CS method.
Dynamics and Thermodynamics of Molecular Machines
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......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...... statistical 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...
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...
Fast dynamics of molecular bridges
Špička, Václav; Kalvová, Anděla; Velický, B.
T151, č. 1 (2012), s. 1-17. ISSN 0031-8949 R&D Projects: GA ČR GAP204/12/0897 Institutional research plan: CEZ:AV0Z10100521; CEZ:AV0Z10100520 Keywords : time quantum dynamics * nonequilibrium Green-functions * Kadanoff-Baym equations * initial correlations * transportequations * mesoscopic systems Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.032, year: 2012
Scalable Molecular Dynamics for Large Biomolecular Systems
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.
Beam dynamics studies of the Heavy Ion Fusion Accelerator injector
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
Molecular Scale Dynamics of Large Ring Polymers
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.
Methane in carbon nanotube - molecular dynamics simulation
Bartuś, Katarzyna; Bródka, Aleksander
2011-01-01
Abstract The behaviour of methane molecules inside carbon nanotube at room temperature is studied using classical molecular dynamics simulations. A methane molecule is represented either by a shapeless super-atom or by rigid set of 5 interaction centres localised on atoms. Different loadings of methane molecules ranging from the dense gas density to the liquid density, and the influence of flexibility of the CNT on structural and dynamics properties of confined molecules are consid...
Neutron Star Crust and Molecular Dynamics Simulation
Horowitz, C J; Schneider, A; Berry, D K
2011-01-01
In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.
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.
Spectral Ewald Acceleration of Stokesian Dynamics for polydisperse suspensions
Wang, Mu
2015-01-01
In this work we develop the Spectral Ewald Accelerated Stokesian Dynamics (SEASD), a novel computational method for dynamic simulations of polydisperse colloidal suspensions with full hydrodynamic interactions. SEASD is based on the framework of Stokesian Dynamics (SD) with extension to compressible solvents, and uses the Spectral Ewald (SE) method [Lindbo & Tornberg, J. Comput. Phys. 229 (2010) 8994] for the wave-space mobility computation. To meet the performance requirement of dynamic simulations, we use Graphic Processing Units (GPU) to evaluate the suspension mobility, and achieve an order of magnitude speedup compared to a CPU implementation. For further speedup, we develop a novel far-field block-diagonal preconditioner to reduce the far-field evaluations in the iterative solver, and SEASD-nf, a polydisperse extension of the mean-field Brownian approximation of Banchio & Brady [J. Chem. Phys. 118 (2003) 10323]. We extensively discuss implementation and parameter selection strategies in SEASD, a...
Molecular dynamics simulation of impact test
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.)
Molecular dynamic simulation of directional crystal growth
Costa, B. V.; Coura, P. Z.; Mesquita, O. N.
1999-01-01
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach experimentally, being an important tool for further experimental and theoretical developments in the area of crystal growth.
Molecular dynamics - NMR experiments and simulations
Dračínský, Martin; Hodgkinson, P.; Kessler, Jiří; Bouř, Petr
Brno : Masaryk University Press, 2015 - (Sklenář, V.). s. 277-278 ISBN 978-80-210-7890-1. [EUROMAR 2015. 05.07.2015-10.07.2015, Praha] Institutional support: RVO:61388963 Keywords : molecular dynamics * NMR spectroscopy * MD simulations Subject RIV: CF - Physical ; Theoretical Chemistry
Reaction dynamics in polyatomic molecular systems
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
Molecular dynamics simulations of weak detonations.
Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie
2011-12-01
Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055
Dynamical quenching of tunneling in molecular magnets
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
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.
GPU accelerated dynamic functional connectivity analysis for functional MRI data.
Akgün, Devrim; Sakoğlu, Ünal; Esquivel, Johnny; Adinoff, Bryon; Mete, Mutlu
2015-07-01
Recent advances in multi-core processors and graphics card based computational technologies have paved the way for an improved and dynamic utilization of parallel computing techniques. Numerous applications have been implemented for the acceleration of computationally-intensive problems in various computational science fields including bioinformatics, in which big data problems are prevalent. In neuroimaging, dynamic functional connectivity (DFC) analysis is a computationally demanding method used to investigate dynamic functional interactions among different brain regions or networks identified with functional magnetic resonance imaging (fMRI) data. In this study, we implemented and analyzed a parallel DFC algorithm based on thread-based and block-based approaches. The thread-based approach was designed to parallelize DFC computations and was implemented in both Open Multi-Processing (OpenMP) and Compute Unified Device Architecture (CUDA) programming platforms. Another approach developed in this study to better utilize CUDA architecture is the block-based approach, where parallelization involves smaller parts of fMRI time-courses obtained by sliding-windows. Experimental results showed that the proposed parallel design solutions enabled by the GPUs significantly reduce the computation time for DFC analysis. Multicore implementation using OpenMP on 8-core processor provides up to 7.7× speed-up. GPU implementation using CUDA yielded substantial accelerations ranging from 18.5× to 157× speed-up once thread-based and block-based approaches were combined in the analysis. Proposed parallel programming solutions showed that multi-core processor and CUDA-supported GPU implementations accelerated the DFC analyses significantly. Developed algorithms make the DFC analyses more practical for multi-subject studies with more dynamic analyses. PMID:25805449
Accelerating the convergence of path integral dynamics with a generalized Langevin equation
Ceriotti, Michele; Parrinello, Michele; 10.1063/1.3556661
2012-01-01
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 quasi-harmonic 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.
Exciton dynamics in perturbed vibronic molecular aggregates.
Brüning, C; Wehner, J; Hausner, J; Wenzel, M; Engel, V
2016-07-01
A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840
Radio Frequency Station - Beam Dynamics Interaction in Circular Accelerators
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
Radio Frequency Station - Beam Dynamics Interaction in Circular Accelerators
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
Radio Frequency Station - Beam Dynamics Interaction in Circular Accelerators
Mastoridis, Themistoklis; /Stanford U., Elect. Eng. Dept. /SLAC
2011-03-01
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
A gas-dynamical approach to radiation pressure acceleration
Schmidt, Peter; Boine-Frankenheim, Oliver
2016-06-01
The study of high intensity ion beams driven by high power pulsed lasers is an active field of research. Of particular interest is the radiation pressure acceleration, for which simulations predict narrow band ion energies up to GeV. We derive a laser-piston model by applying techniques for non-relativistic gas-dynamics. The model reveals a laser intensity limit, below which sufficient laser-piston acceleration is impossible. The relation between target thickness and piston velocity as a function of the laser pulse length yields an approximation for the permissible target thickness. We performed one-dimensional Particle-In-Cell simulations to confirm the predictions of the analytical model. These simulations also reveal the importance of electromagnetic energy transport. We find that this energy transport limits the achievable compression and rarefies the plasma.
Imaging molecular structure and dynamics using laser driven recollisions
Complete test of publication follows. Laser driven electron recollision provides a unique tool for measuring the structure and dynamics of matter. We illustrate this with experiments that use HHG to measure molecular structure with sub-Angstrom spatial and sub-femtosecond temporal resolution. Our recent work has looked in particular at the signal from high order harmonic generation which contains rich information about the structure and intra-molecular dynamics of small molecules. This we will illustrate by two types of experiment; (a) measurements of HHG from aligned molecular samples to observe two-centre recombination interference and electronic structure dependence of the angle dependent yield, (b) reconstruction of intra-molecular proton dynamics from the spectral dependence of the HHG using the intrinsic chirp of recolliding electrons. We experimentally investigate the process of intramolecular quantum interference in high-order harmonic generation in impulsively aligned CO2 molecules. The recombination interference effect is clearly seen through the order dependence of the harmonic yield in an aligned sample. This confirms that the effective de Broglie wavelength of the returning electron wave is not significantly altered by acceleration in the Coulomb field of the molecular ion. For the first time, to our knowledge, we demonstrate that such interference effects can be effectively controlled by changing the ellipticity of the driving laser field. Here we also report the results of angular dependence measurements of high order harmonics (17tth - 27th) from impulsively aligned organic molecules: Acetylene, Ethylene, and Allene. Since these molecules have a relatively low Ip an appropriately short pulse is required to produce as many harmonic orders as possible. This was provided by the ∼ 10 fs beam line of the ASTRA laser at Rutherford Appleton Laboratory whilst a somewhat longer pulse, properly forwarded with respect to the driving pulse, induced the
The Acceleration Scale, Modified Newtonian Dynamics and Sterile Neutrinos
Diaferio, Antonaldo; Angus, Garry W.
General relativity is able to describe the dynamics of galaxies and larger cosmic structures only if most of the matter in the universe is dark, namely, it does not emit any electromagnetic radiation. Intriguingly, on the scale of galaxies, there is strong observational evidence that the presence of dark matter appears to be necessary only when the gravitational field inferred from the distribution of the luminous matter falls below an acceleration of the order of 10^{-10} m s^{-2}. In the standard model, which combines Newtonian gravity with dark matter, the origin of this acceleration scale is challenging and remains unsolved. On the contrary, the full set of observations can be neatly described, and were partly predicted, by a modification of Newtonian dynamics, dubbed MOND, that does not resort to the existence of dark matter. On the scale of galaxy clusters and beyond, however, MOND is not as successful as on the scale of galaxies, and the existence of some dark matter appears unavoidable. A model combining MOND with hot dark matter made of sterile neutrinos seems to be able to describe most of the astrophysical phenomenology, from the power spectrum of the cosmic microwave background anisotropies to the dynamics of dwarf galaxies. Whether there exists a yet unknown covariant theory that contains general relativity and Newtonian gravity in the weak field limit and MOND as the ultra-weak field limit is still an open question.
Open quantum system parameters from molecular dynamics
Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander
2015-01-01
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...
Towards the molecular bases of polymerase dynamics
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 (rf) and RNA polymerase (rt). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking rf and rt 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 rt may depend on the length (λt) 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
Nonadiabatic Molecular Dynamics Based on Trajectories
Felipe Franco de Carvalho
2013-12-01
Full Text Available Performing molecular dynamics in electronically excited states requires the inclusion of nonadiabatic effects to properly describe phenomena beyond the Born-Oppenheimer approximation. This article provides a survey of selected nonadiabatic methods based on quantum or classical trajectories. Among these techniques, trajectory surface hopping constitutes an interesting compromise between accuracy and efficiency for the simulation of medium- to large-scale molecular systems. This approach is, however, based on non-rigorous approximations that could compromise, in some cases, the correct description of the nonadiabatic effects under consideration and hamper a systematic improvement of the theory. With the help of an in principle exact description of nonadiabatic dynamics based on Bohmian quantum trajectories, we will investigate the origin of the main approximations in trajectory surface hopping and illustrate some of the limits of this approach by means of a few simple examples.
Molecular dynamics study of cyclohexane interconversion
Wilson, Michael A.; Chandler, David
1990-12-01
Classical molecular dynamics calculations are reported for one C 6H 12 molecule in a bath of 250 CS 2 molecules at roomtemperature and liquid densities of 1.0, 1.3, 1.4 and 1.5 g/cm 3. The solvent contribution to the free energy of activation for the chair-boat isomerization has been determined to high accuracy. The transmission coefficient and reactive flux correlation functions have also been computed. The results obtained agree with earlier conclusions drawn from RISM integral equation calculations and stochastic molecular dynamics calculations. Namely, the solvent effect on the rate manifests a qualitative breakdown of transition state theory and the RRKM picture of unimolecular kinetics. Analysis of the activated trajectories indicate a significant degree of quasiperiodicity.
Molecular dynamics at constant Cauchy stress
Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio
2016-05-01
The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.
Molecular dynamics simulation for modelling plasma spectroscopy
Talin, B; Calisti, A; Gigosos, M A; González, M A; Gaztelurrutia, T R; Dufty, J W
2003-01-01
The ion-electron coupling properties for an ion impurity in an electron gas and for a two-component plasma are carried out on the basis of a regularized electron-ion potential removing the short-range Coulomb divergence. This work is largely motivated by the study of radiator dipole relaxation in plasmas which makes a real link between models and experiments. Current radiative property models for plasmas include single electron collisions neglecting charge-charge correlations within the classical quasi-particle approach commonly used in this field. The dipole relaxation simulation based on electron-ion molecular dynamics proposed here will provide a means to benchmark and improve model developments. Benefiting from a detailed study of a single ion embedded in an electron plasma, the challenging two-component ion-electron molecular dynamics simulations are proved accurate. They open new possibilities of obtaining reference lineshape data.
Molecular quantum dynamics. From theory to applications
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
Simulation of Abrasive Machining Using Molecular Dynamics
Oluwajobi, Akinjide O.; Chen, Xun
2009-01-01
The development of ultra–precision processes which can achieve excellent surface finish and tolerance at nanometre level is now a critical requirement for many applications in medical, electronics and energy industry. Presently, it is very difficult to observe the diverse microscopic physical phenomena occurring in nanometric machining through experiments. The use of Molecular Dynamics (MD) simulation has proved to be an effective tool for the prediction and the analysis ...
Modelling abrasive machining techniques using molecular dynamics
Oluwajobi, Akinjide O.; Chen, Xun
2008-01-01
The development of ultra–precision processes which can achieve nanometre surface finishes and tolerances is now a critical requirement for many applications in medical, electronics and energy industry. Presently, it is very difficult to observe the diverse microscopic physical phenomena occurring in nanometric machining through experiments. The use Molecular Dynamics (MD) simulation has proved to be an effective tool for the prediction and the analysis of these processes at the nanometre scal...
Molecular dynamics simulation of a chemical reaction
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
Molecular dynamics modelling of solidification in metals
Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)
1997-12-31
Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.
Molecular dynamics simulation of expanding infinite matter
Multi-fragmentation occurred in an expanding infinite system is studied by using molecular dynamics simulation. To evaluate the secondary decay effect, the time evolution of expanding system is proceeded till all fragments are stabilized completely. The fragment mass distribution from the expansion is compared with a percolation model and the cause of the exponential shape is clarified. The cause of small critical temperature is also discussed. (author)
Molecular Dynamics with Helical Periodic Boundary Conditions
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 ostatní: 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
Temperature Dependent Molecular Dynamic Simulation of Friction
Dias, R A; Coura, P Z; Costa, B V
2006-01-01
In this work we present a molecular dynamics simulation of a FFM experiment. The tip-sample interaction is studied by varying the normal force in the tip and the temperature of the surface. The friction force, cA, at zero load and the friction coefficient, $\\mu$, were obtained. Our results strongly support the idea that the effective contact area, A, decreases with increasing temperature and the friction coefficient presents a clear signature of the premelting process of the surface.
Simulating granular flow with molecular dynamics
Ristow, Gerald
1992-01-01
We investigate by means of Molecular Dynamics simulations an assembly of spheres to model a granular medium flowing from an upper rectangular chamber through a hole into a lower chamber. Two different two dimensional models are discussed one of them including rotations of the individual spheres. The outflow properties are investigated and compared to experimental data. The qualitative agreement suggests that our models contain the necessary ingredients to describe the outflow properties of gr...
Molecular dynamics simulations using graphics processing units
Baker, J.A.; Hirst, J.D.
2011-01-01
It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation com...
Molecular Dynamics Studies of Nanofluidic Devices
Zambrano Rodriguez, Harvey Alexander
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 methodology. In the second part of this thesis, we present the results of three different research projects. Fristly, we present a computational study of thermophoresis as a suitable mechanism to drive water droplets confined in different types of carbon nanotubes. We observe a...... motion of the water droplet 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...
The Acceleration Scale, Modified Newtonian Dynamics, and Sterile Neutrinos
Antonaldo DiaferioUniversita' di Torino and INFN Torino; Angus, Garry W.
2015-01-01
General Relativity is able to describe the dynamics of galaxies and larger cosmic structures only if most of the matter in the Universe is dark, namely it does not emit any electromagnetic radiation. Intriguingly, on the scale of galaxies, there is strong observational evidence that the presence of dark matter appears to be necessary only when the gravitational field inferred from the distribution of the luminous matter falls below an acceleration of the order of 10^(-10) m/s^2. In the standa...
Optimally designed fields for controlling molecular dynamics
Rabitz, Herschel
1991-10-01
This research concerns the development of molecular control theory techniques for designing optical fields capable of manipulating molecular dynamic phenomena. Although is has been long recognized that lasers should be capable of manipulating dynamic events, many frustrating years of intuitively driven laboratory studies only serve to illustrate the point that the task is complex and defies intuition. The principal new component in the present research is the recognition that this problem falls into the category of control theory and its inherent complexities require the use of modern control theory tools largely developed in the engineering disciplines. Thus, the research has initiated a transfer of the control theory concepts to the molecular scale. Although much contained effort will be needed to fully develop these concepts, the research in this grant set forth the basic components of the theory and carried out illustrative studies involving the design of optical fields capable of controlling rotational, vibrational and electronic degrees of freedom. Optimal control within the quantum mechanical molecular realm represents a frontier area with many possible ultimate applications. At this stage, the theoretical tools need to be joined with merging laboratory optical pulse shaping capabilities to illustrate the power of the concepts.
Control Volume Representation of Molecular Dynamics
Smith, E R; Dini, D; Zaki, T A
2012-01-01
A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of [1] Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' Transport Theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-Control-Volume (LCV) conversion function \\vartheta_{i}, for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the Volume Average (VA, [2] Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, [3] Todd et al, Phys. Rev. E 52, 1627 (1995)) emerges natu...
Atomic dynamics of alumina melt: A molecular dynamics simulation study
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
A Concurrent Multiscale Micromorphic Molecular Dynamics. Part I. Theoretical Formulation
Li, Shaofan
2014-01-01
Based on a novel concept of multiplicative multiscale decomposition, we have derived a multiscale micromorphic molecular dynamics (MMMD)to extent the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and macroscale. The multiscale micromorphic molecular dynamics is a con-current three-scale particle dynamics that couples a fine scale molecular dynamics, a mesoscale particle dynamics of micromorphic medium, and a coarse scale nonlocal particle dynamics of nonlinear continuum. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and it is a special case of the proposed multiscale micromorphic molecular dynamics. The discovered mutiscale structure and the corresponding multiscale dynamics reveal a seamless transition channel from atomistic scale to continuum scale and the intrinsic coupling relation among them, and it can be used to solve finite size nanoscale sc...
Mechanisms of Acceleration and Retardation of Water Dynamics by Ions
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 ostatní: 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
Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces
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.
Molecular Dynamics Studies of Initiation in Energetic Materials
Haskins, P.
1995-01-01
In this paper an overview of Molecular Dynamics simulations of chemically reacting systems is described. In particular, molecular dynamics simulations of shock initiation in a model energetic material are reported. The use of Molecular Dynamics to model thermal initiation and determine reactions rates in energetic materials is also discussed. Finally, the future potential of MD techniques for energetic materials applications is considered.
Dynamical structure of fluid mercury: Molecular-dynamics simulations
Hoshino, Kozo; Tanaka, Shunichiro; Shimojo, Fuyuki
2007-01-01
We have carried out molecular-dynamics simulations for nonmetallic fluid mercury in liquid and vapor phases using a Lennard-Jones type effective potential and shown that the structure factors S(Q) and the dynamic structure factors S(Q, omega) of nonmetallic fluid mercury obtained by our MD simulations are in good agreement with recent X-ray diffraction and inelastic X-ray scattering experiments. We conclude from these results that, though the fluid mercury which shows a metal-nonmetal transit...
Application of optimal prediction to molecular dynamics
Barber IV, John Letherman
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is {delta}-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
We investigated the characteristics of a capacitive nano-accelerometer based on a telescoping carbon nanotube by means of classical molecular dynamics simulations. The position of the telescoping nanotube was controlled by an externally applied force, and feedback sensing was based on the capacitance change. The capacitance variations, which were almost linearly proportional to the applied acceleration, were monitored within an error tolerance
The Acceleration Scale, Modified Newtonian Dynamics, and Sterile Neutrinos
Diaferio, Antonaldo
2012-01-01
General Relativity is able to describe the dynamics of galaxies and larger cosmic structures only if most of the matter in the Universe is dark, namely it does not emit any electromagnetic radiation. Intriguingly, on the scale of galaxies, there is strong observational evidence that the presence of dark matter appears to be necessary only when the gravitational field inferred from the distribution of the luminous matter falls below an acceleration of the order of 10^(-10) m/s^2. In the standard model, which combines Newtonian gravity with dark matter, the origin of this acceleration scale is challenging and remains unsolved. On the contrary, the full set of observations can be neatly described, and were partly predicted, by a modification of Newtonian dynamics, dubbed MOND, that does not resort to the existence of dark matter. On the scale of galaxy clusters and beyond, however, MOND is not as successful as on the scale of galaxies, and the existence of some dark matter appears unavoidable. A model combining ...
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...
Cell Molecular Dynamics for Cascades (CMDC): A new tool for cascade simulation
We present a new Molecular Dynamics (MD) scheme for the simulation of cascades: Cell Molecular Dynamics for Cascades (CMDC). It is based on the decomposition of the material in nanometric cells which are added and removed on the fly from the MD simulation and the dynamics of which are treated with a local time step. An acceleration of several orders of magnitude is observed compared to standard calculation. The capacity of the method is demonstrated on the test cases of 60 keV He implantation and self-cascades in iron up to 1.8 MeV
Nano-tribology through molecular dynamics simulations
WANG; Hui(
2001-01-01
［1］Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.［2］Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.［3］Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.［4］Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.［5］Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.［6］Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.［7］Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.［8］Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.［9］Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.［10］Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.［11］Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.［12］Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.［13］Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.
Molecular dynamic results on transport properties
Alder, B.J.; Alley, W.E.
1978-06-01
Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so.
Molecular dynamic results on transport properties
Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so
Electronic continuum model for molecular dynamics simulations.
Leontyev, I V; Stuchebrukhov, A A
2009-02-28
A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627
Molecular dynamics studies of aromatic hydrocarbon liquids
This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules
Continuous Finite Element Methods of Molecular Dynamics Simulations
Qiong Tang; Luohua Liu; Yujun Zheng
2015-01-01
Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite elemen...
Parallelization of quantum molecular dynamics simulation code
A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)
Ab Initio Molecular Dynamics: A Virtual Laboratory
Hobbi Mobarhan, Milad
2014-01-01
In this thesis, we perform ab initio molecular dynamics (MD) simulations at the Hartree-Fock level, where the forces are computed on-the-fly using the Born-Oppenheimer approximation. The theory behind the Hartree-Fock method is discussed in detail and an implementation of this method based on Gaussian basis functions is explained. We also demonstrate how to calculate the analytic energy derivatives needed for obtaining the forces acting on the nuclei. Hartree-Fock calculations on the ground s...
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.
Electrostatic Energy Calculations for Molecular Dynamics
Love, M J; Comment, Henri J.F. Jansen; Love, Michael J.
1995-01-01
The evaluation of Coulomb forces is a difficult task. The summations that are involved converge only conditionally and care has to be taken in selecting the appropriate procedure to define the limits. The Ewald method is a standard method for obtaining Coulomb forces, but this method is rather slow, since it depends on the square of the number of atoms in a unit cell. In this paper we have adapted the plane-wise summation method for the evaluation of Coulomb forces. The use of this method allows for larger computational cells in molecular dynamics calculations.
Molecular beam studies of reaction dynamics
Lee, Y.T.
1987-03-01
Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.
Molecular dynamics at constant temperature and pressure
Toxvaerd, S.
1993-01-01
Algorithms for molecular dynamics (MD) at constant temperature and pressure are investigated. The ability to remain in a regular orbit in an intermittent chaotic regime is used as a criterion for long-time stability. A simple time-centered algorithm (leap frog) is found to be the most stable of the commonly used algorithms in MD. A model of N one-dimensional dimers with a double-well intermolecular potential, for which the distribution functions at constant temperature T and pressure P can be calculated, is used to investigate MD-NPT dynamics. A time-centered NPT algorithm is found to sample correctly and to be very robust with respect to volume scaling.
Fermionic Molecular Dynamics and short range correlations
Feldmeier, H; Roth, R S; Schnack, J
1998-01-01
Fermionic Molecular Dynamics (FMD) models a system of fermions by means of many-body states which are composed of antisymmetrized products of single-particle states. These consist of one or several Gaussians localized in coordinate and momentum space. The parameters specifying them are the dynamical variables of the model. As the repulsive core of the nucleon-nucleon interaction induces short range correlations which cannot be accommodated by a Slater determinant, a novel approach, the unitary correlation operator method (UCOM), is applied. The unitary correlator moves two particles away from each other whenever their relative distance is within the repulsive core. The time-dependent variational principle yields the equations of motion for the variables. Energies of the stationary ground states are calculated and compared to exact many-body results for nuclei up to Ca 48. Time-dependent solutions are shown for collisions between nuclei.
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.
Beam Dynamics Measurements for the SLAC Laser Acceleration Experiment
The NLC Test Accelerator (NLCTA) was built to address beam dynamics issues for the Next Linear Collider and beyond. An S-Band RF gun, diagnostics and low energy spectrometer (LES) at 6 MeV together with a large-angle extraction line at 60 MeV have now been built and commissioned for the laser acceleration experiment, E163. Following a four quad matching section after the NLCTA chicane, the extraction section is followed by another matching section, final focus and buncher. The laser-electron interaction point (IP) is followed by a broad range, high resolving power spectrometer (HES) for electron bunch analysis. Optical symmetries in the design of the 25.5 degree extraction line provide 1:1 phase space transfer without sextupoles for a large, 6D phase space volume and range of input conditions. Spot sizes down to a few microns at the IP (HES object) allow testing microscale structures with high resolving power at the HES image. Tolerances, tuning sensitivities, diagnostics and the latest commissioning results are discussed and compared to design expectations
Spin dynamics of electron beams in circular accelerators
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.
Beam Dynamics Studies for a Laser Acceleration Experiment
The NLC Test Accelerator (NLCTA) at SLAC was built to address various beam dynamics issues for the Next Linear Collider. An S-Band RF gun is being installed together with a large-angle extraction line at 60 MeV followed by a matching section, buncher and final focus 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. Another spectrometer at 6 MeV will be used for analysis of bunch charges up to 1 nC. Emittance compensating solenoids and the low energy spectrometer (LES) will be used to tune for best operating point and match to the linac. Optical symmetries in the design of the 25.5o extraction line provide 1:1 phase space transfer without use of sextupoles for a large, 6D phase space volume and range of input conditions. Design techniques, tolerances, tuning sensitivities and orthogonal knobs are discussed
Molecular dynamics simulations through GPU video games technologies
Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia
2016-01-01
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations.
Step by step parallel programming method for molecular dynamics code
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)
GPU-enabled molecular dynamics simulations of ankyrin kinase complex
Gautam, Vertika; Chong, Wei Lim; Wisitponchai, Tanchanok; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.; Tayapiwatana, Chatchai; Lee, Vannajan Sanghiran
2014-10-01
The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein-protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.
Active microrheology of Brownian suspensions via Accelerated Stokesian Dynamics simulations
Chu, Henry; Su, Yu; Gu, Kevin; Hoh, Nicholas; Zia, Roseanna
2015-11-01
The non-equilibrium rheological response of colloidal suspensions is studied via active microrheology utilizing Accelerated Stokesian Dynamics simulations. In our recent work, we derived the theory for micro-diffusivity and suspension stress in dilute suspensions of hydrodynamically interacting colloids. This work revealed that force-induced diffusion is anisotropic, with qualitative differences between diffusion along the line of the external force and that transverse to it, and connected these effects to the role of hydrodynamic, interparticle, and Brownian forces. This work also revealed that these forces play a similar qualitative role in the anisotropy of the stress and in the evolution of the non-equilibrium osmotic pressure. Here, we show that theoretical predictions hold for suspensions ranging from dilute to near maximum packing, and for a range of flow strengths from near-equilibrium to the pure-hydrodynamic limit.
Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations
Byutner, Oleksiy; Smith, Grant
2001-03-01
In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.
Multiple branched adaptive steered molecular dynamics
Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto
2014-08-01
Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of nonequilibrium trajectories. The recently proposed adaptive steered molecular dynamics, ASMD, introduced a new idea for selecting important events and eliminating the non-contributing trajectories, thus decreasing the overall computation needed. ASMD was shown to reduce the number of trajectories needed by a factor of 10 in a benchmarking study of decaalanine stretching. Here we propose a novel, highly efficient "multiple branching" (MB) version, MB-ASMD, which obtains a more complete enhanced sampling of the important trajectories, while still eliminating non-contributing segments. Compared to selecting a single configuration in ASMD, MB-ASMD offers to select multiple configurations at each segment along the reaction coordinate based on the distribution of work trajectories. We show that MB-ASMD has all benefits of ASMD such as faster convergence of the PMF even when pulling 1000 times faster than the reversible limit while greatly reducing the probability of getting trapped in a non-significant path. We also analyze the hydrogen bond breaking within the decaalanine peptide as we force the helix into a random coil and confirm ASMD results with less noise in the numerical averages.
Dynamics of Ag clusters on complex surfaces: Molecular dynamics simulations
Alkis, S.; Krause, J. L.; Fry, J. N.; Cheng, H.-P.
2009-03-01
We study the diffusion of silver nanoparticles on self-assembled monolayers (SAMs). Silver clusters Agn of sizes n=55 , 147, and 1289 were evolved in contact with an alkanethiol (12 carbon, dodecanethiol) SAM deposited on a gold (111) surface. Analysis based on classical molecular dynamics simulations reveals that these systems exhibit a rich variety of behaviors, from superdiffusive for the lightest cluster to pinned for the heaviest, evolution self-similar in lengths and times for the lightest cluster but with characteristic time scales and directional anisotropies emerging for the heavier clusters.
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics
Erban, Radek
2015-01-01
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.
Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow
Archereau, Aurelien Y M; Willmott, Geoff R
2016-01-01
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...
The 2011 Dynamics of Molecular Collisions Conference
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
A scheme to combine molecular dynamics and dislocation dynamics
Many engineering challenges occur on multiple interacting length scales, e.g. during fracture atoms separate on the atomic scale while plasticity develops on the micrometer scale. To investigate the details of these events, a concurrent multiscale model is required which studies the problem at appropriate length- and time-scales: the atomistic scale and the dislocation dynamics scale. The AtoDis multiscale model is introduced, which combines atomistics and dislocation dynamicsinto a fully dynamic model that is able to simulate deformation mechanisms at finite temperature. The model uses point forces to ensure mechanical equilibrium and kinematic continuity at the interface. By resolving each interface atom analytically, and not numerically, the framework uses a coarse FEM mesh and intrinsically filters out atomistic vibrations. This multiscale model allows bi-directional dislocation transition at the interface of both models with no remnant atomic disorder. Thereby, the model is able to simulate a larger plastic zone than conventional molecular dynamics while reducing the need for constitutive dislocation dynamics equations. This contribution studies dislocation nucleation at finite temperature and investigates the absorption of dislocations into the crack wake. (paper)
Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.
2009-01-01
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 mu...
Color Molecular-Dynamics for High Density Matter
Maruyama, Toshiki; Hatsuda, Tetsuo
1999-01-01
We propose a microscopic simulation for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with the meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Statistical feature and the dynamical change between confinement and deconfinement phases are studied with this molecular dynamics simulation.
Improved scaling of temperature-accelerated dynamics using localization.
Shim, Yunsic; Amar, Jacques G
2016-07-01
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. PMID:27394097
Single particle dynamics and nonlinear resonances in circular accelerators
The purpose of this paper is to introduce the reader to single particle dynamics in circular accelerators with an emphasis on nonlinear resonances. We begin with the Hamiltonian and the equations of motion in the neighborhood of the design orbit. In the linear theory this yields linear betatron oscillations about a closed orbit. It is useful then to introduce the action-angle variables of the linear problem. Next we discuss the nonlinear terms which are present in an actual accelerator, and in particular, we motivate the inclusion of sextupoles to cure chromatic effects. To study the effects of the nonlinear terms, we next discuss canonical perturbation theory which leads us to nonlinear resonances. After showing a few examples of perturbation theory, we abandon it when very close to a resonance. This leads to the study of an isolated resonance in one degree of freedom with a 'time'-dependent Hamiltonian. We see the familiar resonance structure in phase space which is simply closed islands when the nonlinear amplitude dependence of the frequency or 'tune' is included. To show the limits of the validity of the isolated resonance approximation, we discuss two criteria for the onset of chaotic motion. Finally, we study an isolated coupling resonance in two degrees of freedom with a 'time'-dependent Hamiltonian and calculate the two invariants in this case. This leads to a surface of section which is a 2-torus in 4-dimensional phase space. However, we show that it remains a 2-torus when projected into particular 3-dimensional subspaces, and thus can be viewed in perspective
Single particle dynamics and nonlinear resonances in circular accelerators
Ruth, R.D.
1985-11-01
The purpose of this paper is to introduce the reader to single particle dynamics in circular accelerators with an emphasis on nonlinear resonances. We begin with the Hamiltonian and the equations of motion in the neighborhood of the design orbit. In the linear theory this yields linear betatron oscillations about a closed orbit. It is useful then to introduce the action-angle variables of the linear problem. Next we discuss the nonlinear terms which are present in an actual accelerator, and in particular, we motivate the inclusion of sextupoles to cure chromatic effects. To study the effects of the nonlinear terms, we next discuss canonical perturbation theory which leads us to nonlinear resonances. After showing a few examples of perturbation theory, we abandon it when very close to a resonance. This leads to the study of an isolated resonance in one degree of freedom with a 'time'-dependent Hamiltonian. We see the familiar resonance structure in phase space which is simply closed islands when the nonlinear amplitude dependence of the frequency or 'tune' is included. To show the limits of the validity of the isolated resonance approximation, we discuss two criteria for the onset of chaotic motion. Finally, we study an isolated coupling resonance in two degrees of freedom with a 'time'-dependent Hamiltonian and calculate the two invariants in this case. This leads to a surface of section which is a 2-torus in 4-dimensional phase space. However, we show that it remains a 2-torus when projected into particular 3-dimensional subspaces, and thus can be viewed in perspective.
Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS
Astuti, A. D.; Mutiara, A. B.
2009-01-01
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example of molecular dynamics application developed by Groningen University. This application is a non-commercial and able to work in the operating system Linux. The main ability of Gromacs is to perform molecular dynamics simulation and minimization energy. In this...
Development of semiclassical molecular dynamics simulation method.
Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi
2016-04-28
Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383
DMS: A Package for Multiscale Molecular Dynamics
Somogyi, Endre; Ortoleva, Peter J
2013-01-01
Advances in multiscale theory and computation provide a novel paradigm for simulating many-classical particle systems. The Deductive Multiscale Simulator (DMS) is a multiscale molecular dynamics (MD) program built on two of these advances, i.e., multiscale Langevin (ML) and multiscale factorization (MF). Both capture the coevolution of the the coarse-grained (CG) state and the microstate. This provides these methods with great efficiency over conventional MD. Neither involve the introduction of phenomenological governing equations for the CG state with attendant uncertainty in both their form of the governing equations and the data needed to calibrate them. The design and implementation of DMS as an open source computational platform is presented here. DMS is written in Python, uses Gromacs to achieve the microphase, and then advances the microstate via a CG-guided evolution. DMS uses MDAnalysis, a Python library for analyzing MD trajectories, to perform computations required to construct CG-related variables...
Molecular dynamics simulations of shock compressed graphite
We present molecular dynamic simulations of the shock compression of graphite with the LCBOPII potential. The range of shock intensities covers the full range of available experimental data, including near-tera-pascal pressures. The results are in excellent agreement with the available DFT data and point to a graphite-diamond transition for shock pressures above 65 GPa, a value larger than the experimental data (20 to 50 GPa). The transition mechanism leads preferentially to hexagonal diamond through a diffusion-less process but is submitted to irreversible re-graphitization upon release: this result is in good agreement with the lack of highly ordered diamond observed in post-mortem experimental samples. Melting is found for shock pressures ranging from 200 to 300 GPa, close to the approximate LCBOPII diamond melting line. A good overall agreement is found between the calculated and experimental Hugoniot data up to 46% compression rate. (authors)
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
Schwabe, Tobias
2015-08-20
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273
Nano-tribology through molecular dynamics simulations
王慧; 胡元中; 邹鲲; 冷永胜
2001-01-01
The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.
Molecular dynamics simulation of laser shock phenomena
Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).
2001-10-01
Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)
Statistical mechanics and dynamics of molecular fragmentation
Quack, M. (Goettingen Univ. (Germany, F.R.). Inst. fuer Physikalische Chemie)
1981-05-11
The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored.
Statistical mechanics and dynamics of molecular fragmentation
The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored. (author)
Cell list algorithms for nonequilibrium molecular dynamics
Dobson, Matthew; Fox, Ian; Saracino, Alexandra
2016-06-01
We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.
Superdeformed $\\Lambda$ hypernuclei with antisymmetrized molecular dynamics
Isaka, Masahiro; Kimura, Masaaki; Hiyama, Emiko; Sagawa, Hiroyuki; Yamamoto, Yasuo
2014-01-01
The response to the addition of a $\\Lambda$ hyperon is investigated for the deformed states such as superdeformation in $^{41}_\\Lambda$Ca, $^{46}_\\Lambda $Sc and $^{48}_\\Lambda$Sc. In the present study, we use the antisymmetrized molecular dynamics (AMD) model. It is pointed out that many kinds of deformed bands appear in $^{45}$Sc and $^{47}$Sc. Especially, it is found that there exists superdeformed states in $^{45}$Sc. By the addition of a $\\Lambda$ particle to $^{40}$Ca, $^{45}$Sc and $^{47}$Sc, it is predicted, for the first time, that the superdeformed states exist in the hypernuclei $^{41}_\\Lambda$Ca and $^{46}_\\Lambda$Sc. The manifestation of the dependence of the $\\Lambda$-separation energy on nuclear deformation such as spherical, normal deformation and superdeformation is shown in the energy spectra of $^{41}_\\Lambda$Ca, $^{46}_\\Lambda $Sc and $^{48}_\\Lambda$Sc hypernuclei.
Molecular Dynamics Simulations for Predicting Surface Wetting
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
Nonequilibrium molecular dynamics: The first 25 years
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments
Dynamics of dewetting at the nanoscale using molecular dynamics.
Bertrand, E; Blake, T D; Ledauphin, V; Ogonowski, G; Coninck, J De; Fornasiero, D; Ralston, J
2007-03-27
Large-scale molecular dynamics simulations are used to model the dewetting of solid surfaces by partially wetting thin liquid films. Two levels of solid-liquid interaction are considered that give rise to large equilibrium contact angles. The initial length and thickness of the films are varied over a wide range at the nanoscale. Spontaneous dewetting is initiated by removing a band of molecules either from each end of the film or from its center. As observed experimentally and in previous simulations, the films recede at an initially constant speed, creating a growing rim of liquid with a constant receding dynamic contact angle. Consistent with the current understanding of wetting dynamics, film recession is faster on the more poorly wetted surface to an extent that cannot be explained solely by the increase in the surface tension driving force. In addition, the rates of recession of the thinnest films are found to increase with decreasing film thickness. These new results imply not only that the mobility of the liquid molecules adjacent to the solid increases with decreasing solid-liquid interactions, but also that the mobility adjacent to the free surface of the film is higher than in the bulk, so that the effective viscosity of the film decreases with thickness. PMID:17328565
Continuous Finite Element Methods of Molecular Dynamics Simulations
Qiong Tang
2015-01-01
Full Text Available Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite element method is also a reliable method to simulate long-time classical trajectory of molecular systems.
Molecular Dynamic Simulation of Failure of Ettringite
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
Molecular Dynamic Simulation of Failure of Ettringite
Sun, W.; Wang, D.; Wang, L.
2013-03-01
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
The increasing use of biodegradable devices in tissue engineering and regenerative medicine means it is essential to study and understand their degradation behaviour. Accelerated degradation systems aim to achieve similar degradation profiles within a shorter period of time, compared with standard conditions. However, these conditions only partially mimic the actual situation, and subsequent analyses and derived mechanisms must be treated with caution and should always be supported by actual long-term degradation data obtained under physiological conditions. Our studies revealed that polycaprolactone (PCL) and PCL-composite scaffolds degrade very differently under these different degradation conditions, whilst still undergoing hydrolysis. Molecular weight and mass loss results differ due to the different degradation pathways followed (surface degradation pathway for accelerated conditions and bulk degradation pathway for simulated physiological conditions). Crystallinity studies revealed similar patterns of recrystallization dynamics, and mechanical data indicated that the scaffolds retained their functional stability, in both instances, over the course of degradation. Ultimately, polymer degradation was shown to be chiefly governed by molecular weight, crystallinity susceptibility to hydrolysis and device architecture considerations whilst maintaining its thermodynamic equilibrium
Cryogenic molecular separation system for radioactive 11C ion acceleration
A 11C molecular production/separation system (CMPS) has been developed as part of an isotope separation on line system for simultaneous positron emission tomography imaging and heavy-ion cancer therapy using radioactive 11C ion beams. In the ISOL system, 11CH4 molecules will be produced by proton irradiation and separated from residual air impurities and impurities produced during the irradiation. The CMPS includes two cryogenic traps to separate specific molecules selectively from impurities by using vapor pressure differences among the molecular species. To investigate the fundamental performance of the CMPS, we performed separation experiments with non-radioactive 12CH4 gases, which can simulate the chemical characteristics of 11CH4 gases. We investigated the separation of CH4 molecules from impurities, which will be present as residual gases and are expected to be difficult to separate because the vapor pressure of air molecules is close to that of CH4. We determined the collection/separation efficiencies of the CMPS for various amounts of air impurities and found desirable operating conditions for the CMPS to be used as a molecular separation device in our ISOL system
Molecular beam studies of reaction dynamics
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Molecular dynamics studies on nanoscale gas transport
Barisik, Murat
Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the
Junghans, Christoph; Perez, Danny; Vogel, Thomas
2014-01-01
We show direct formal relationship between the Wang-Landau iteration [PRL 86, 2050 (2001)], metadynamics [PNAS 99, 12562 (2002)] and statistical temperature molecular dynamics [PRL 97, 050601 (2006)], the major Monte Carlo and molecular dynamics work-horses for sampling from a generalized, multicanonical ensemble. We demonstrate that statistical temperature molecular dynamics (which is formally derived from the Wang-Landau method), augmented by the introduction of kernel updates of the statis...
Polarizable molecular dynamics in a polarizable continuum solvent.
Lipparini, Filippo; Lagardère, Louis; Raynaud, Christophe; Stamm, Benjamin; Cancès, Eric; Mennucci, Benedetta; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip
2015-02-10
We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-term energy conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique. PMID:26516318
Hybrid particle-field molecular dynamics simulation for polyelectrolyte systems.
Zhu, You-Liang; Lu, Zhong-Yuan; Milano, Giuseppe; Shi, An-Chang; Sun, Zhao-Yan
2016-04-14
To achieve simulations on large spatial and temporal scales with high molecular chemical specificity, a hybrid particle-field method was proposed recently. This method is developed by combining molecular dynamics and self-consistent field theory (MD-SCF). The MD-SCF method has been validated by successfully predicting the experimentally observable properties of several systems. Here we propose an efficient scheme for the inclusion of electrostatic interactions in the MD-SCF framework. In this scheme, charged molecules are interacting with the external fields that are self-consistently determined from the charge densities. This method is validated by comparing the structural properties of polyelectrolytes in solution obtained from the MD-SCF and particle-based simulations. Moreover, taking PMMA-b-PEO and LiCF3SO3 as examples, the enhancement of immiscibility between the ion-dissolving block and the inert block by doping lithium salts into the copolymer is examined by using the MD-SCF method. By employing GPU-acceleration, the high performance of the MD-SCF method with explicit treatment of electrostatics facilitates the simulation study of many problems involving polyelectrolytes. PMID:27001709
Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wave packet calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics
Molecular Dynamics Investigated by Neutron Scattering
A short review of the present state of the problem of applicability of the Krieger-Nelkin theory as well as of the Griffing theory to gases is made. Then, on the basis of experiments with liquid methane, the applicability of the mass-tensor concept to molecules in condensed states is criticized. Strong arguments against the application of the Krieger-Nelkin theory to condensed states are: a shift of neutron energy distribution after scattering towards higher energies and the lack of dependence of the Inelastic part on the scattering angle. Further sections deal with the rotational dynamics of ammonium groups in ammonium compounds. Most of the experimental material is discussed in connection with ammonium halides on the basis of experiments by different authors. For some substances a freedom of rotation of NH4 groups was obtained from neutron measurements, whereas for some others the rotation goes over into torsional vibration. In this case, frequencies of torsional vibrations obtained by various authors from neutron experiments were compared with those obtained from infrared spectroscopy and specific heat measurements. The barrier-to-rotation evaluation from total neutron cross-section measurements is also discussed. Further a comparison is made of the rotational dynamics of NH4 groups in NH4CIO4 and H3O groups in H3OCIO4 on the basis of neutron inelastic scattering experiments. A free rotation of the NH4 group in ammonium perchlorate was obtained even at temperatures as low as liquid nitrogen temperature. For H3OCIO4 a torsional vibration of the H3O group with a frequency of 497 cm-1 was obtained. So in spite of the identity of the crystal lattices of NH4CIO4 and H3OCIO4 the dynamics of the NH4 and H3O groups are different. The results are compared with those known from Raman spectroscopy and nuclear magnetic resonance. Finally, a number of other substances is discussed from the point of view of molecular dynamics. (author)
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom
Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics
Rakesh, L.
2009-09-01
Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the
Nanoscale deicing by molecular dynamics simulation
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-07-01
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice
How Dynamic Visualization Technology Can Support Molecular Reasoning
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
Static and dynamic properties of confined, cold ion plasmas: MD (molecular dynamics) simulations
Schiffer, J.P.
1989-01-01
Some four years ago it was suggested that in the new generation of heavy ion accelerator storage rings for multiply charged ions, being planned in Europe, one may well attain internal temperatures that would correspond to very cold plasmas. Since that time, the techniques of electron or laser cooling of such beams has evolved and it may well be possible to reach temperatures corresponding to a plasma coupling parameter {Gamma} >> 100. I was fortunate to have had an opportunity to collaborate during 1986-87 with my former colleague Aneesur Rahman, of Molecular Dynamics fame, and we adapted the MD method to the calculation of the properties of cold confined plasmas. After Rahman's premature death two years ago I have continued the exploration of these systems and would like to summarize the results here. 9 refs., 10 figs.
Report of the workshop on accelerator-based atomic and molecular science
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
Imaging the Breakdown of Molecular Frame Dynamics through Rotational Uncoupling
Zipp, Lucas J; Bucksbaum, Philip H
2016-01-01
We have observed directly in the time domain the uncoupling of electron motion from the molecular frame due to rotational-electronic coupling in a molecular Rydberg system. In contrast to Born- Oppenheimer dynamics, in which the electron is firmly fixed to the molecular frame, there exists a regime of molecular dynamics known as $l$-uncoupling where the motion of a non-penetrating Rydberg electron decouples from the instantaneous alignment of the molecular frame. We have imaged this unusual regime in time-dependent photoelectron angular distributions of a coherently prepared electron wave packet in the 4$f$ manifold of $N_2$.
Multimillion atom molecular dynamics simulations of glasses and ceramic materials
Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed. (c) 1999 American Institute of Physics
A molecular dynamics simulation code ISIS
Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)
Quantum molecular dynamics simulations of dense matter
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
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
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. 1018 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
Dynamics of a current bridge in a coaxial plasma accelerator
Voronin, A. V.; Gusev, V. K.; Kobyakov, S. V.
2011-07-01
The pioneering investigation of the behavior of a current bridge in a coaxial accelerator with pulsed delivery of a working gas liberated from titanium hydride by an electrical discharge is reported. A new method to trace the motion of the current bridge using LEDs is suggested. The behavior of the current bridge in accelerators with axial and radial gas injection is studied. The parameters of an accelerator generating a pure plasma jet with a high kinetic energy (such as the size and polarity of electrodes, gas flow direction, and time delay between the delivery of the gas to the accelerator and its ionization) are optimized. The applicability of an electrodynamic model to this type of accelerator is discussed. Good agreement between experimental data and calculation results is obtained.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Research highlights: → Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. → Half height widths are used in modeling of Lorentzian doublets. → Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy)
2011-01-07
Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
The invention claims equipment for stabilizing the position of the front covers of the accelerator chamber in cyclic accelerators which significantly increases accelerator reliability. For stabilizing, it uses hydraulic cushions placed between the electromagnet pole pieces and the front chamber covers. The top and the bottom cushions are hydraulically connected. The cushions are disconnected and removed from the hydraulic line using valves. (J.P.)
Scale Invariance at low accelerations (aka MOND) and the dynamical anomalies in the Universe
Milgrom, Mordehai
2016-01-01
Galactic systems, and the Universe at large, exhibit large dynamical anomalies: The observed matter in them falls very short of providing enough gravity to account for their dynamics. The mainstream response to this conundrum is to invoke large quantities of `dark matter' (DM) -- which purportedly supplies the needed extra gravity -- and also of `dark energy' (DE), to account for further anomalies in cosmology, such as the observed, accelerated expansion. The MOND paradigm offers a different solution: a breakdown of standard dynamics (gravity and/or inertia) in the limit of low accelerations -- below some acceleration $a_0$. In this limit, dynamics become space-time scale invariant, and is controlled by a gravitational constant $\\mathcal{A}_0\\equiv Ga_0$, which replaces Newton's $G$. With the new dynamics, the various detailed manifestations of the anomalies in galaxies disappear with no need for DM. The cosmological anomalies could, but need not have to do with small accelerations. For example, the need for ...
Modeling shockwave deformation via molecular dynamics
Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too
Analysis of the Time Reversible Born-Oppenheimer Molecular Dynamics
Lin, Lin; Shao, Sihong
2013-01-01
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 dynamic simulation. We connect and compare TRBOMD with the 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.
Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics
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.
Frail, Dale A
2011-01-01
We review the class of galactic supernova remnants which show strong interactions with molecular clouds, revealed through shock-excited hydroxyl masers. These remnants are preferentially found among the known GeV and TeV detections of supernova remnants. It has been argued that the masers trace out the sites of hadronic particle acceleration. We discuss what is known about the physical conditions of these shocked regions and we introduce a potential new maser tracer for identifying the sites of cosmic ray acceleration. This review includes a reasonably complete bibliography for researchers new to the topic of shock-excited masers and supernova remnants.
Beam and spin dynamics of hadron beams in intermediate-energy ring accelerators
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)
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-01
Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.
Molecular dynamics of immiscible fluids in chemically patterned nanochannels
Cieplak, Marek; Banavar, Jayanth R.
2008-03-01
Molecular dynamics simulations of chain molecules are used to elucidate physical phenomena involved in flows of dense immiscible fluids in nanochannels. We first consider a force driven flow in which the channel walls are homogeneous and wetting to one fluid and nonwetting to the other fluid. The coating of the walls by the wetting fluid provides a fluctuating surface that confines the flow of the nonwetting fluid. The resulting dissipation yields stationary Poiseuille-like flows in contrast to the accelerating nature of flow in the absence of the coating. We then consider walls consisting of patches whose wetting preferences to a fluid alternate along the walls. In the resulting flow, the immiscible components exhibit periodic structures in their velocity fields such that the crests are located at the wettability steps in contrast to the behavior of a single fluid for which the crest occurs in the wetting region. We demonstrate that for a single fluid, the modulated velocity field scales with the size of the chain molecules.
Exploring the free energy surface using ab initio molecular dynamics.
Samanta, Amit; Morales, Miguel A; Schwegler, Eric
2016-04-28
Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525
Visualization and orchestration of the dynamic molecular society in cells
Xuebiao Yao; Guowei Fang
2009-01-01
@@ Visualization of specific molecules and their interactions in real space and time is essential to delineate how cellular plasticity and dynamics are achieved and orchestrated as perturbation of cellular plasticity and dynamics is detrimental to health. Elucidation of cellular dynamics requires molecular imaging at nanometer scale at millisecond resolution. The 1st International Conference on Cellular Dynamics and Chemical Biology held in Hefei, China (from 12 September to 15 September,2008) launched the quest by bringing synergism among photonics, chemistry and biology.
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to
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.
Brown, W. Michael; Kohlmeyer, Axel; Plimpton, Steven J.; Tharrington, Arnold N.
2012-03-01
The use of accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. In this paper, we present a continuation of previous work implementing algorithms for using accelerators into the LAMMPS molecular dynamics software for distributed memory parallel hybrid machines. In our previous work, we focused on acceleration for short-range models with an approach intended to harness the processing power of both the accelerator and (multi-core) CPUs. To augment the existing implementations, we present an efficient implementation of long-range electrostatic force calculation for molecular dynamics. Specifically, we present an implementation of the particle-particle particle-mesh method based on the work by Harvey and De Fabritiis. We present benchmark results on the Keeneland InfiniBand GPU cluster. We provide a performance comparison of the same kernels compiled with both CUDA and OpenCL. We discuss limitations to parallel efficiency and future directions for improving performance on hybrid or heterogeneous computers.
Stochastic dynamics and Fokker-Planck equation in accelerator physics
Mais, H.; Zorzano, M.P.
1999-01-01
The aim of this contribution is to study the particle dynamics in a storage ring under the influence of noise. Some simplified stochastic beam dynamics problems are treated by solving the corresponding Fokker-Planck equations numerically.
Beam dynamics in a long-pulse linear induction accelerator
Ekdahl, Carl [Los Alamos National Laboratory; Abeyta, Epifanio O [Los Alamos National Laboratory; Aragon, Paul [Los Alamos National Laboratory; Archuleta, Rita [Los Alamos National Laboratory; Cook, Gerald [Los Alamos National Laboratory; Dalmas, Dale [Los Alamos National Laboratory; Esquibel, Kevin [Los Alamos National Laboratory; Gallegos, Robert A [Los Alamos National Laboratory; Garnett, Robert [Los Alamos National Laboratory; Harrison, James F [Los Alamos National Laboratory; Johnson, Jeffrey B [Los Alamos National Laboratory; Jacquez, Edward B [Los Alamos National Laboratory; Mc Cuistian, Brian T [Los Alamos National Laboratory; Montoya, Nicholas A [Los Alamos National Laboratory; Nath, Subrato [Los Alamos National Laboratory; Nielsen, Kurt [Los Alamos National Laboratory; Oro, David [Los Alamos National Laboratory; Prichard, Benjamin [Los Alamos National Laboratory; Rose, Chris R [Los Alamos National Laboratory; Sanchez, Manolito [Los Alamos National Laboratory; Schauer, Martin M [Los Alamos National Laboratory; Seitz, Gerald [Los Alamos National Laboratory; Schulze, Martin [Los Alamos National Laboratory; Bender, Howard A [Los Alamos National Laboratory; Broste, William B [Los Alamos National Laboratory; Carlson, Carl A [Los Alamos National Laboratory; Frayer, Daniel K [Los Alamos National Laboratory; Johnson, Douglas E [Los Alamos National Laboratory; Tom, C Y [Los Alamos National Laboratory; Trainham, C [Los Alamos National Laboratory; Williams, John [Los Alamos National Laboratory; Scarpetti, Raymond [LLNL; Genoni, Thomas [VOSS; Hughes, Thomas [VOSS; Toma, Carsten [VOSS
2010-01-01
The second axis of the Dual Axis Radiography of Hydrodynamic Testing (DARHT) facility produces up to four radiographs within an interval of 1.6 microseconds. It accomplishes this by slicing four micro-pulses out of a long 1.8-kA, 16.5-MeV electron beam pulse and focusing them onto a bremsstrahlung converter target. The long beam pulse is created by a dispenser cathode diode and accelerated by the unique DARHT Axis-II linear induction accelerator (LIA). Beam motion in the accelerator would be a problem for radiography. High frequency motion, such as from beam breakup instability, would blur the individual spots. Low frequency motion, such as produced by pulsed power variation, would produce spot to spot differences. In this article, we describe these sources of beam motion, and the measures we have taken to minimize it.
Beam dynamics in a long-pulse linear induction accelerator
The second axis of the Dual Axis Radiography of Hydrodynamic Testing (DARHT) facility produces up to four radiographs within an interval of 1.6 microseconds. It accomplishes this by slicing four micro-pulses out of a long 1.8-kA, 16.5-MeV electron beam pulse and focusing them onto a bremsstrahlung converter target. The long beam pulse is created by a dispenser cathode diode and accelerated by the unique DARHT Axis-II linear induction accelerator (LIA). Beam motion in the accelerator would be a problem for radiography. High frequency motion, such as from beam breakup instability, would blur the individual spots. Low frequency motion, such as produced by pulsed power variation, would produce spot to spot differences. In this article, we describe these sources of beam motion, and the measures we have taken to minimize it.
Resonance, particle dynamics, and particle transmission in the micro-accelerator platform
We describe particle dynamics in the Micro-Accelerator Platform (MAP), a slab-symmetric dielectric laser accelerator (DLA), and model the expected performance of recently fabricated MAP structures. The quality of the structure resonances has been characterized optically, and results are compared with simulation. 3D trajectory analysis is used to model acceleration in those same structures “as built.” Results are applied to ongoing beam transmission and acceleration tests at NLCTA/E-163, in which transmission of 60 MeV injected electrons through the beam channel of the MAP was clearly observed, despite the overfilling of the structure by the beam.
Modelling of Spectroscopic and Structural Properties using Molecular Dynamics
Francesco Muniz Miranda
2013-01-01
The following dissertation is about the study that I performed at the Chemistry Department of the University of Florence and at the European Laboratory for Non- Linear Spectroscopy (LENS) to recover and elucidate structural, dynamical, and spectroscopic molecular features adopting computer simulations. In particular, here ab initio molecular dynamics simulations and time-frequency analysis are the most employed “tools”, in order to have a better understanding of the origins ...
Multi CPU clusters and calculations by molecular dynamics method
The technical characteristics of multi CPU (Central Processor Unit) clusters in Institute of Ion-Plasma and Laser Technologies AS RUz and Institute of Mathematics and Information Technologies AS RUz are described. There is detail information about cluster s architecture, installed programs and their productivity for decision of molecular dynamics tasks. Molecular dynamics program packages GROMACS, OPENMX and AutoDock-4.2.3 are described. The results of calculations using these program packages are presented. (author)
Applications of Molecular Dynamics in Atmospheric and Solution Chemistry
Li, Xin
2011-01-01
This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial ch...
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding
Yaman Arkun; Mert Gur
2012-01-01
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding Yaman Arkun1*, Mert Gur2¤ 1 Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey, 2 Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey Abstract A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamic...
HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.
Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G
2016-04-12
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features. PMID:26949976
Dynamical analysis of highly excited molecular spectra
Kellman, M.E. [Univ. of Oregon, Eugene (United States)
1993-12-01
The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.
Electron beam dynamics in the DARHT-II linear induction accelerator
Ekdahl, Carl A [Los Alamos National Laboratory; Abeyta, Epifanio O [Los Alamos National Laboratory; Aragon, Paul [Los Alamos National Laboratory; Archuleta, Rita [Los Alamos National Laboratory; Cook, Gerald [Los Alamos National Laboratory; Dalmas, Dale [Los Alamos National Laboratory; Esquibel, Kevin [Los Alamos National Laboratory; Gallegos, Robert A [Los Alamos National Laboratory; Garnett, Robert [Los Alamos National Laboratory; Harrison, James F [Los Alamos National Laboratory; Johnson, Jeffrey B [Los Alamos National Laboratory; Jacquez, Edward B [Los Alamos National Laboratory; Mccuistian, Brian T [Los Alamos National Laboratory; Montoya, Nicholas A [Los Alamos National Laboratory; Nath, Subrata [Los Alamos National Laboratory; Nielsen, Kurt [Los Alamos National Laboratory; Oro, David [Los Alamos National Laboratory; Prichard, Benjamin [Los Alamos National Laboratory; Rowton, Lawrence [Los Alamos National Laboratory; Sanchez, Manolito [Los Alamos National Laboratory; Scarpetti, Raymond [Los Alamos National Laboratory; Schauer, Martin M [Los Alamos National Laboratory; Seitz, Gerald [Los Alamos National Laboratory; Schulze, Martin [Los Alamos National Laboratory; Bender, Howard A [Los Alamos National Laboratory; Broste, William B [Los Alamos National Laboratory; Carlson, Carl A [Los Alamos National Laboratory; Frayer, Daniel K [Los Alamos National Laboratory; Johnson, Douglas E [Los Alamos National Laboratory; Tom, C Y [Los Alamos National Laboratory; Trainham, C [NSTEC/STL; Williams, John [Los Alamos National Laboratory; Genoni, Thomas [VOSS; Hughes, Thomas [VOSS; Toma, Carsten [VOSS
2008-01-01
The DARHT-II linear induction accelerator (LIA) accelerates a 2-kA electron beam to more than 17 MeV. The beam pulse has a greater than 1.5-microsecond flattop region over which the electron kinetic energy is constant to within 1%. The beam dynamics are diagnosed with 21 beam-position monitors located throughout the injector, accelerator, and after the accelerator exit, where we also have beam imaging diagnostics. We discuss the tuning of the injector and accelerator, and present data for the resulting beam dynamics. We discuss the tuning procedures and other methods used to minimize beam motion, which is undesirable for its application as a bremsstrahlung source for multi-pulse radiography of exlosively driven hydrodynamic experiments. We also present beam stability measurements, which we relate to previous stability experiments at lower current and energy.
Electron beam dynamics in the DARHT-II linear induction accelerator
The DARHT-II linear induction accelerator (LIA) accelerates a 2-kA electron beam to more than 17 MeV. The beam pulse has a greater than 1.5-microsecond flattop region over which the electron kinetic energy is constant to within 1%. The beam dynamics are diagnosed with 21 beam-position monitors located throughout the injector, accelerator, and after the accelerator exit, where we also have beam imaging diagnostics. We discuss the tuning of the injector and accelerator, and present data for the resulting beam dynamics. We discuss the tuning procedures and other methods used to minimize beam motion, which is undesirable for its application as a bremsstrahlung source for multi-pulse radiography of exlosively driven hydrodynamic experiments. We also present beam stability measurements, which we relate to previous stability experiments at lower current and energy.
Acceleration of Early-Photon Fluorescence Molecular Tomography with Graphics Processing Units
Xin Wang; Bin Zhang; Xu Cao; Fei Liu; Jianwen Luo; Jing Bai
2013-01-01
Fluorescence molecular tomography (FMT) with early-photons can improve the spatial resolution and fidelity of the reconstructed results. However, its computing scale is always large which limits its applications. In this paper, we introduced an acceleration strategy for the early-photon FMT with graphics processing units (GPUs). According to the procedure, the whole solution of FMT was divided into several modules and the time consumption for each module is studied. In this strategy, two most...
Current-driven dynamics in molecular-scale devices
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)
A fermionic molecular dynamics technique to model nuclear matter
Full text: At sub-nuclear densities of about 1014 g/cm3, 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)
Unified rotational dynamics of molecular crystals with orientational phase transition
Michel, K.H.; Raedt, H. De
1976-01-01
A unified theory for the rotational dynamics of molecular crystals with orientational phase transitions is given. As basic secular variables one takes symmetry adapted functions, which describe the molecular orientations, and the angular momenta of the molecules. Using Mori’s projection operator tec
Elucidation of molecular dynamics of invasive species of rice
Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...
Shapiro like steps reveals molecular nanomagnets' spin dynamics
Babak Abdollahipour; Jahanfar Abouie; Navid Ebrahimi
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 junct...
Jet acceleration of the fast molecular outflows in the Seyfert galaxy IC5063
Tadhunter, C; Rose, M; Oonk, J B R; Oosterloo, T
2014-01-01
Massive outflows driven by active galactic nuclei (AGN) are widely recognised to play a key role in the evolution of galaxies, heating the ambient gas, expelling it from the nuclear regions, and thereby affecting the star formation histories of the galaxy bulges. It has been proposed that the powerful jets of relativistic particles launched by some AGN can both accelerate and heat the molecular gas, which often dominates the mass budgets of the outflows. However, clear evidence for this mechanism in the form of detailed associations between the molecular gas kinematics and features in the radio-emitting jets has been lacking. Here we show that the warm molecular hydrogen gas in the western radio lobe of the Seyfert galaxy IC5063 is moving at high velocities - up to 600 km/s - relative to the galaxy disk. This suggests that the molecules have been accelerated by fast shocks driven into the interstellar medium (ISM) by the expanding radio jets. These results demonstrate the general feasibility of accelerating m...
Lee, S. Y.
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.
Tunable Interfacial Thermal Conductance by Molecular Dynamics
Shen, Meng
We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1
Dynamics and transport of laser-accelerated particle beams
The subject of this thesis is the investigation and optimization of beam transport elements in the context of the steadily growing field of laser-driven particle acceleration. The first topic is the examination of the free vacuum expansion of an electron beam at high current density. It could be shown that particle tracking codes which are commonly used for the calculation of space charge effects will generate substantial artifacts in the regime considered here. The artifacts occurring hitherto predominantly involve insufficient prerequisites for the Lorentz transformation, the application of inadequate initial conditions and non negligible retardation artifacts. A part of this thesis is dedicated to the development of a calculation approach which uses a more adequate ansatz calculating space charge effects for laser-accelerated electron beams. It can also be used to validate further approaches for the calculation of space charge effects. The next elements considered are miniature magnetic quadrupole devices for the focusing of charged particle beams. General problems involved with their miniaturization concern distorting higher order field components. If these distorting components cannot be controlled, the field of applications is very limited. In this thesis a new method for the characterization and compensation of the distorting components was developed, which might become a standard method when assembling these permanent magnet multipole devices. The newly developed characterization method has been validated at the Mainz Microtron (MAMI) electron accelerator. Now that we can ensure optimum performance, the first application of permanent magnet quadrupole devices in conjunction with laser-accelerated ion beams is presented. The experiment was carried out at the Z-Petawatt laser system at Sandia National Laboratories. A promising application for laser-accelerated electron beams is the FEL in a university-scale size. The first discussion of all relevant aspects
Dynamics and transport of laser-accelerated particle beams
Becker, Stefan
2010-04-19
The subject of this thesis is the investigation and optimization of beam transport elements in the context of the steadily growing field of laser-driven particle acceleration. The first topic is the examination of the free vacuum expansion of an electron beam at high current density. It could be shown that particle tracking codes which are commonly used for the calculation of space charge effects will generate substantial artifacts in the regime considered here. The artifacts occurring hitherto predominantly involve insufficient prerequisites for the Lorentz transformation, the application of inadequate initial conditions and non negligible retardation artifacts. A part of this thesis is dedicated to the development of a calculation approach which uses a more adequate ansatz calculating space charge effects for laser-accelerated electron beams. It can also be used to validate further approaches for the calculation of space charge effects. The next elements considered are miniature magnetic quadrupole devices for the focusing of charged particle beams. General problems involved with their miniaturization concern distorting higher order field components. If these distorting components cannot be controlled, the field of applications is very limited. In this thesis a new method for the characterization and compensation of the distorting components was developed, which might become a standard method when assembling these permanent magnet multipole devices. The newly developed characterization method has been validated at the Mainz Microtron (MAMI) electron accelerator. Now that we can ensure optimum performance, the first application of permanent magnet quadrupole devices in conjunction with laser-accelerated ion beams is presented. The experiment was carried out at the Z-Petawatt laser system at Sandia National Laboratories. A promising application for laser-accelerated electron beams is the FEL in a university-scale size. The first discussion of all relevant aspects
Molecular Dynamics Simulations of Protein Dynamics and their relevance to drug discovery
Salsbury, Freddie R.
2010-01-01
Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy systems. In this article, the methods and principles of all-atom molecular dynamics will be elucidated with several examples provided of their utility to investigators interested on drug discovery.
Energy conservation in molecular dynamics simulations of classical systems
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...
The Computer Simulation of Liquids by Molecular Dynamics.
Smith, W.
1987-01-01
Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)
Beam dynamics at the main LEBT of RAON accelerator
Jin, Hyunchang
2015-01-01
The high-intensity rare-isotope accelerator (RAON) of the Rare Isotope Science Project (RISP) in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams. The ion beams, which are generated by Electron Cyclotron Resonance Ion Source (ECR-IS), will be transported through the main Low Energy Beam Transport (LEBT) system to the Radio Frequency Quadrupole (RFQ). While passing the beams through LEBT, we should keep the transverse beam size and longitudinal emittance small. Furthermore, the matching of required twiss parameter at the RFQ entrance will be performed by using electro-static quadrupoles at the main LEBT matching section which is from the multi-harmonic buncher (MHB) to the entrance of RFQ. We will briefly review the new aspects of main LEBT lattice and the beam matching at the main LEBT matching section will be presented. In addition, the effects of various errors on the beam orbit and the correction of distorted orbit will be discussed.
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
Lau, E Y; Krishnan, V V
2007-07-18
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
Self-accelerating Universe in modified gravity with dynamical torsion
Nikiforova, V; Rubakov, V
2016-01-01
We consider a model belonging to the class of Poincare gauge gravities. The model is free of ghosts and gradient instabilities about Minkowski and torsionless Einstein backgrounds. We find that at zero cosmological constant, the model admits a self-accelerating solution with non-Riemannian connection. Small value of the effective cosmological constant is obtained at the expense of the hierarchy between the dimensionless couplings.
Makarov, G N
2001-01-01
The method is described for shaping the intensive secondary pulsed molecular beam, wherein the molecules kinetic energy may be controlled through the powerful IR laser radiation by means of the molecules oscillatory excitation in the source itself. The thickening jump (the shock wave), which is formed by interaction of the intensive pulsed supersonic molecular beam (or flux) with a solid surface, is used as the secondary beam source. The intensive (>= 10 sup 2 sup 0 molecules/stere. s) beams of the SF sub 6 and CF sub 3 I molecules with the kinetic energy correspondingly equal to approximately 1.5 eV and 1.2 eV without gas-carrier and molecular SF sub 6 beams with kinetic energy approx = 2.5 eV are obtained. The spectral and energy characteristics of the SF sub 6 molecules acceleration in the secondary beam are studied. The possibility of obtaining the accelerated radicals in the secondary molecular beam is indicated
Order parameter prediction from molecular dynamics simulations in proteins
Perilla, Juan R
2011-01-01
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy barriers and within a complex energy landscape. This makes it very difficult to reliably connect, for example by all-atom molecular dynamics calculations, the states, their energies and the pathways between them. A major issue needed to improve sampling on the intermediate states is an order parameter -- a reduced descriptor for the major subset of degrees of freedom -- that can be used to aid sampling for the large conformational change. We present a novel way to combine information from molecular dynamics using non-linear time series and dimensionality reduction, in order to quantitatively determine an order parameter connecting two large-scale conformationally distinct protein states. This new method suggests an implementation for molecular dynamics calculations that ma...
Molecular Dynamics Simulation of Amyloid Beta Dimer Formation
Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V
2004-01-01
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...
Interfacial Molecular Searching Using Forager Dynamics
Monserud, Jon H.; Schwartz, Daniel K.
2016-03-01
Many biological and technological systems employ efficient non-Brownian intermittent search strategies where localized searches alternate with long flights. Coincidentally, molecular species exhibit intermittent behavior at the solid-liquid interface, where periods of slow motion are punctuated by fast flights through the liquid phase. Single-molecule tracking was used here to observe the interfacial search process of DNA for complementary DNA. Measured search times were qualitatively consistent with an intermittent-flight model, and ˜10 times faster than equivalent Brownian searches, suggesting that molecular searches for reactive sites benefit from similar efficiencies as biological organisms.
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...
Dynamics Studies on Molecular Diffusion in Zeolites
王秋霞; 樊建芬; 肖鹤鸣
2003-01-01
A review about the applications of molecular dynamics（MD）simulation in zeolites is presented. MD simulation has been proved to be a useful tool due to its applications in this field for the recent two decades. The fundamental theory of MD is introduced and the hydrocarbon diffusion in zeolites is mainly focused on in this paper.
De Martino, Salvatore; De Siena, Silvio; Illuminati, Fabrizio
1998-01-01
A recent proposal (see quant-ph/9803068) to simulate semiclassical corrections to classical dynamics by suitable classical stochastic fluctuations is applied to the specific instance of charged beam dynamics in particle accelerators. The resulting picture is that the collective beam dynamics, at the leading semiclassical order in Planck constant can be described by a particular diffusion process, the Nelson process, which is time-reversal invariant. Its diffusion coefficient $\\sqrt{N}\\lambda_...
Implicit Time Integration for Multiscale Molecular Dynamics Using Transcendental Padé Approximants.
Abi Mansour, Andrew; Ortoleva, Peter J
2016-04-12
Molecular dynamics systems evolve through the interplay of collective and localized disturbances. As a practical consequence, there is a restriction on the time step imposed by the broad spectrum of time scales involved. To resolve this restriction, multiscale factorization was introduced for molecular dynamics as a method that exploits the separation of time scales by coevolving the coarse-grained and atom-resolved states via Trotter factorization. Developing a stable time-marching scheme for this coevolution, however, is challenging because the coarse-grained dynamical equations depend on the microstate; therefore, these equations cannot be expressed in closed form. The objective of this paper is to develop an implicit time integration scheme for multiscale simulation of large systems over long periods of time and with high accuracy. The scheme uses Padé approximants to account for both the stochastic and deterministic features of the coarse-grained dynamics. The method is demonstrated for a protein either undergoing a conformational change or migrating under the influence of an external force. The method shows promise in accelerating multiscale molecular dynamics without a loss of atomic precision or the need to conjecture the form of coarse-grained governing equations. PMID:26845510
Particle acceleration by turbulent magnetohydro-dynamic reconnection
Matthaeus, W. H.; Ambrosiano, J. J.; Goldstein, M. L.
1984-01-01
Test particles in a two dimensional, turbulent MHD simulation are found to undergo significant acceleration. The magnetic field configuration is a periodic sheet pinch which undergoes reconnection. The test particles are trapped in the reconnection region for times of order an Alfven transit time in the large electric fields that characterize the turbulent reconnection process at the relatively large magnetic Reynolds number used in the simulation. The maximum speed attained by these particles is consistent with an analytic estimate which depends on the reconnection electric field, the Alfven speed, and the ratio of Larmor period to the Alfven transit time.
Single Particle Dynamics in a Quasi-Integrable Nonlinear Accelerator Lattice
Antipov, Sergey A; Valishev, Alexander
2016-01-01
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 el...
Käshammer, Peter; Borgardt, Nikolai I.; Seibt, Michael; Sinno, Talid
2016-09-01
Molecular dynamics based on the empirical Tersoff potential was used to simulate the deposition of amorphous silicon and germanium on silicon(111) at various deposition rates and temperatures. The resulting films were analyzed quantitatively by comparing one-dimensional atomic density profiles to experimental measurements. It is found that the simulations are able to capture well the structural features of the deposited films, which exhibit a gradual loss of crystalline order over several monolayers. A simple mechanistic model is used to demonstrate that the simulation temperature may be used to effectively accelerate the surface relaxation processes during deposition, leading to films that are consistent with experimental samples grown at deposition rates many orders-of-magnitude slower than possible in a molecular dynamics simulation.
Dynamic strength of molecular adhesion bonds.
Evans, E; Ritchie, K
1997-01-01
In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction k...
Dynamic response of an accelerator driven system to accelerator beam interruptions for criticality
Subcritical nuclear reactors driven by intense neutron sources can be very suitable tools for nuclear waste transmutation, particularly in the case of minor actinides with very low fractions of delayed neutrons. A proper control of these systems needs to know at every time the absolute value of the reactor subcriticality (negative reactivity), which must be measured by fully reliable methods, usually conveying a short interruption of the accelerator beam in order to assess the neutron flux reduction. Those interruptions should be very short in time, for not disturbing too much the thermal magnitudes of the reactor. Otherwise, the cladding and the fuel would suffer from thermal fatigue produced by those perturbations, and the mechanical integrity of the reactor would be jeopardized. It is shown in this paper that beam interruptions of the order of 400 μs repeated every second would not disturb significantly the reactor thermal features, while enabling for an adequate measurement of the negative reactivity
Beam dynamics simulations of post low energy beam transport section in RAON heavy ion accelerator
Jin, Hyunchang, E-mail: hcjin@ibs.re.kr; Jang, Ji-Ho; Jang, Hyojae; Hong, In-Seok [Institute for Basic Science, Yuseong-daero 1689-gil, Yuseong-gu, Daejeon (Korea, Republic of)
2016-02-15
RAON (Rare isotope Accelerator Of Newness) heavy ion accelerator of the rare isotope science project in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams to be used for various science programs. In the RAON accelerator, the rare isotope beams which are generated by an isotope separation on-line system with a wide range of nuclei and charges will be transported through the post Low Energy Beam Transport (LEBT) section to the Radio Frequency Quadrupole (RFQ). In order to transport many kinds of rare isotope beams stably to the RFQ, the post LEBT should be devised to satisfy the requirement of the RFQ at the end of post LEBT, simultaneously with the twiss parameters small. We will present the recent lattice design of the post LEBT in the RAON accelerator and the results of the beam dynamics simulations from it. In addition, the error analysis and correction in the post LEBT will be also described.
Electron cloud dynamics in the Cornell Electron Storage Ring Test Accelerator wiggler
Celata, C. M.
2011-01-01
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 th...
Acceleration-Extended Galilean Symmetries with Central Charges and their Dynamical Realizations
Lukierski, J.; Stichel, P. C.; Zakrzewski, W. J.
2007-01-01
We add to Galilean symmetries the transformations describing constant accelerations. The corresponding extended Galilean algebra allows, in any dimension $D=d+1$, the introduction of one central charge $c$ while in $D=2+1$ we can have three such charges: c, \\theta and \\theta'. We present nonrelativistic classical mechanics models, with higher order time derivatives and show that they give dynamical realizations of our algebras. The presence of central charge $c$ requires the acceleration squa...
Tunneling Dynamics Between Atomic and Molecular Bose-Einstein Condensates
CHEN Chang-Yong
2004-01-01
Tunneling dynamics of multi-atomic molecules between atomic and multi-atomic molecular Bose-Einstein condensates with Feshbach resonance is investigated.It is indicated that the tunneling in the two Bose-Einstein condensates depends on not only the inter-atomic-molecular nonlinear interactions and the initial number of atoms in these condensates,but also the tunneling coupling between the atomic condensate and the multi-atomic molecular condensate.It is discovered that besides oscillating tunneling current between the atomic condensate and the multi-atomic molecular condensate,the nonlinear multi-atomic molecular tunneling dynamics sustains a self-locked population imbalance:a macroscopic quantum self-trapping effect.The influence of de-coherence caused by non-condensate atoms on the tunneling dynamics is studied.It is shown that de-coherence suppresses the multi-atomic molecular tunneling.Moreover,the conception of the molecular Bose-Einstein condensate,which is different from the conventional single-atomic Bose-Einstein condensate,is specially emphasized in this paper.
LOW MOLECULAR WEIGHT HEPARIN ENHANCES THE EFFECT OF aFGF IN ACCELERATING NEOVASCULA- RIZATION
陈书艳; 荣烨之; 吕宝经; 赵美华; 张建军
2003-01-01
Objective To explore the potential of low molecular weight heparin (LMWH) in combination cooperated with aFGF in accelerating neovascularization in vivo. Methods Ischemic model was set up in the right hindlimbs of 28 New Zealand white rabbits. Four groups of animals treated with saline, LMWH, aFGF and aFGF plus LMWH were allocated equally in group Ⅰ, group Ⅱ, group Ⅲ and group Ⅳ respectively. Vascular neovascularization and smooth muscular thickness of the ischemic hindlimb vessels of each animal in different groups were compared with each other on the 28th day postoperatively by angiography with DSA and the standard immunoperoxidase technique. Results No significant neovascularization was seen when aFGF adiministered in low dosage by venous infusion. But when the same dosage of aFGF plus LMWH were administered by venous infusion, a significant neovascularization was observed. Conclusion LMWH can potentiate aFGF in accelerating neovascularization.
Passage from quantum to classical molecular dynamics in the presence of Coulomb interactions
Ambrosio, Luigi; Friesecke, Gero; Giannoulis, Jannis
2009-01-01
We present a rigorous derivation of classical molecular dynamics (MD) from quantum molecular dynamics (QMD) that applies to the standard Hamiltonians of molecular physics with Coulomb interactions. The derivation is valid away from possible electronic eigenvalue crossings.
DTL cavity design and beam dynamics for a TAC linear proton accelerator
Caliskan, A.; Yılmaz, M.
2012-02-01
A 30 mA drift tube linac (DTL) accelerator has been designed using SUPERFISH code in the energy range of 3-55 MeV in the framework of the Turkish Accelerator Center (TAC) project. Optimization criteria in cavity design are effective shunt impedance (ZTT), transit-time factor and electrical breakdown limit. In geometrical optimization we have aimed to increase the energy gain in each RF gap of the DTL cells by maximizing the effective shunt impedance (ZTT) and the transit-time factor. Beam dynamics studies of the DTL accelerator have been performed using beam dynamics simulation codes of PATH and PARMILA. The results of both codes have been compared. In the beam dynamical studies, the rms values of beam emittance have been taken into account and a low emittance growth in both x and y directions has been attempted.
DTL cavity design and beam dynamics for a TAC linear proton accelerator
A 30 mA drift tube linac (DTL) accelerator has been designed using SUPERFISH code in the energy range of 3-55 MeV in the framework of the Turkish Accelerator Center (TAC) project. Optimization criteria in cavity design are effective shunt impedance (ZTT), transit-time factor and electrical breakdown limit. In geometrical optimization we have aimed to increase the energy gain in each RF gap of the DTL cells by maximizing the effective shunt impedance (ZTT) and the transit-time factor. Beam dynamics studies of the DTL accelerator have been performed using beam dynamics simulation codes of PATH and PARMILA. The results of both codes have been compared. In the beam dynamical studies, the rms values of beam emittance have been taken into account and a low emittance growth in both x and y directions has been attempted. (authors)
Wavelet approach to accelerator problems. 1: Polynomial dynamics
This is the first part of a series of talks in which the authors present applications of methods from wavelet analysis to polynomial approximations for a number of accelerator physics problems. In the general case they have the solution as a multiresolution expansion in the base of compactly supported wavelet basis. The solution is parameterized by solutions of two reduced algebraical problems, one is nonlinear and the second is some linear problem, which is obtained from one of the next wavelet constructions: Fast Wavelet Transform, Stationary Subdivision Schemes, the method of Connection Coefficients. In this paper the authors consider the problem of calculation of orbital motion in storage rings. The key point in the solution of this problem is the use of the methods of wavelet analysis, relatively novel set of mathematical methods, which gives one a possibility to work with well-localized bases in functional spaces and with the general type of operators (including pseudodifferential) in such bases
Phase Space Dynamics of Ionization Injection in Plasma Based Accelerators
Xu, X L; Li, F; Zhang, C J; Yan, L X; Du, Y C; Huang, W H; Chen, H B; Tang, C X; Lu, W; Yu, P; An, W; Mori, W B; Joshi, C
2013-01-01
The evolution of beam phase space in ionization-induced injection into plasma wakefields is studied using theory and particle-in-cell (PIC) simulations. The injection process causes special longitudinal and transverse phase mixing leading initially to a rapid emittance growth followed by oscillation, decay, and eventual slow growth to saturation. An analytic theory for this evolution is presented that includes the effects of injection distance (time), acceleration distance, wakefield structure, and nonlinear space charge forces. Formulas for the emittance in the low and high space charge regimes are presented. The theory is verified through PIC simulations and a good agreement is obtained. This work shows how ultra-low emittance beams can be produced using ionization-induced injection.
Soft matter dynamics: Accelerated fluid squeeze-out during slip
Hutt, W.; Persson, B. N. J.
2016-03-01
Using a Leonardo da Vinci experimental setup (constant driving force), we study the dependency of lubricated rubber friction on the time of stationary contact and on the sliding distance. We slide rectangular rubber blocks on smooth polymer surfaces lubricated by glycerol or by a grease. We observe a remarkable effect: during stationary contact the lubricant is only very slowly removed from the rubber-polymer interface, while during slip it is very rapidly removed resulting (for the grease lubricated surface) in complete stop of motion after a short time period, corresponding to a slip distance typically of order only a few times the length of the rubber block in the sliding direction. For an elastically stiff material, poly(methyl methacrylate), we observe the opposite effect: the sliding speed increases with time (acceleration), and the lubricant film thickness appears to increase. We propose an explanation for the observed effect based on transient elastohydrodynamics, which may be relevant also for other soft contacts.
Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics
Ehrlicher, Allen
2012-02-01
Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.
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.
Jang, Seogjoo
2013-01-01
An exact real time quantum dynamics preaveraged over imaginary time path integral is formulated for general condensed phase equilibrium ensemble. This formulation results in the well-known centroid dynamics approach upon filtering of centroid constraint, and provides a rigorous framework to understand and analyze a related quantum dynamics approximation method called ring polymer molecular dynamics. The formulation also serves as the basis for developing new kinds of quantum dynamics that uti...
Nonlocalized cluster dynamics and nuclear molecular structure
Zhou, Bo; Funaki, Yasuro; Horiuchi, Hisashi; Ren, Zhongzhou; Röpke, Gerd; Schuck, Peter; Tohsaki, Akihiro; Xu, Chang; Yamada, Taiichi
2013-01-01
A container picture is proposed for understanding cluster dynamics where the clusters make nonlocalized motion occupying the lowest orbit of the cluster mean-field potential characterized by the size parameter $``B"$ in the THSR (Tohsaki-Horiuchi-Schuck-R\\"{o}pke) wave function. The nonlocalized cluster aspects of the inversion-doublet bands in $^{20}$Ne which have been considered as a typical manifestation of localized clustering are discussed. So far unexplained puzzling features of the THS...
EXCITON DYNAMICS IN ORGANIC MOLECULAR CRYSTALS
A. Matsui; Mizuno, K.; Kobayashi, M.
1985-01-01
Dynamical behavior of Frenkel excitons in aromatic hydrocarbon crystals, pyrene, α-perylene, β-perylene, and tetracene are overviewed based on the published references and in terms of the self-trap depth. Then pressure-induced instability in exciton states (the change in the self-trap depth) in α-perylene and anthracene is demonstrated and discussed. Finally a quasi-free exciton state is suggested to be the origin of the luminescence in anthracene at room temperature.
On the stochastic dynamics of molecular conformation
无
2007-01-01
An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamiltonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.
Theoretical analysis of dynamic processes for interacting molecular motors
Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. (paper)
Molecular dynamics insights into human aquaporin 2 water channel.
Binesh, A R; Kamali, R
2015-12-01
In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney. PMID:26489820
Molecular phenomena in dynamic wetting: superspreading and precursors
Isele-Holder, Rolf Erwin
2015-01-01
Wetting is a multiscale process that can be controlled simultaneously by complex flow patterns on the macroscale and contact line phenomena at the Ångstrom scale. While resolving the latter scale is often circumvented by usage of boundary conditions, there are molecular wetting phenomena in which this approach is infeasible. The focus of this study is to use molecular dynamics simulations to examine two of these phenomena: superspreading, the ultra-rapid wetting of aqueous solutions facilitat...
Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Lipparini, Filippo; Lagardère, Louis; Raynaud, Christophe; Stamm, Benjamin; Cancès, Eric; Mennucci, Benedetta; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip
2015-01-01
We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a rob...
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps
Paolo Ruggerone; Vargiu, Attilio V.; Francesca Collu; Nadine Fischer; Christian Kandt
2013-01-01
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 conformation...
Acceleration-extended Galilean symmetries with central charges and their dynamical realizations
Lukierski, J. [Institute for Theoretical Physics, University of Wroclaw, pl. Maxa Borna 9, 50-205 Wroclaw (Poland)]. E-mail: lukier@ift.uni.wroc.pl; Stichel, P.C. [An der Krebskuhle 21, D-33619 Bielefeld (Germany)]. E-mail: peter@physik.uni-bielefeld.de; Zakrzewski, W.J. [Department of Mathematical Sciences, University of Durham, Durham DH1 3LE (United Kingdom)]. E-mail: W.J.Zakrzewski@durham.ac.uk
2007-06-28
We add to Galilean symmetries the transformations describing constant accelerations. The corresponding extended Galilean algebra allows, in any dimension D=d+1, the introduction of one central charge c while in D=2+1 we can have three such charges: c,{theta} and {theta}{sup '}. We present nonrelativistic classical mechanics models, with higher order time derivatives and show that they give dynamical realizations of our algebras. The presence of central charge c requires the acceleration square Lagrangian term. We show that the general Lagrangian with three central charges can be reinterpreted as describing an exotic planar particle coupled to a dynamical electric and a constant magnetic field.
Acceleration-Extended Galilean Symmetries with Central Charges and their Dynamical Realizations
Lukierski, J; Zakrzewski, W J
2007-01-01
We add to Galilean symmetries the transformations describing constant accelerations. The corresponding extended Galilean algebra allows, in any dimension $D=d+1$, the introduction of one central charge $c$ while in $D=2+1$ we can have three such charges: c, \\theta and \\theta'. We present nonrelativistic classical mechanics models, with higher order time derivatives and show that they give dynamical realizations of our algebras. The presence of central charge $c$ requires the acceleration square Lagrangian term. We show that the general Lagrangian with three central charges can be reinterpreted as describing an exotic planar particle coupled to a dynamical electric and a constant magnetic field.
Acceleration-extended Galilean symmetries with central charges and their dynamical realizations
We add to Galilean symmetries the transformations describing constant accelerations. The corresponding extended Galilean algebra allows, in any dimension D=d+1, the introduction of one central charge c while in D=2+1 we can have three such charges: c,θ and θ'. We present nonrelativistic classical mechanics models, with higher order time derivatives and show that they give dynamical realizations of our algebras. The presence of central charge c requires the acceleration square Lagrangian term. We show that the general Lagrangian with three central charges can be reinterpreted as describing an exotic planar particle coupled to a dynamical electric and a constant magnetic field
GPU accelerated Trotter-Suzuki solver for quantum spin dynamics
Dente, Axel D; Zangara, Pablo R; Pastawski, Horacio M
2013-01-01
The resolution of dynamics in out of equilibrium quantum spin systems relies at the heart of fundamental questions among Quantum Information Processing, Statistical Mechanics and Nano-Technologies. Efficient computational simulations of interacting many-spin systems are extremely valuable tools for tackling such questions. Here, we use the Trotter-Suzuki (TS) algorithm, a well-known strategy that provides the evolution of quantum systems, to address the spin dynamics. We present a GPU implementation of a particular TS version, which has been previously implemented on single cores in CPUs. We develop a massive parallel version of this algorithm and compare the efficiency between CPU and GPU implementations. This boosted method reduces the execution time in several hundred times and is capable to deal with systems of up to 27 spins (only limited by the GPU memory).
Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations.
Semrouni, David; Sharma, Ashwani; Dognon, Jean-Pierre; Ohanessian, Gilles; Clavaguéra, Carine
2014-08-12
Infrared spectra of biomolecules are obtained from molecular dynamics simulations at finite temperature using the AMOEBA force field. Diverse examples are presented such as N-methylacetamide and its derivatives and a helical peptide. The computed spectra from polarizable molecular dynamics are compared in each case to experimental ones at various temperatures. The role of high-level electrostatic treatment and explicit polarization, including parameters improvements, is highlighted for obtaining spectral sensitivity to the environment including hydrogen bonds and water molecules and a better understanding of the observed experimental bands. PMID:26588289
The application of molecular dynamics in the uracil
Under the (N, V, T) system, the position, speed, strength and direction of under stress and the changes of bond distance and bond angle of the evolution of each atom in uracil molecule are calculated by using the semiempirical molecular dynamics. The calculations come to the conclusions which are difficult or failed to be obtained on the microcosmic information of particles during the experiment be- cause of the limit of today's technology. It is to provide the theoretical basis that will go a step further to know molecular inner dynamics. (authors)
State-to-state dynamics of molecular energy transfer
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.
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
Electron-phonon interaction within classical molecular dynamics
Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.
2016-07-01
We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e -ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.
Shapiro like steps reveals molecular nanomagnets' spin dynamics
Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid
2015-09-01
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet's spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.
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.
Ion and neutral dynamics in Hall plasma accelerator ionization instabilities
Lucca Fabris, Andrea; Young, Christopher; Cappelli, Mark
2015-09-01
Hall thrusters, the extensively studied E × B devices used for space propulsion applications, are rife with instabilities and fluctuations. Many are thought to be fundamentally linked to microscopic processes like electron transport across magnetic field lines and propellant ionization that in turn affect macroscopic properties like device performance and lifetime. One of the strongest oscillatory regimes is the ``breathing mode,'' characterized by a propagating ionization front, time-varying ion acceleration profiles, and quasi-periodic 10-50 kHz current oscillations. Determining the temporal and spatial evolution of plasma properties is critical to achieving a fundamental physical understanding of these processes. We present non-intrusive laser-induced fluorescence measurements of the local ion and neutral velocity distribution functions synchronized with the breathing mode oscillations. Measurements reveal strong ion velocity fluctuations, multiple ion populations arising in narrow time windows throughout the near-field plume, and the periodic population and depopulation of neutral excited states. Analyzing these detailed experimental results in the context of the existing literature clarifies the fundamental physical processes underlying the breathing mode. This work is sponsored by the U.S. Air Force Office of Scientific Research with Dr. M. Birkan as program manager. C.Y. acknowledges support from the DOE NSSA Stewardship Science Graduate Fellowship under contract DE-FC52-08NA28752.
Embarrassingly Parallel Acceleration of Global Tractography via Dynamic Domain Partitioning
Wu, Haiyong; Chen, Geng; Jin, Yan; Shen, Dinggang; Yap, Pew-Thian
2016-01-01
Global tractography estimates brain connectivity by organizing signal-generating fiber segments in an optimal configuration that best describes the measured diffusion-weighted data, promising better stability than local greedy methods with respect to imaging noise. However, global tractography is computationally very demanding and requires computation times that are often prohibitive for clinical applications. We present here a reformulation of the global tractography algorithm for fast parallel implementation amendable to acceleration using multi-core CPUs and general-purpose GPUs. Our method is motivated by the key observation that each fiber segment is affected by a limited spatial neighborhood. In other words, a fiber segment is influenced only by the fiber segments that are (or can potentially be) connected to its two ends and also by the diffusion-weighted signal in its proximity. This observation makes it possible to parallelize the Markov chain Monte Carlo (MCMC) algorithm used in the global tractography algorithm so that concurrent updating of independent fiber segments can be carried out. Experiments show that the proposed algorithm can significantly speed up global tractography, while at the same time maintain or even improve tractography performance. PMID:27468263
Imaging the molecular dynamics of dissociative electron attachment to water
Adaniya, Hidihito; Rudek, B.; Osipov, Timur; Haxton, Dan; Weber, Thorsten; Rescigno, Thomas N.; McCurdy, C.W.; Belkacem, Ali
2009-10-19
Momentum imaging experiments on dissociative electron attachment to the water molecule are combined with ab initio theoretical calculations of the angular dependence of the quantum mechanical amplitude for electron attachment to provide a detailed picture of the molecular dynamics of dissociation attachment via the two lowest energy Feshbach resonances. The combination of momentum imaging experiments and theory can reveal dissociation dynamics for which the axial recoil approximation breaks down and thus provides a powerful reaction microscope for DEA to polyatomics.
Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties
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: 0.530, year: 2014 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf
Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field
Pabis, Anna; Geronimo, Inacrist; York, Darrin M.; Paneth, Piotr
2014-01-01
Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specif...
Molecular Dynamics Study of Iron-Nickel Alloys
Meyer, R.; Entel, P.
1995-01-01
We present results of molecular dynamics simulations of disordered iron-nickel alloys. In particular we discuss the α-γ transition and associated anharmonic properties by making use of semiempirical potentials. Our results show that the structural transformation in these alloys is driven by local disorder. From data of specific heat and thermal expansion we conclude that the lattice dynamics at elevated temperatures (above the Curie temperature) can be described correctly without considering ...
ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics
Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
2013-01-01
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates `GROMACS wrapper' to initiate MD simula...
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Allen, Joshua W.; Green, William H; Suleimanov, Yu. V.
2013-01-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett–Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any ...
Micellar Crystals in Solution from Molecular Dynamics Simulations
Anderson, J A; Lorenz, C. D.; Travesset, A.
2008-01-01
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our result...
Dynamics of excess electrons in atomic and molecular clusters
Young, Ryan Michael
2011-01-01
Femtosecond time-resolved photoelectron imaging (TRPEI) is applied to the study of excess electrons in clusters as well as to microsolvated anion species. This technique can be used to perform explicit time-resolved as well as one-color (single- or multiphoton) studies on gas phase species. The first part of this dissertation details time-resolved studies done on atomic clusters with an excess electron, the excited-state dynamics of solvated molecular anions, and charge-transfer dynamics to...
Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation
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
Deposition of Small Clusters on Surface: a Molecular Dynamics Simulation
DUAN Xiang-Mei; GONG Xin-Gao
2000-01-01
By using the molecular dynamics simulation, we have studied the dynamic behaviors of small energetic clusters deposited on the surface. We find that, at incident energy as low as 1.0eV/atom, the structure of the cluster is destroyed and cluster atoms form an epitaxial layer above the surface. At high energy incidence, the site exchange between cluster atom and surface atom is observed. The effects of the cluster size and orientation are discussed.
The target of the present paper is the study of chirality effects in molecular dynamics from both a theoretical and an experimental point of view under the hypothesis of a molecular dynamics mechanism as the origin of chiral discrimination. This is a fundamental problem per se, and of possible relevance for the problem of the intriguing homochirality in Nature, so far lacking satisfactory explanations. We outline the steps that have been taken so far toward this direction, motivated by various experimental studies of supersonic molecular beams carried out in this laboratory, such as the detection of aligned oxygen in gaseous streams and further evidence on nitrogen, benzene and various hydrocarbons, showing the insurgence of molecular orientation in the dynamics of molecules in flows and in molecular collisions. Chiral effects are theoretically demonstrated to show up in the differential scattering of oriented molecules, also when impinging on surfaces. Focus on possible mechanisms for chiral bio-stereochemistry of oriented reactants may be of pre-biotical interest, for example when flowing in atmospheres of rotating bodies, specifically the planet Earth, as well as in vortex motions of celestial objects. Molecular dynamics simulations and experimental verifications of the hypothesis are reviewed and objectives of future research activity proposed.
Aquilanti, Vincenzo; Grossi, Gaia; Lombardi, Andrea; Maciel, Glauciete S; Palazzetti, Federico [Dipartimento di Chimica, Universita di Perugia, Via Elce di Sotto 8, 06123 Perugia (Italy)], E-mail: abulafia@dyn.unipg.it
2008-10-15
The target of the present paper is the study of chirality effects in molecular dynamics from both a theoretical and an experimental point of view under the hypothesis of a molecular dynamics mechanism as the origin of chiral discrimination. This is a fundamental problem per se, and of possible relevance for the problem of the intriguing homochirality in Nature, so far lacking satisfactory explanations. We outline the steps that have been taken so far toward this direction, motivated by various experimental studies of supersonic molecular beams carried out in this laboratory, such as the detection of aligned oxygen in gaseous streams and further evidence on nitrogen, benzene and various hydrocarbons, showing the insurgence of molecular orientation in the dynamics of molecules in flows and in molecular collisions. Chiral effects are theoretically demonstrated to show up in the differential scattering of oriented molecules, also when impinging on surfaces. Focus on possible mechanisms for chiral bio-stereochemistry of oriented reactants may be of pre-biotical interest, for example when flowing in atmospheres of rotating bodies, specifically the planet Earth, as well as in vortex motions of celestial objects. Molecular dynamics simulations and experimental verifications of the hypothesis are reviewed and objectives of future research activity proposed.
Simplistic Coulomb Forces in Molecular Dynamics
Hansen, Jesper Schmidt; Schrøder, Thomas; Dyre, J. C.
2012-01-01
salt model the SF approximation overall reproduces the structural and dynamical properties as accurately as does the Wolf method. It is shown that the optimal Wolf damping parameter depends on the property in focus and that neither the potential energy nor the radial distribution function are useful...... measures for the convergence of the Wolf method to the Ewald summation method. The SF approximation is also tested for the SPC/Fw model of liquid water at room temperature, showing good agreement with both the Wolf and the particle mesh Ewald methods; this confirms previous findings [Fennell, C. J......In this paper we compare the Wolf method to the shifted forces (SF) method for efficient computer simulation of bulk systems with Coulomb forces, taking results from the Ewald summation and particle mesh Ewald methods as representing the true behavior. We find that for the Hansen–McDonald molten...
Superspreading: molecular dynamics simulations and experimental results
Theodorakis, Panagiotis; Kovalchuk, Nina; Starov, Victor; Muller, Erich; Craster, Richard; Matar, Omar
2015-11-01
The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Recently, we have observed that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. Here, we present the structural characteristics and kinetics of the droplet spreading during the different stages of this process, and we compare our results with experimental data for trisiloxane and poly oxy ethylene surfactants. In this way, we highlight and explore the differences between surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting. EPSRC Platform Grant MACIPh (EP/L020564/).
New ways to boost molecular dynamics simulations.
Krieger, Elmar; Vriend, Gert
2015-05-15
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. PMID:25824339
Molecular circuits for dynamic noise filtering.
Zechner, Christoph; Seelig, Georg; Rullan, Marc; Khammash, Mustafa
2016-04-26
The invention of the Kalman filter is a crowning achievement of filtering theory-one that has revolutionized technology in countless ways. By dealing effectively with noise, the Kalman filter has enabled various applications in positioning, navigation, control, and telecommunications. In the emerging field of synthetic biology, noise and context dependency are among the key challenges facing the successful implementation of reliable, complex, and scalable synthetic circuits. Although substantial further advancement in the field may very well rely on effectively addressing these issues, a principled protocol to deal with noise-as provided by the Kalman filter-remains completely missing. Here we develop an optimal filtering theory that is suitable for noisy biochemical networks. We show how the resulting filters can be implemented at the molecular level and provide various simulations related to estimation, system identification, and noise cancellation problems. We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using flow cytometry measurements of a light-inducible circuit in Escherichia coli. PMID:27078094
Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics
The Nose-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ''demon,'' which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature. We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations
Molecular evolution of scorpion a-toxins--Accelerated substitutions and functional divergence
无
2002-01-01
Scorpion α-toxins are a family of toxic proteins with similar scaffold, but possess divergent pharmacological properties.Analysis of cDNA sequences reveals that the numbers of nucleotide substitutions per site (K) for 5' and 3' UTRs are smaller than those per synonymous site (Ks) for the mature peptide-coding sequences, whereas the numbers of nucleotide substitutions per nonsynonymous site (Ka) are close to or larger than Ks values for relevant pairs of cDNAs. These results, together with phylogenetic analysis, indicate that scorpion a-toxins have evolved by accelerated substitutions in the mature toxin regions. In addition, the 15 amino acids, absolutely conserved in all the scorpion α-toxins described so far, are mostly located in molecular interior, which may be involved in structural constraints for stabilizing the CSαβ fold in evolution of these molecules. Four hot spot mutation sites in the molecular surface are found to dis tribute in the putative functional regions of α-toxins, suggesting that positive Darwinian selection drives the accelerated evolution of scorpion α-toxins. These findings reasonably explain the relationship between three-dimensional structure conservation and functional divergence of scorpion α-toxins and are of important value in guiding us in our engineering experiments to obtain higher affinity ligands to Na+ channels.
Scale Invariance at low accelerations (aka MOND) and the dynamical anomalies in the Universe
Milgrom, Mordehai
2016-01-01
Galactic systems, and the Universe at large, exhibit large dynamical anomalies: The observed matter in them falls very short of providing enough gravity to account for their dynamics. The mainstream response to this conundrum is to invoke large quantities of `dark matter' -- which purportedly supplies the needed extra gravity -- and also of `dark energy', to account for further anomalies in cosmology, such as the observed, accelerated expansion. The MOND paradigm offers a different solution: ...
Stability of molecular dynamics simulations of classical systems
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 method is also used to investigate higher-order central difference algorithms, which are symplectic and also have shadow Hamiltonians, and for which one can also determine the exact criteria for the limit of stability of a single harmonic mode. A fourth-order central difference algorithm gives...
Probing Molecular Dynamics by Laser-Induced Backscattering Holography
Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B.
2016-04-01
We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H2 and D2 molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H2 and D2 with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules.
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.
C60 molecular dynamics studied by muon spin relaxation
In muonium-substituted organic radicals, the muon spin can serve as a probe of molecular dynamics. The motional perturbation induces transitions between the coupled spin states of muon and unpaired electron. Studies of the resultant muon spin relaxation in C60Mu, the species formed by muon implantation in solid C60, yield the correlation time characteristic of the reorientational motion
THE REFINEMENT OF NMR STRUCTURES BY MOLECULAR-DYNAMICS SIMULATION
TORDA, AE; VANGUNSTEREN, WF
1991-01-01
We discuss the use of molecular dynamics simulations as a tool for the refinement of structures based on NMR data. The procedure always involves the construction of a pseudo-energy term to model the experimental data and we consider the various approaches to this problem. We detail recent work where
Active site modeling in copper azurin molecular dynamics simulations
Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R
2004-01-01
Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po
Reasoning with Atomic-Scale Molecular Dynamic Models
Pallant, Amy; Tinker, Robert F.
2004-01-01
The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…
Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
Menon, Madhu
1998-01-01
In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
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.
Molecular Dynamics ofa Coulomb System with Deformable Periodic Boundary Conditions
Totsuji, Hiroo; Shirokoshi, Hideki; Nara, Shigetoshi
1991-01-01
Variable shape molecular dynamics is formulated for the one-component plasma and the structural transition from the fcc lattice to the bcc lattice has been observed. It is emphasized that the condition of constant volume should be imposed when deformations of periodic boundary conditions are taken into account.
Molecular Dynamics Simulations Study on Chiral Room -Temperature Ionic Liquids
Lísal, Martin; Chvál, Z.; Storch, Jan; Izák, Pavel; Aim, Karel
Frankfurt : DECHEMA, 2012, P2-35. ISBN N. [European Symposium on Applied Thermodynamics - ESAT 2012 /26./. Potsdam (DE), 07.10.2012-10.10.2012] Institutional support: RVO:67985858 Keywords : ionic liquids * molecular dynamics simulations * thermodynamics properties Subject RIV: CF - Physical ; Theoretical Chemistry http://events.dechema.de/events/en/esat2012.html
Open boundary molecular dynamics of sheared star-polymer melts.
Sablić, Jurij; Praprotnik, Matej; Delgado-Buscalioni, Rafael
2016-02-28
Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution. PMID:26820315
Molecular dynamics simulations on PGLa using NMR orientational constraints
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 on PGLa using NMR orientational constraints
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 of flows in the Knudsen regime
Cieplak, Marek; Koplik, Joel; Banavar, Jayanth R.
2000-01-01
Novel technological applications often involve fluid flows in the Knudsen regime in which the mean free path is comparable to the system size. We use molecular dynamics simulations to study the transition between the dilute gas and the dense fluid regimes as the fluid density is increased.
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-10-01
Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.
Molecular dynamics simulation of the Ni(001) surface
Chirita, V.; Pailthorpe, B.A. (School of Physics, Univ. of Sydney, New South Wales (Australia))
1992-02-10
A Lennard-Jones two-body interatomic potential is used in a molecular dynamics simulation of bulk nickel and of the Ni(001) surface stabilized using a Dion-Barker-Merrill substrate interaction. It is found that the bulk and surface Debye temperatures and surface atomic displacements compare well with previous theoretical and experimental studies. (orig.).
Enhanced molecular dynamics performance with a programmable graphics processor
Rapaport, D C
2009-01-01
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of multistream processor hardware necessitates a reformulation of the underlying algorithm. Performance measurements demonstrate the considerable benefit and cost-effectiveness of such an approach.
A Molecular Dynamics Approach to Grain Boundary Structure and Migration
Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans
1974-01-01
It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...
Molecular dynamics simulation of a charged biological membrane
López Cascales, J.J.; García de la Torre, J.; Marrink, S.J.; Berendsen, H.J.C.
1996-01-01
A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as counterions and water molecules. The behavior of this membrane differs from that was shown by other me
Watching coherent molecular structural dynamics during photoreaction: beyond kinetic description
Lemke, Henrik T; Hartsock, Robert; van Driel, Tim Brandt; Chollet, Matthieu; Glownia, J M; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Nielsen, Martin M; Benfatto, Maurizio; Gaffney, Kelly J; Collet, Eric; Cammarata, Marco
2015-01-01
A deep understanding of molecular photo-transformations occurring is challenging because of the complex interaction between electronic and nuclear structure. The initially excited electronic energy dissipates into electronic and structural reconfigurations often in less than a billionth of a second. Molecular dynamics induced by photoexcitation have been very successfully studied with femtosecond optical spectroscopies, but electronic and nuclear dynamics are often very difficult to disentangle. X-ray based spectroscopies can reduce the ambiguity between theoretical models and experimental data, but it is only with the recent development of bright ultrafast X-ray sources, that key information during transient molecular processes can be obtained on their intrinsic timescale. We use Free Electron Laser (FEL) based time-resolved X-ray Absorption Near Edge Structure (XANES) measurements around the Iron K-edge of a spin crossover prototypical compound. We reveal its transformation from the ligand-located electroni...
Collisional dynamics in a gas of molecular super-rotors
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh.
2015-07-01
Recently, femtosecond laser techniques have been developed that are capable of bringing gas molecules to extremely fast rotation in a very short time, while keeping their translational motion relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a metastable `gyroscopic stage' in the course of which the molecules maintain their fast rotation and orientation of the angular momentum through many collisions. The inhibited rotational-translational relaxation is characterized by a persistent anisotropy in the molecular angular distribution, and is manifested in the optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the `gyroscopic stage' is abruptly terminated by an explosive rotational-translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules.
Heru Suhartanto
2012-03-01
Full Text Available Implementation of virtual laboratory on scientific research has produced huge acceleration. One of the virtual scientific research activity is molecular dynamic simulation. The virtual experiments need high computing resources to solve the problem. AMBER is one of the software that provides molecular dynamic simulation that can utilize the parallel computing facilities. In this paper, we conduct the molecular dynamic experiments in order to know reliability of cluster computing environment. The results show that an implicit solvent simulation takes longer time than that in vacuum scenario since one has to consider existence of solvent surround the molecules so the computation is much longer than in vacuum; that the speed up will likely to remain constant on certain additional number of processors; and that there is no significant speed up for case in the LOX-Curcumin explicit solvent simulation.
Influence of conformational molecular dynamics on matter wave interferometry
Gring, Michael; Eibenberger, Sandra; Nimmrichter, Stefan; Berrada, Tarik; Arndt, Markus; Ulbricht, Hendrik; Hornberger, Klaus; Müri, Marcel; Mayor, Marcel; Böckmann, Marcus; Doltsinis, Nikos
2014-01-01
We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum object, our experiment demonstrates that the translational quantum phase is sensitive to dynamic conformational state changes inside the diffracted molecules. The structural flexibility of tailor-made hot organic particles is sufficient to admit a mixture of strongly fluctuating dipole moments. These modify the electric susceptibility and through this the quantum interference pattern in the presence of an external electric field. Detailed molecular dynamics simulations combined with density functional theory allow us to quantify the time-dependent structural reconfigurations and to predict the ensemble-averaged square of the dipole moment which is found to be in good agreement with the interferometric result. The experiment thus opens a new perspective on matter wave interfe...
Molecular dynamics computer simulation of permeation in solids
Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M. [Sandia National Labs., Albuquerque, NM (United States)
1997-12-31
In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.
Laser-enhanced dynamics in molecular rate processes
George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.
1978-01-01
The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
Chiappori, Federica; Merelli, Ivan; Colombo, Giorgio; Milanesi, Luciano; Morra, Giulia
2012-01-01
Author Summary Allostery, or the capability of proteins to respond to ligand binding events with a variation in structure or dynamics at a distant site, is a common feature for biomolecular function and regulation in a large number of proteins. Intra-protein connections and inter-residue coordinations underlie allosteric mechanisms and react to binding primarily through a finely tuned modulation of motions and structures at the microscopic scale. Hence, all-atom molecular dynamics simulations...
Scherer, Christoph
2015-01-01
Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industri...
MD or DM? Modified dynamics at low accelerations vs dark matter
Milgrom, Mordehai
2011-01-01
The MOND paradigm posits a departure from standard Newtonian dynamics, and from General Relativity, in the limit of small accelerations. The resulting modified dynamics aim to account for the mass discrepancies in the universe without non-baryonic dark matter. I briefly review this paradigm with its basic tenets, and its underlying theories--nonrelativistic and relativistic--including a novel, bimetric MOND gravity theory. I also comment on MOND's possible connection to, and origin in, the cosmological state of the universe at large. Some of its main predictions, achievements, and remaining desiderata are listed. I then succinctly pit MOND against the competing paradigm of standard dynamics with cold, dark matter. (Abridged)
Start-to-end simulations for beam dynamics in the RISP heavy-ion accelerator
Kim, Eun-San, E-mail: eskim1@knu.ac.kr [Department of Physics, Kyungpook National University, Deagu (Korea, Republic of); Bahng, JungBae [Department of Physics, Kyungpook National University, Deagu (Korea, Republic of); Hwang, Ji-Gwang [KIRAMS, Seoul (Korea, Republic of); Choi, Bong-Hyuk; Kim, Hye-Jin; Jeon, Dong-O [Institute for Basic Science, Daejeon (Korea, Republic of)
2015-09-11
RAON has been designed as a rare isotope accelerator facility for the Rare Isotope Science Project (RISP). The main accelerator for the in-flight system accelerates uranium and proton beams to 200 MeV/u and 660 MeV, respectively, with a beam power of 400 kW. The front-end system consists of two 28 GHz electron cyclotron resonance ion sources (10 keV/u), a low-energy beam transport (LEBT) line with two 90° bends, a multi-harmonic buncher with three different rf frequencies, a radio-frequency quadrupole (RFQ), and a medium-energy beam transport line (MEBT) with three rebunchers and eight quadrupoles. A driver linac system consisting of Linac-1 and Linac-2 has been designed to optimize the beam and accelerator parameters so as to meet the required design goals. A charge stripper section is located between Linac-1 and Linac-2. To optimize these designs, we performed start-to-end simulations with the beams from the LEBT to Linac-2 using 1 million macroparticles. We present the resulting beam dynamics to evaluate the performance of the accelerator. Our simulation results predict that the transmission rate of the uranium beam is 85.8% from the LEBT to Linac-2. The designed facility is expected to achieve the required beam loss condition of less than 1 W/m. The RAON driver linac lattice design was developed and an overview of the beam dynamics is presented.
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik
2010-03-17
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
Molecular dynamics analysis on impact behavior of carbon nanotubes
Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler–Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation
Molecular dynamics analysis on impact behavior of carbon nanotubes
Seifoori, Sajjad, E-mail: sajjad.seifoori@vru.ac.ir
2015-01-30
Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler–Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation.
We investigate the consequences of Birkhoff's theorem in general relativity (GR) and in modified Newtonian dynamics (MOND). We study, in particular, the system of a finite-mass test particle inside a spherical shell. In both GR and MOND, we find nonvanishing acceleration for that test particle. The direction of the acceleration is such that it pushes the test particle toward the center of the shell. In GR, the acceleration is found analytically in the case of a small test mass with a small displacement from the center of the shell. In MOND, the acceleration is found analytically in the limit of large test mass and small displacement, and a comparison to numerical values is made. Numerical simulations are done for more general cases with parameters that mimic the system of a galaxy in a cluster. In GR, the acceleration is highly suppressed and physically insignificant. In MOND, on the contrary, the acceleration of the point particle can be a significant fraction of the field just outside of the spherical shell.
Dynamics of Particles in Non Scaling Fixed Field Alternating Gradient Accelerators
Jones J. K.
2010-01-01
Full Text Available Non scaling Fixed-Field Alternating Gradient (FFAG accelerators have an unprece- dented potential for muon acceleration, as well as for medical purposes based on car- bon and proton hadron therapy. They also represent a possible active element for an Accelerator Driven Subcritical Reactor (ADSR. Starting from first principle the Hamil- tonian formalism for the description of the dynamics of particles in non-scaling FFAG machines has been developed. The stationary reference (closed orbit has been found within the Hamiltonian framework. The dependence of the path length on the energy deviation has been described in terms of higher order dispersion functions. The latter have been used subsequently to specify the longitudinal part of the Hamiltonian. It has been shown that higher order phase slip coefficients should be taken into account to adequately describe the acceleration in non-scaling FFAG accelerators. A complete theory of the fast (serpentine acceleration in non-scaling FFAGs has been developed. An example of the theory is presented for the parameters of the Electron Machine with Many Applications (EMMA, a prototype electron non-scaling FFAG to be hosted at Daresbury Laboratory.
Dynamics of Particles in Non Scaling Fixed Field Alternating Gradient Accelerators
Tzenov S. I.
2010-01-01
Full Text Available Non scaling Fixed-Field Alternating Gradient (FFAG accelerators have an unprecedented potential for muon acceleration, as well as for medical purposes based on carbon and proton hadron therapy. They also represent a possible active element for an Accelerator Driven Subcritical Reactor (ADSR. Starting from first principle the Hamiltonian formalism for the description of the dynamics of particles in non-scaling FFAG machines has been developed. The stationary reference (closed orbit has been found within the Hamiltonian framework. The dependence of the path length on the energy deviation has been described in terms of higher order dispersion functions. The latter have been used subsequently to specify the longitudinal part of the Hamiltonian. It has been shown that higher order phase slip coefficients should be taken into account to adequately describe the acceleration in non-scaling FFAG accelerators. A complete theory of the fast (serpentine acceleration in non-scaling FFAGs has been developed. An example of the theory is presented for the parameters of the Electron Machine with Many Applications (EMMA, a prototype electron non-scaling FFAG to be hosted at Daresbury Laboratory.
Orbital free molecular dynamics; Approche sans orbitale des plasmas denses
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)
rf-induced beam dynamics in rf guns and accelerating cavities
Floettmann, Klaus
2015-01-01
In this paper, a detailed discussion of the rf-related beam dynamics in rf guns and accelerating cavities is presented. Other rf-gun-related aspects such as space charge and cathode physics are not treated. An effective start phase is introduced in order to yield a better description for the synchronous phase, the energy gain, and the bunch compression factor in gun cavities. Energy spread and longitudinal emittance are treated in a form applicable to guns as well as to accelerating cavities....
Rarefied Gas Flow in Rough Microchannels by Molecular Dynamics Simulation
曹炳阳; 陈民; 过增元
2004-01-01
The molecular dynamics simulation method is applied to investigate the rarefied gas flow in a submicron channel with surface roughness which is modelled by an array of triangle modules. The boundary conditions are found to be determined not only by the Knudsen number but also the roughness, which implies that the breakdown of the Maxwell slip model under the conditions that the surface roughness is comparable to the molecular mean free path. The effects of the rarefaction and the surface roughness on the boundary conditions and the flow characteristics are strongly coupled. The flow friction increases with increasing roughness and with decreasing Knudsen number.
Spectra modelling combining molecular dynamics and quantum mechanics
Novák, Vít; Bouř, Petr
2015-01-01
Roč. 22, č. 1 (2015), s. 48. ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /13./. 19.03.2015-21.03.2015, Nové Hrady] R&D Projects: GA ČR GAP208/11/0105; GA ČR GA15-09072S Grant ostatní: GA MŠk(CZ) LM2010005; GA MŠk(CZ) ED3.2.00/08.0144 Institutional support: RVO:61388963 Keywords : Raman scattering * molecular dynamics * autocorrelation function Subject RIV: CF - Physical ; Theoretical Chemistry
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Andrzej Koliński
2013-05-01
Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej
2013-01-01
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-03-14
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Molecular-Level Organization of the Tear Film Lipid Layer: A Molecular Dynamics Simulation Study
Wizert, A.; Iskander, D. R.; Jungwirth, Pavel; Cwiklik, Lukasz
Elsevier. Roč. 106, č. 2 (2014), 710A. ISSN 0006-3495. [Annual Meeting of the Biophysical Society /58./. 15.02.2014-19.02.2014, San Francisco] Institutional support: RVO:61388963 ; RVO:61388955 Keywords : tear film * lipid layer * molecular dynamics simulations Subject RIV: BO - Biophysics
Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.
2010-01-01
As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…
Molecular co-catalyst accelerating hole transfer for enhanced photocatalytic H2 evolution
Bi, Wentuan; Li, Xiaogang; Zhang, Lei; Jin, Tao; Zhang, Lidong; Zhang, Qun; Luo, Yi; Wu, Changzheng; Xie, Yi
2015-10-01
In artificial photocatalysis, sluggish kinetics of hole transfer and the resulting high-charge recombination rate have been the Achilles' heel of photocatalytic conversion efficiency. Here we demonstrate water-soluble molecules as co-catalysts to accelerate hole transfer for improved photocatalytic H2 evolution activity. Trifluoroacetic acid (TFA), by virtue of its reversible redox couple TFA./TFA-, serves as a homogeneous co-catalyst that not only maximizes the contact areas between co-catalysts and reactants but also greatly promotes hole transfer. Thus K4Nb6O17 nanosheet catalysts achieve drastically increased photocatalytic H2 production rate in the presence of TFA, up to 32 times with respect to the blank experiment. The molecular co-catalyst represents a new, simple and highly effective approach to suppress recombination of photogenerated charges, and has provided fertile new ground for creating high-efficiency photosynthesis systems, avoiding use of noble-metal co-catalysts.
Kotter, John P
2012-11-01
The old ways of setting and implementing strategy are failing us, writes the author of Leading Change, in part because we can no longer keep up with the pace of change. Organizational leaders are torn between trying to stay ahead of increasingly fierce competition and needing to deliver this year's results. Although traditional hierarchies and managerial processes--the components of a company's "operating system"--can meet the daily demands of running an enterprise, they are rarely equipped to identify important hazards quickly, formulate creative strategic initiatives nimbly, and implement them speedily. The solution Kotter offers is a second system--an agile, networklike structure--that operates in concert with the first to create a dual operating system. In such a system the hierarchy can hand off the pursuit of big strategic initiatives to the strategy network, freeing itself to focus on incremental changes to improve efficiency. The network is populated by employees from all levels of the organization, giving it organizational knowledge, relationships, credibility, and influence. It can Liberate information from silos with ease. It has a dynamic structure free of bureaucratic layers, permitting a level of individualism, creativity, and innovation beyond the reach of any hierarchy. The network's core is a guiding coalition that represents each level and department in the hierarchy, with a broad range of skills. Its drivers are members of a "volunteer army" who are energized by and committed to the coalition's vividly formulated, high-stakes vision and strategy. Kotter has helped eight organizations, public and private, build dual operating systems over the past three years. He predicts that such systems will lead to long-term success in the 21st century--for shareholders, customers, employees, and companies themselves. PMID:23155997
De Martino, S; Illuminati, F; Martino, Salvatore De; Siena, Silvio De; Illuminati, Fabrizio
1999-01-01
A recent proposal (see quant-ph/9803068) to simulate semiclassical corrections to classical dynamics by suitable classical stochastic fluctuations is applied to the specific instance of charged beam dynamics in particle accelerators. The resulting picture is that the collective beam dynamics, at the leading semiclassical order in Planck constant can be described by a particular diffusion process, the Nelson process, which is time-reversal invariant. Its diffusion coefficient $\\sqrt{N}\\lambda_{c}$ represents a semiclassical unit of emittance (here $N$ is the number of particles in the beam, and $\\lambda_{c}$ is the Compton wavelength). The stochastic dynamics of the Nelson type can be easily recast in the form of a Schroedinger equation, with the semiclassical unit of emittance replacing Planck constant. Therefore we provide a physical foundation to the several quantum-like models of beam dynamics proposed in recent years. We also briefly touch upon applications of the Nelson and Schroedinger formalisms to inc...
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
Microscopic study of nuclear 'pasta' by quantum molecular dynamics
Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. and be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape. We also observe intermediate phases, which has complicated nuclear shapes. Geometrical structures of matter are analyzed with Minkowski functionals, and it is found out that intermediate phases can be characterized as ones with negative Euler characteristic. Our result suggests the existence of these kinds of phases in addition to the simple 'pasta' phases in neutron star crusts. (author)
Ab initio molecular dynamics study of liquid methanol
Handgraaf, J W; Meijer, E J; Handgraaf, Jan-Willem; Erp, Titus S. van; Meijer, Evert Jan
2003-01-01
We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms
Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R
2005-02-02
Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.
Coalescence of silver unidimensional structures by molecular dynamics simulation
The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)
Molecular dynamical simulations of melting behaviors of metal clusters
The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures
The chaos and order in nuclear molecular dynamics
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 12C, 16O and 20Ne 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
Excitation Dynamics and Relaxation in a Molecular Heterodimer
Balevicius, V; Abramavicius, D; Mancal, T; Valkunas, L
2011-01-01
The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the energy gap of the molecular excitation, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.
Coherent Amplification of Ultrafast Molecular Dynamics in an Optical Oscillator
Aharonovich, Igal; Pe'er, Avi
2016-02-01
Optical oscillators present a powerful optimization mechanism. The inherent competition for the gain resources between possible modes of oscillation entails the prevalence of the most efficient single mode. We harness this "ultrafast" coherent feedback to optimize an optical field in time, and show that, when an optical oscillator based on a molecular gain medium is synchronously pumped by ultrashort pulses, a temporally coherent multimode field can develop that optimally dumps a general, dynamically evolving vibrational wave packet, into a single vibrational target state. Measuring the emitted field opens a new window to visualization and control of fast molecular dynamics. The realization of such a coherent oscillator with hot alkali dimers appears within experimental reach.
Fermionic molecular dynamics for ground states and collisions of nuclei
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.)
Kinetic distance and kinetic maps from molecular dynamics simulation
Noe, Frank
2015-01-01
Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine...
Serine Proteases an Ab Initio Molecular Dynamics Study
De Santis, L
1999-01-01
In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.
Tensor-optimized antisymmetrized molecular dynamics in nuclear physics
Myo, Takayuki; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro
2015-01-01
We develop a new formalism to treat nuclear many-body systems using bare nucleon-nucleon interaction. It has become evident that the tensor interaction plays important role in nuclear many-body systems due to the role of the pion in strongly interacting system. We take the antisymmetrized molecular dynamics (AMD) as a basic framework and add a tensor correlation operator acting on the AMD wave function using the concept of the tensor-optimized shell model (TOSM). We demonstrate a systematical and straightforward formulation utilizing the Gaussian integration and differentiation method and the antisymmetrization technique to calculate all the matrix elements of the many-body Hamiltonian. We can include the three-body interaction naturally and calculate the matrix elements systematically in the progressive order of the tensor correlation operator. We call the new formalism "tensor-optimized antisymmetrized molecular dynamics".
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.
Surface hopping methodology in laser-driven molecular dynamics
Fiedlschuster, T; Gross, E K U; Schmidt, R
2016-01-01
A theoretical justification of the empirical surface hopping method for the laser-driven molecular dynamics is given utilizing the formalism of the exact factorization of the molecular wavefunction [Abedi et al., PRL $\\textbf{105}$, 123002 (2010)] in its quantum-classical limit. Employing an exactly solvable $\\textrm H_2^{\\;+}$-like model system, it is shown that the deterministic classical nuclear motion on a single time-dependent surface in this approach describes the same physics as stochastic (hopping-induced) motion on several surfaces, provided Floquet surfaces are applied. Both quantum-classical methods do describe reasonably well the exact nuclear wavepacket dynamics for extremely different dissociation scenarios. Hopping schemes using Born-Oppenheimer surfaces or instantaneous Born-Oppenheimer surfaces fail completely.
Reaction dynamics of molecular hydrogen on silicon surfaces
Bratu, P.; Brenig, W.; Gross, A.; Hartmann, M.; Höfer, U.; Kratzer, Peter; Russ, R.
1996-01-01
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...... 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...... five-dimensional model is presented taking lattice distortion, corrugation, and molecular vibrations into account within the framework of coupled-channel calculations. While the temperature dependence of the sticking is dominated by lattice distortion, the main effect of corrugation is a reduction of...
An implicit divalent counterion force field for RNA molecular dynamics
Henke, Paul S.; Mak, Chi H.
2016-03-01
How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg2+ screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.
Shock induced phase transition of water: Molecular dynamics investigation
Neogi, Anupam, E-mail: anupamneogi@atdc.iitkgp.ernet.in [Advanced Technology Development Center, Indian Institute of Technology Kharagpur, Kharagpur 721302 (India); Mitra, Nilanjan, E-mail: nilanjan@civil.iitkgp.ernet.in [Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302 (India)
2016-02-15
Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns.
Shock induced phase transition of water: Molecular dynamics investigation
Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns
Tensor-optimized antisymmetrized molecular dynamics in nuclear physics
Myo, Takayuki; Toki, Hiroshi; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro
2015-07-01
We develop a new formalism to treat nuclear many-body systems using the bare nucleon-nucleon interaction. It has become evident that the tensor interaction plays an important role in nuclear many-body systems due to the role of the pion in strongly interacting systems. We take the antisymmetrized molecular dynamics (AMD) as a basic framework and add a tensor correlation operator acting on the AMD wave function using the concept of the tensor-optimized shell model. We demonstrate a systematical and straightforward formulation utilizing the Gaussian integration and differentiation method and the antisymmetrization technique to calculate all the matrix elements of the many-body Hamiltonian. We can include the three-body interaction naturally and calculate the matrix elements systematically in the progressive order of the tensor correlation operator. We call the new formalism "tensor-optimized antisymmetrized molecular dynamics".
Ab initio molecular dynamics on the electronic Boltzmann equilibrium distribution
Alonso, J L; Echenique, P [Departamento de Fisica Teorica, Universidad de Zaragoza, Pedro Cerbuna 12, E-50009 Zaragoza (Spain); Castro, A; Polo, V [Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, E-50018 Zaragoza (Spain); Rubio, A [Nano-Bio Spectroscopy group and ETSF Scientific Development Centre, Departamento de Fisica de Materiales, Universidad del PaIs Vasco, Centro de Fisica de Materiales, CSIC-UPV/EHU-MPC and DIPC, E-20018 San Sebastian (Spain); Zueco, D, E-mail: dzueco@unizar.e [Instituto de Ciencia de Materiales de Aragon and Departamento de Fisica de la Materia Condensada, CSIC-Universidad de Zaragoza, E-50009 Zaragoza (Spain)
2010-08-15
We prove that for a combined system of classical and quantum particles, it is possible to describe a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In addition, these molecular dynamics (MD) do not need to assume that the electrons immediately follow the nuclear motion (in contrast to any adiabatic approach) and do not present problems in the presence of crossing points between different potential energy surfaces (conical intersections or spin-crossings). A practical application of this MD to the study of the effect of temperature on molecular systems presenting (nearly) degenerate states-such as the avoided crossing in the ring-closure process of ozone-is presented.
Nonequilibrium Molecular Dynamics Simulation of the Thermocapillary Effect
Maier, Holger Andreas
2011-01-01
A natural convection occurs at lateral spatially variable solid-fluid or liquid-fluid interfaces [probstein1994]. It can play an important role in the transport of heat or mass across such interfaces, e.g. in evaporation or solvent extraction as they are often employed in chemical engineering [sherwood1975]. Model systems of such interfacial systems have been studied by different methods [colinet2001]. A very fundamental method is the usage of so-called molecular dynamics (MD) simulation...
Molecular Dynamics Study of the Primary Ferrofluid Aggregate Formation
Tanygin, B. M.; Kovalenko, V. F.; Petrychuk, M.V.; Dzyan, S. A.
2011-01-01
Investigations of the phase transitions and self-organization in the magnetic aggregates are of the fundamental and applied interest. The long-range ordering structures described in the Tom\\'anek's systematization (M. Yoon, and D. Tom\\'anek, 2010 [1]) are not yet obtained in the direct molecular dynamics simulations. The resulted structures usually are the linear chains or circles, or, else, amorphous (liquid) formations. In the present work, it was shown, that the thermodynamically equilibri...
Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane.
Bernèche, S; Nina, M; Roux, B
1998-01-01
Molecular dynamics trajectories of melittin in an explicit dimyristoyl phosphatidylcholine (DMPC) bilayer are generated to study the details of lipid-protein interactions at the microscopic level. Melittin, a small amphipathic peptide found in bee venom, is known to have a pronounced effect on the lysis of membranes. The peptide is initially set parallel to the membrane-solution interfacial region in an alpha-helical conformation with unprotonated N-terminus. Solid-state nuclear magnetic reso...
Nonlinear dynamics of zigzag molecular chains (in Russian)
Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth;
1999-01-01
Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...... types (such as extension and compression varieties) develop simultaneously in the chain. Accordingly, the inclusion of chain geometry is necessary if physical phenomena are to be described in terms of solitary waves...
Ab initio molecular dynamics simulation of laser melting of silicon
Silvestrelli, P.-L.; Alavi, A; Parrinello, M.; Frenkel, D
1996-01-01
The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting transition to a metallic state. In contrast to ordinary liquid silicon, the new liquid is characterized by a high coordination number and a strong reduction of covalent bonding effects.
Understanding disordered and membrane protein recognition by molecular dynamics
Stanley, Nathaniel H., 1983-
2015-01-01
This thesis has been about the use of a simulation technique, known as molecular dynamics simulations, to study biophysics in proteins that have historically been difficult to study with other methods. We have studied numerous systems, namely binding to the membrane proteins Fatty acid amide hydrolase (FAAH) and the sphingosine-1-phosphate receptor 1 (S1P1R), and folding in the disordered protein kinase inducible domain (KID). In each case we have been able to analyze processes and uncover be...
Automated processing of data generated by molecular dynamics
A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)
Efficient stochastic thermostatting of path integral molecular dynamics
Ceriotti, Michele; Parrinello, Michele; Markland, Thomas E.; Manolopoulos, David E.
2010-01-01
The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high-frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat...
Quantum tunneling splittings from path-integral molecular dynamics.
Mátyus, Edit; Wales, David J; Althorpe, Stuart C
2016-03-21
We illustrate how path-integral molecular dynamics can be used to calculate ground-state tunnelling splittings in molecules or clusters. The method obtains the splittings from ratios of density matrix elements between the degenerate wells connected by the tunnelling. We propose a simple thermodynamic integration scheme for evaluating these elements. Numerical tests on fully dimensional malonaldehyde yield tunnelling splittings in good overall agreement with the results of diffusion Monte Carlo calculations. PMID:27004863
Viscosity in molecular dynamics with periodic boundary conditions
Viscardy, S.; Gaspard, P.
2003-01-01
We report a study of viscosity by the method of Helfand moment in systems with periodic boundary conditions. We propose a new definition of Helfand moment which takes into account the minimum image convention used in molecular dynamics with periodic boundary conditions. Our Helfand-moment method is equivalent to the method based on the Green-Kubo formula and is not affected by ambiguities due to the periodic boundary conditions. Moreover, in hard-ball systems, our method is equivalent to the ...
Coupling Lattice Boltzmann and Molecular Dynamics models for dense fluids
Dupuis, A.; Kotsalis, E. M.; Koumoutsakos, P.
2006-01-01
We propose a hybrid model, coupling Lattice Boltzmann and Molecular Dynamics models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with r...
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
Rapaport, D C
2009-01-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Molecular dynamics simulations of HIV-1 protease complexed with saquinavir
Watson, S. J.
2009-01-01
Inhibition of the Human Immunode�ficiency virus type-1 (HIV-1) protease enzyme blocks HIV-1 replication. Protease inhibitor drugs have successfully been used as a therapy for HIV-infected individuals to reduce their viral loads and slow the progression to Acquired Immune Defi�ciency Syndrome (AIDS). However, mutations readily and rapidly accrue in the protease gene resulting in a reduced sensitivity of the protein to the inhibitor. In this thesis, molecular dynamics simulations (MDS)...
Molecular dynamics simulation of nanoindentation on nanocomposite pearlite
Ghaffarian, Hadi; Taheri, Ali Karimi; Ryu, Seunghwa; Kang, Keonwook
2016-01-01
We carry out molecular dynamics simulations of nanoindentation to investigate the effect of cementite size and temperature on the deformation behavior of nanocomposite pearlite composed of alternating ferrite and cementite layers. We find that, instead of the coherent transmission, dislocation propagates by forming a widespread plastic deformation in cementite layer. We also show that increasing temperature enhances the distribution of plastic strain in the ferrite layer, which reduces the st...
Molecular Dynamics for Low Temperature Plasma-Surface Interaction Studies
Graves, David B.; Brault, Pascal
2009-01-01
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms through integration of atomic equations of motion, using inter-atomic potentials that can account for bond breaking and formation that result when energetic species from the plasma impact surfaces. This article summarizes the current status of the technique for ...
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
Rapaport, D. C.
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
DNA basepair step deformability inferred from molecular dynamics simulations
Lankaš, Filip; Šponer, Jiří; Langowski, J.; Cheatham III, T. E.
2003-01-01
Roč. 85, č. 5 (2003), s. 2872-2883. ISSN 0006-3495 R&D Projects: GA MŠk LN00A032 Grant ostatní: National Science Foundation(US) CHE-0218739; Wellcome Trust(GB) GR067507MF Institutional research plan: CEZ:AV0Z5004920; CEZ:AV0Z4040901 Keywords : molecular dynamics simulations * DNA basepair step deformability Subject RIV: BO - Biophysics Impact factor: 4.463, year: 2003
Spin dynamics of an ultra-small nanoscale molecular magnet
Ciftja Orion
2007-01-01
Full Text Available AbstractWe present mathematical transformations which allow us to calculate the spin dynamics of an ultra-small nanoscale molecular magnet consisting of a dimer system of classical (high Heisenberg spins. We derive exact analytic expressions (in integral form for the time-dependent spin autocorrelation function and several other quantities. The properties of the time-dependent spin autocorrelation function in terms of various coupling parameters and temperature are discussed in detail.
Molecular Dynamics Simulation of Myoglobin Collision with Low Energy Ions
CHENG Wei; ZHANG Feng-Shou; ZHOU Hong-Yu
2007-01-01
Collisions of a low energy heavy ion with a myoglobin in water are simulated by molecular dynamics model. The increase of total energy is very small. The mean squared fluctuation decreases at 300 K and increases at 250K.This is an important novel cooling effect that protects the protein from ion damage. The possible collision side effect is the change of tertiary structure that blocks the normal functions of the myogiobin.
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche
1997-09-01
Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.
Thermal conductivity of ZnTe investigated by molecular dynamics
The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
Leone, Stephen 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 me...
Molecular dynamics in electrospun amorphous plasticized polylactide fibers
MONNIER, X; DELPOUVE, N; BASSON, N; GUINAULT, A; DOMENEK, S; Saiter, A; MALLON, P.E; Dargent, E
2015-01-01
The molecular dynamics in the amorphous phase of electrospun fibers of polylactide (PLA) has been investigated using the cooperative rearranging region concept. An unusual and significant increase of the cooperativity length at the glass transition induced by the electrospinning has been observed. This behavior is attributed to the singularity of the amorphous phase organization. Electrospun PLA fibers rearrange in a pre-ordered metastable state which is characterized by highly oriented but n...
Enhanced molecular dynamics performance with a programmable graphics processor
Rapaport, D. C.
2009-01-01
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware necessitates a reformulation of the underlying algorithm. Performance measurements demonstrate the considerable benefit and cost-effectiveness of such an approach, which produces a factor of 2.5 speed improvement over previous work for the case of the soft-sp...
Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit
Xu, Ji; Ren, Ying; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai
2010-01-01
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU ar...
Molecular dynamics simulations of complex shaped particles using Minkowski operators
Galindo-Torres, Sergio-Andres; Alonso-Marroquin, Fernando
2008-01-01
The Minkowski operators (addition and substraction of sets in vectorial spaces) has been extensively used for Computer Graphics and Image Processing to represent complex shapes. Here we propose to apply those mathematical concepts to extend the Molecular Dynamics (MD) Methods for simulations with complex-shaped particles. A new concept of Voronoi-Minkowski diagrams is introduced to generate random packings of complex-shaped particles with tunable particle roundness. By extending the classical...
Molecular Dynamics study of Pb overlayer on Cu(100)
Karimi, M.; Tibbits, P.; Ila, D.; Dalins, I.; Vidali, G.
1991-01-01
Isothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2x2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.
Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins
Fogolari, Federico; Brigo, Alessandro; Molinari, Henriette
2003-01-01
Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poi...
Molecular dynamics investigation of radiation damage in semiconductors
Good, Brian S.
1991-01-01
Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.
Molecular dynamics simulation study of polyelectrolyte adsorption on cellulose surfaces
Biermann, Oliver
2002-01-01
The adsorption of two polyelectrolyte ((carboxy methyl) cellulose and poly(acrylate) in water on crystalline cellulose is studied in this work. The multi-component problem has been splitted up into simulations of solutions of the polyelectrolyte (polyanions including sodium counterions) in water, into simulations of the interface of crystalline cellulose towards water. Finally polyelectrolyte-cellulose systems were studied. Molecular dynamics simulations of diluted (_ 2:5 weight percent) aque...
Hydration of polyelectrolytes studied by molecular dynamics simulation
Biermann, Oliver; Haedicke, Erich; Koltzenburg, Sebastian; Seufert, Michael; Mueller-Plathe, Florian
2001-01-01
Molecular dynamics simulations of diluted (~2.5 weight percent) aqueous solutions of two polyelectrolytes, namely sodium carboxy methyl cellulose (CMC) and sodium poly(acrylate) (PAA) have been performed. Water and counterions were taken into account explicitly. For CMC the substitution pattern and starting conformation is all-important. Two simulations of CMC oligomers resulted in different structures: One molecule takes a stretched conformation, while the second one keeps a globule-like, to...
Incorporation of quantum statistical features in molecular dynamics
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 packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation
Pedersen, U.R.; Peters, Günther H.j.; Westh, P.
2007-01-01
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......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...... 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 C...
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
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
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
Abdollahipour, Babak, E-mail: b-abdollahi@tabrizu.ac.ir [Faculty of Physics, University of Tabriz, Tabriz 51666-16471 (Iran, Islamic Republic of); Abouie, Jahanfar, E-mail: jahan@iasbs.ac.ir; Ebrahimi, Navid [Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731 (Iran, Islamic Republic of)
2015-09-15
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
Babak Abdollahipour
2015-09-01
Full Text Available We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.
Molecular dynamics of a water jet from a carbon nanotube.
Hanasaki, Itsuo; Yonebayashi, Toru; Kawano, Satoyuki
2009-04-01
A carbon nanotube (CNT) can be viewed as a molecular nozzle. It has a cylindrical shape of atomistic regularity, and the diameter can be even less than 1 nm. We have conducted molecular-dynamics simulations of water jet from a (6,6) CNT that confines water in a form of single-file molecular chain. The results show that the water forms nanoscale clusters at the outlet and they are released intermittently. The jet breakup is dominated by the thermal fluctuations, which leads to the strong dependence on the temperature. The cluster size n decreases and the release frequency f increases at higher temperatures. The f roughly follows the reaction kinetics by the transition state theory. The speed of a cluster is proportional to the 1/sqrt[n] because of the central limit theorem. These properties make great contrast with the macroscopic liquid jets. PMID:19518333
Molecular Dynamics Studies on the Buffalo Prion Protein
Zhang, Jiapu
2015-01-01
It was reported that buffalo is a low susceptibility species resisting to TSEs (Transmissible Spongiform Encephalopathies) (same as rabbits, horses and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (in humans prion diseases are (v)CJDs, GSS, FFI, and kulu etc). It was reported that buffalo is a low susceptibility species resisting to prion diseases (as rabbits, dogs, horses). In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to find out the reason why buffaloes are resistant to prion diseases. We first did molecular modeling a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonanc...
Applications of the molecular dynamics flexible fitting method.
Trabuco, Leonardo G; Schreiner, Eduard; Gumbart, James; Hsin, Jen; Villa, Elizabeth; Schulten, Klaus
2011-03-01
In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to landmark advances in experimental and computational techniques, resulting in sub-nanometer resolution structures being obtained routinely. The remaining gap between these data and revealing the mechanisms of molecular function can be closed through hybrid modeling tools that incorporate known atomic structures into the cryo-EM data. One such tool, molecular dynamics flexible fitting (MDFF), uses molecular dynamics simulations to combine structures from X-ray crystallography with cryo-EM density maps to derive atomic models of large biomolecular complexes. The structures furnished by MDFF can be used subsequently in computational investigations aimed at revealing the dynamics of the complexes under study. In the present work, recent applications of MDFF are presented, including the interpretation of cryo-EM data of the ribosome at different stages of translation and the structure of a membrane-curvature-inducing photosynthetic complex. PMID:20932910
Exploiting molecular dynamics in Nested Sampling simulations of small peptides
Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor
2016-04-01
Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.
The dynamical correlation between quantum entanglement and intramolecular energy in realistic molecular vibrations is explored using the Lie algebraic approach. The explicit expression of entanglement measurement can be achieved using algebraic operations. The common and different characteristics of dynamical entanglement in different molecular vibrations are also provided. The dynamical study of quantum entanglement and intramolecular energy in small molecular vibrations can be helpful for controlling the entanglement and further understanding the intramolecular dynamics. (atomic and molecular physics)
Beam dynamics of a double-gap acceleration cell for ion implantation with multiple atomic species
As a result of our work on ion implantation, we derived equations for the beam dynamics of a two-gap-resonator cavity for accelerating and bunching various ion species of varying energies with the cavity designed for one particular ion species of a given energy (the design-reference particle). A two gap structure is useful at low resonant frequencies where lumped circuit elements (inductors) can be used and the structure kept small. A single gap structure has the advantage that each gap can be independently phased to produce the desired beam dynamics behavior for various ion species and ion energies. However at low frequencies, single gap resonant structures can be large. We find that the two-gap structure, where the phase difference between gaps, for the design reference particle, is fixed at π radians can give acceptable performance provided that the individual two gap cells in the entire accelerator are optimized for the ion species having the largest mass to charge ratio and having the maximum required output energy. Our equations show how to adjust the cavity phases and electric fields to obtain equivalent first-order accelerator performance for various ion species and energies. These equations allow for the effective evaluation of various accelerator concepts and can facilitate the tuning of a linac when changing energies and ion species. Extensive simulations have confirmed the efficacy of our equations. copyright 1997 American Institute of Physics
Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A
2013-03-21
The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio
Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators
Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.
1999-11-13
In this paper, we present an object-oriented three-dimensional parallel particle-in-cell code for beam dynamics simulation in linear accelerators. A two-dimensional parallel domain decomposition approach is employed within a message passing programming paradigm along with a dynamic load balancing. Implementing object-oriented software design provides the code with better maintainability, reusability, and extensibility compared with conventional structure based code. This also helps to encapsulate the details of communications syntax. Performance tests on SGI/Cray T3E-900 and SGI Origin 2000 machines show good scalability of the object-oriented code. Some important features of this code also include employing symplectic integration with linear maps of external focusing elements and using z as the independent variable, typical in accelerators. A successful application was done to simulate beam transport through three superconducting sections in the APT linac design.
NONLINEAR DYNAMICS OF AXIALLY ACCELERATING VISCOELASTIC BEAMS BASED ON DIFFERENTIAL QUADRATURE
Hu Ding; Liqun Chen
2009-01-01
This paper investigates nonlinear dynamical behaviors in transverse motion of an axially accelerating viscoelastic beam via the differential quadrature method. The governing equa-tion, a nonlinear partial-differential equation, is derived from the viscoelastic constitution relation using the material derivative. The differential quadrature scheme is developed to solve numeri-cally the governing equation. Based on the numerical solutions, the nonlinear dynamical behaviors presented in the case that the mean axial speed and the amplitude of the speed fluctuation are respectively varied while other parameters are fixed. The Lyapunov exponent and the initial value sensitivity of the different points of the beam, calculated from the time series based on the numer-ical solutions, are used to indicate periodic motions or chaotic motions occurring in the transverse motion of the axially accelerating viscoelastic beam.
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, perf
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, perf
Hall, G.E.
2011-05-31
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.
Hall G. E.; Goncharov, V.
2012-05-29
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.
Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer
Casuyac Miqueas; Bantaculo Rolando
2016-01-01
This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNR)using the classical molecular dynamic (MD) simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H...
Sasagawa, Shun; Shinya, Masahiro; Nakazawa, Kimitaka
2014-01-01
Recent studies have demonstrated that human quiet standing is a multijoint movement, whereby the central nervous system (CNS) is required to deal with dynamic interactions among the joints to achieve optimal motor performance. The purpose of this study was to investigate how the CNS deals with such interjoint interaction during quiet standing by examining the relationship between the kinetics (torque) and kinematics (angular acceleration) within the multi-degree of freedom system. We modeled quiet standing as a double-link inverted pendulum involving both ankle and hip joints and conducted an "induced acceleration analysis." We found that the net ankle and hip torques induced angular accelerations of comparable magnitudes to the ankle (3.8 ± 1.4°/s(2) and 3.3 ± 1.2°/s(2)) and hip (9.1 ± 3.2°/s(2) and 10.5 ± 3.5°/s(2)) joints, respectively. Angular accelerations induced by the net ankle and hip torques were modulated in a temporally antiphase pattern to one another in each of the two joints. These quantitative and temporal relationships allowed the angular accelerations induced by the two net torques to countercompensate one another, thereby substantially (∼70%) reducing the resultant angular accelerations of the individual joints. These results suggest that, by taking advantage of the interjoint interaction, the CNS prevents the net torques from producing large amplitudes of the resultant angular accelerations when combined with the kinematic effects of all other torques in the chain. PMID:24089399
Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations.
Zhonghua Shen
Full Text Available Human microsomal cytochrome P450 2E1 (CYP2E1 can oxidize not only low molecular weight xenobiotic compounds such as ethanol, but also many endogenous fatty acids. The crystal structure of CYP2E1 in complex with indazole reveals that the active site is deeply buried into the protein center. Thus, the unbinding pathways and associated unbinding mechanisms remain elusive. In this study, random acceleration molecular dynamics simulations combined with steered molecular dynamics and potential of mean force calculations were performed to identify the possible unbinding pathways in CYP2E1. The results show that channel 2c and 2a are most likely the unbinding channels of CYP2E1. The former channel is located between helices G and I and the B-C loop, and the latter resides between the region formed by the F-G loop, the B-C loop and the β1 sheet. Phe298 and Phe478 act as the gate keeper during indazole unbinding along channel 2c and 2a, respectively. Previous site-directed mutagenesis experiments also supported these findings.
Machado, N C F; Dos Santos, L; Carvalho, B G; Singh, P; Téllez Soto, C A; Azoia, N G; Cavaco-Paulo, A; Martin, A A; Favero, P P
2016-08-01
The present work, involves the simulation of the transport of a vitamin C derivative, Ascorbyl Tetraisopalmitate (ATI), through human skin by molecular dynamics. Percutaneous absorption of the ATI molecule through the infundibulum, an important route of absorption into the hair follicle of the human skin, has been modeled and compared with the stratum corneum membrane. The comparative study was done using molecular dynamics with Martini force field. In infundibulum, a single ATI molecule require more time to penetrate, and the data obtained suggested that a high concentration of ATI molecule accelerated the process of penetration. In conclusion, the ATI molecule was found to have more affinity towards the stratum corneum as compared with the infundibulum, and it followed a straight pathway to penetrate (until 600ns of simulation). In the infundibulum, it showed less affinity, more mobility and followed a lateral pathway. Thus, this work contributes to a better understanding of the different molecular interactions during percutaneous absorption of active molecules in these two different types of biological membranes. PMID:27289538
Wittenberg, Nathan J.; Zheng, Leiliang; Winograd, Nicholas; Ewing, Andrew G.
2008-01-01
We have used amperometric measurements in a model system consisting of two liposomes connected with a membrane nanotube to monitor catechol release during artificial exocytosis and thereby to elucidate the effect of small-chain alcohols on this dynamic membrane process. To determine the rate of membrane shape change, catechol release during membrane distention was monitored amperometrically, and the presence of alcohols in the buffer was shown to accelerate the membrane distention process in ...
Predictive Simulation and Design of Materials by Quasicontinuum and Accelerated Dynamics Methods
Luskin, Mitchell [University of Minnesota; James, Richard; Tadmor, Ellad
2014-03-30
This project developed the hyper-QC multiscale method to make possible the computation of previously inaccessible space and time scales for materials with thermally activated defects. The hyper-QC method combines the spatial coarse-graining feature of a finite temperature extension of the quasicontinuum (QC) method (aka “hot-QC”) with the accelerated dynamics feature of hyperdynamics. The hyper-QC method was developed, optimized, and tested from a rigorous mathematical foundation.
The classical and quantum dynamics of molecular spins on graphene.
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2016-02-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices. PMID:26641019
Molecular dynamics investigation of tracer diffusion in a simple liquid
Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs
Wave packet dynamics in molecular excited electronic states
We theoretically explore the use of UV pump – UV probe schemes to resolve in time the dynamics of nuclear wave packets in excited electronic states of the hydrogen molecule. The pump pulse ignites the dynamics in singly excited states, that will be probed after a given time delay by a second identical pulse that will ionize the molecule. The field-free molecular dynamics is first explored by analyizing the autocorrelation function for the pumped wave packet and the excitation probabilities. We investigate both energy and angle differential ionization probabilities and demonstrate that the asymmetry induced in the electron angular distributions gives a direct map of the time evolution of the pumped wave packet
Molecular dynamics of coalescence and collisions of silver nanoparticles
We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy
Steered molecular dynamics simulations of protein-ligand interactions
XU Yechun; SHEN Jianhua; LUO Xiaomin; SHEN Xu; CHEN Kaixian; JIANG Hualiang
2004-01-01
Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and kinetic processes of ligand-receptor binding and unbinding, which cannot be accessed by the experimental methods. In this article, the methodology of SMD is described, and the applications of SMD simulations for obtaining dynamic insights into protein-ligand interactions are illustrated through two of our own examples. One is associated with the simulations of binding and unbinding processes between huperzine A and acetylcholinesterase, and the other is concerned with the unbinding process of α-APA from HIV-1 reverse transcriptase.
Molecular dynamics of coalescence and collisions of silver nanoparticles
Guevara-Chapa, Enrique, E-mail: enrique_guevara@hotmail.com [Universidad Autónoma de Nuevo León, Facultad de Ciencias Físico Matemáticas (Mexico); Mejía-Rosales, Sergio [Universidad Autónoma de Nuevo León, Center for Innovation, Research and Development in Engineering and Technology (CIIDIT), and CICFIM-Facultad de Ciencias Físico Matemáticas (Mexico)
2014-12-15
We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy.
Two methods for molecular dynamics on curved surfaces
Paquay, Stefan
2014-01-01
Lateral diffusion along membranes is an important transport mechanism in biology. Dynamical simulations of this transport can greatly aid in understanding biological processes where this diffusion plays a role. Brownian dynamics simulations in local coordinates are one possibility, but we show here that it is also possible to combine constraint algorithms with a velocity Verlet scheme to perform molecular dynamics simulations of particles confined on arbitrary time-independent curved surfaces. The main advantage is that this method is based on Cartesian coordinates instead of local coordinates, allowing the reuse of many other standard tools, including parallelisation through domain decomposition, without adapting those to local coordinates. Of the two constraint algorithms we considered, RATTLE is more computationally efficient and easier to implement, while the symmetric projection method has slightly better energy conservation. By applying the schemes to the Langevin equation, Brownian motion on various cu...
The classical and quantum dynamics of molecular spins on graphene
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2016-02-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.
Koniakhin, S V; Terterov, I N; Shvidchenko, A V; Eidelman, E D; Dubina, M V
2016-01-01
The determination of particle size by dynamic light scattering uses the Stokes-Einstein relation, which can break down for nanoscale objects. Here we employ a molecular dynamics simulation of fully solvated 1-5 nm carbon nanoparticles for the refinement of the experimental data obtained for nanodiamonds in water by using dynamic light scattering. We performed molecular dynamics simulations in differently sized boxes and calculated nanoparticles diffusion coefficients using the velocity autocorrelation function and mean-square displacement. We found that the predictions of the Stokes-Einstein relation are accurate for nanoparticles larger than 3 nm while for smaller nanoparticles the diffusion coefficient should be corrected and different boundary conditions should be taken into account.
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
Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N
2016-07-12
We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step. PMID:27267207
Molecular imaging with dynamic contrast-enhanced computed tomography
Dynamic contrast-enhanced computed tomography (DCE-CT) is a quantitative technique that employs rapid sequences of CT images after bolus administration of intravenous contrast material to measure a range of physiological processes related to the microvasculature of tissues. By combining knowledge of the molecular processes underlying changes in vascular physiology with an understanding of the relationship between vascular physiology and CT contrast enhancement, DCE-CT can be redefined as a molecular imaging technique. Some DCE-CT derived parameters reflect tissue hypoxia and can, therefore, provide information about the cellular microenvironment. DCE-CT can also depict physiological processes, such as vasodilatation, that represent the physiological consequences of molecular responses to tissue hypoxia. To date the main applications have been in stroke and oncology. Unlike some other molecular imaging approaches, DCE-CT benefits from wide availability and ease of application along with the use of contrast materials and software packages that have achieved full regulatory approval. Hence, DCE-CT represents a molecular imaging technique that is applicable in clinical practice today.
Molecular-dynamics analysis of the diffusion of molecular hydrogen in all-silica sodalite
Van den Berg, A.W.C.; Bromley, S.T.; Flikkema, E.; Wojdel, J.; Maschmeyer, T; Jansen, J C
2004-01-01
In order to investigate the technical feasibility of crystalline porous silicates as hydrogen storage materials, the self-diffusion of molecular hydrogen in all-silica sodalite is modeled using large-scale classical molecular-dynamics simulations employing full lattice flexibility. In the temperature range of 700–1200 K, the diffusion coefficient is found to range from 1.6⋅10−10 to 1.8⋅10−9 m2/s. The energy barrier for hydrogen diffusion is determined from the simulations allowing the applica...
Accelerating molecular simulations of proteins using Bayesian inference on weak information
Perez, Alberto; MacCallum, Justin L.; Dill, Ken A.
2015-01-01
Atomistic molecular dynamics (MD) simulations of protein molecules are too computationally expensive to predict most native structures from amino acid sequences. Here, we integrate “weak” external knowledge into folding simulations to predict protein structures, given their sequence. For example, we instruct the computer “to form a hydrophobic core,” “to form good secondary structures,” or “to seek a compact state.” This kind of information has been too combinatoric, nonspecific, and vague to help guide MD simulations before. Within atomistic replica-exchange molecular dynamics (REMD), we develop a statistical mechanical framework, modeling using limited data with coarse physical insight(s) (MELD + CPI), for harnessing weak information. As a test, we apply MELD + CPI to predict the native structures of 20 small proteins. MELD + CPI samples to within less than 3.2 Å from native for all 20 and correctly chooses the native structures (<4 Å) for 15 of them, including ubiquitin, a millisecond folder. MELD + CPI is up to five orders of magnitude faster than brute-force MD, satisfies detailed balance, and should scale well to larger proteins. MELD + CPI may be useful where physics-based simulations are needed to study protein mechanisms and populations and where we have some heuristic or coarse physical knowledge about states of interest. PMID:26351667
Dynamical properties of liquid Al near melting. An orbital-free molecular dynamics study
Gonzalez, David J; Gonzalez, Luis Enrique; Lopez, Jose Manuel; Stott, Malcolm J.
2001-01-01
The static and dynamic structure of liquid Al is studied using the orbital free ab-initio molecular dynamics method. Two thermodynamic states along the coexistence line are considered, namely T = 943 K and 1323 K for which X-ray and neutron scattering data are available. A new kinetic energy functional, which fulfills a number of physically relevant conditions is employed, along with a local first principles pseudopotential. In addition to a comparison with experiment, we also compare our ab-...