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...
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
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.
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.
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 ...
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...
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.
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
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.
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)
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.
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.
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.
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
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.
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
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.
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
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 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)
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.
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...
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.
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.
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 ...
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.
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.
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
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 ...
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...
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 ...
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.
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.
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.
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.
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
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...
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 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
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
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.
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
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
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
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
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.
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.
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 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
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 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
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
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.
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...
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.
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...
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...
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.
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
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.
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 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
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...
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.
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...
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)
Molecular beam studies of reaction dynamics
Lee, Y.T.
1987-03-01
Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.
Molecular dynamics simulation of 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.
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.
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.
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
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
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.
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
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...
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)
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
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)
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.
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.
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.
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.
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
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.
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)
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.
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.
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.
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
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
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 ...