Substructured multibody molecular dynamics.
Energy Technology Data Exchange (ETDEWEB)
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
Conference on Multibody Dynamics
Multibody Dynamics : Computational Methods and Applications
2014-01-01
By having its origin in analytical and continuum mechanics, as well as in computer science and applied mathematics, multibody dynamics provides a basis for analysis and virtual prototyping of innovative applications in many fields of contemporary engineering. With the utilization of computational models and algorithms that classically belonged to different fields of applied science, multibody dynamics delivers reliable simulation platforms for diverse highly-developed industrial products such as vehicle and railway systems, aeronautical and space vehicles, robotic manipulators, smart structures, biomechanical applications and nano-technologies. The chapters of this volume are based on the revised and extended versions of the selected scientific papers from amongst 255 original contributions that have been accepted to be presented within the program of the distinguished international ECCOMAS conference. It reflects state-of-the-art in the advances of multibody dynamics, providing excellent insight in the recen...
How to combine binary collision approximation and multi-body potential for molecular dynamics
International Nuclear Information System (INIS)
Saito, Seiki; Nakamura, Hiroaki; Takayama, Arimichi; Ito, Atsushi M.; Kenmotsu, Takahiro
2010-01-01
Our group has been developing a hybrid simulation of the molecular dynamics (MD) and the binary collision approximation (BCA) simulation. One of the main problems of this hybridization model is that the multi-body potential suddenly appears at the moment when the simulation method switches from the BCA to the MD. This instantaneously emerged multi-body potential causes the acceleration or deceleration of atoms of the system. To solve this problem, the kinetic energy of atoms should be corrected to conserve the total energy in the system. This paper gives the solution. The hybrid simulation for hydrogen atom injection into a graphite material is executed in order to demonstrate the solution. (author)
Multibody system dynamics, robotics and control
Gerstmayr, Johannes
2013-01-01
The volume contains 19 contributions by international experts in the field of multibody system dynamics, robotics and control. The book aims to bridge the gap between the modeling of mechanical systems by means of multibody dynamics formulations and robotics. In the classical approach, a multibody dynamics model contains a very high level of detail, however, the application of such models to robotics or control is usually limited. The papers aim to connect the different scientific communities in multibody dynamics, robotics and control. Main topics are flexible multibody systems, humanoid robots, elastic robots, nonlinear control, optimal path planning, and identification.
Numerical methods in multibody dynamics
Eich-Soellner, Edda
1998-01-01
Today computers play an important role in the development of complex mechanical systems, such as cars, railway vehicles or machines. Efficient simulation of these systems is only possible when based on methods that explore the strong link between numerics and computational mechanics. This book gives insight into modern techniques of numerical mathematics in the light of an interesting field of applications: multibody dynamics. The important interaction between modeling and solution techniques is demonstrated by using a simplified multibody model of a truck. Different versions of this mechanical model illustrate all key concepts in static and dynamic analysis as well as in parameter identification. The book focuses in particular on constrained mechanical systems. Their formulation in terms of differential-algebraic equations is the backbone of nearly all chapters. The book is written for students and teachers in numerical analysis and mechanical engineering as well as for engineers in industrial research labor...
Fu, Yao; Song, Jeong-Hoon
2014-08-01
Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.
ECCOMAS Thematic Conference on Multibody Dynamics
Multibody Dynamics : Computational Methods and Applications
2016-01-01
This book includes selected papers from the ECCOMAS Thematic Conference on Multibody Dynamics, that took place in Barcelona, Spain, from June 29 to July 2, 2015. By having its origin in analytical and continuum mechanics, as well as in computer science and applied mathematics, multibody dynamics provides a basis for analysis and virtual prototyping of innovative applications in many fields of contemporary engineering. With the utilization of computational models and algorithms that classically belonged to different fields of applied science, multibody dynamics delivers reliable simulation platforms for diverse highly-developed industrial products such as vehicle and railway systems, aeronautical and space vehicles, robotic manipulators, smart structures, biomechanical systems,and nanotechnologies.
ECCOMAS Thematic Conference on Multibody Dynamics
Fisette, Paul; Multibody Dynamics : Computational Methods and Applications
2013-01-01
This volume provides the international multibody dynamics community with an up-to-date view on the state of the art in this rapidly growing field of research which now plays a central role in the modeling, analysis, simulation and optimization of mechanical systems in a variety of fields and for a wide range of industrial applications. This book contains selected contributions delivered at the ECCOMAS Thematic Conference on Multibody Dynamics, which was held in Brussels, Belgium and organized by the Université catholique de Louvain, from 4th to 7th July 2011. Each paper reflects the State-of-Art in the application of Multibody Dynamics to different areas of engineering. They are enlarged and revised versions of the communications, which were enhanced in terms of self-containment and tutorial quality by the authors. The result is a comprehensive text that constitutes a valuable reference for researchers and design engineers which helps to appraise the potential for the application of multibody dynamics meth...
Planar multibody dynamics formulation, programming and applications
Nikravesh, Parviz E
2007-01-01
Introduction Multibody Mechanical Systems Types of Analyses Methods of Formulation Computer Programming Application Examples Unit System Remarks Preliminaries Reference Axes Scalars and Vectors Matrices Vector, Array, and Matrix Differentiation Equations and Expressions Remarks Problems Fundamentals of Kinematics A Particle Kinematics of a Rigid Body Definitions Remarks Problems Fundamentals of Dynamics Newton's Laws of Motion Dynamics of a Body Force Elements Applied Forces Reaction Force Remarks Problems Point-Coordinates: Kinematics Multipoint
Nonlinear Multibody Dynamics of Wind Turbines
DEFF Research Database (Denmark)
Holm-Jørgensen, Kristian
individually and next couple them by use of joints. This gives a high level of modelling flexibility, where parts of the structure with relative ease can be interchanged to analyze other possibilities in a design process, or if a higher detail level is wanted for some components. In a multibody formulation...... turbine blade with large nonlinear displacements it has shown most favorable to use the end points in the substructure for updating the moving frames. For speeding up dynamical simulations for use in e.g. active control or parameter studies, system reduction of substructures in the multibody formulation...... element parameters also can determine e.g. torsional stiffness and the position of the shear center. The method makes use of three node triangular elements where the different material layers in the blade profile are taken into consideration. The results are compared to a similar tool which makes use...
Elastic Multibody Dynamics A Direct Ritz Approach
Bremer, H
2008-01-01
This textbook is an introduction to and exploration of a number of core topics in the field of applied mechanics: On the basis of Lagrange's Principle, a Central Equation of Dynamics is presented which yields a unified view on existing methods. From these, the Projection Equation is selected for the derivation of the motion equations of holonomic and of non-holonomic systems. The method is applied to rigid multibody systems where the rigid body is defined such that, by relaxation of the rigidity constraints, one can directly proceed to elastic bodies. A decomposition into subsystems leads to a minimal representation and to a recursive representation, respectively, of the equations of motion. Applied to elastic multibody systems one obtains, along with the use of spatial operators, a straight-on procedure for the interconnected partial and ordinary differential equations and the corresponding boundary conditions. The spatial operators are eventually applied to a RITZ series for approximation. The resulting equ...
Developments of multibody system dynamics: computer simulations and experiments
International Nuclear Information System (INIS)
Yoo, Wan-Suk; Kim, Kee-Nam; Kim, Hyun-Woo; Sohn, Jeong-Hyun
2007-01-01
It is an exceptional success when multibody dynamics researchers Multibody System Dynamics journal one of the most highly ranked journals in the last 10 years. In the inaugural issue, Professor Schiehlen wrote an interesting article explaining the roots and perspectives of multibody system dynamics. Professor Shabana also wrote an interesting article to review developments in flexible multibody dynamics. The application possibilities of multibody system dynamics have grown wider and deeper, with many application examples being introduced with multibody techniques in the past 10 years. In this paper, the development of multibody dynamics is briefly reviewed and several applications of multibody dynamics are described according to the author's research results. Simulation examples are compared to physical experiments, which show reasonableness and accuracy of the multibody formulation applied to real problems. Computer simulations using the absolute nodal coordinate formulation (ANCF) were also compared to physical experiments; therefore, the validity of ANCF for large-displacement and large-deformation problems was shown. Physical experiments for large deformation problems include beam, plate, chain, and strip. Other research topics currently being carried out in the author's laboratory are also briefly explained
Constraint Embedding Technique for Multibody System Dynamics
Woo, Simon S.; Cheng, Michael K.
2011-01-01
Multibody dynamics play a critical role in simulation testbeds for space missions. There has been a considerable interest in the development of efficient computational algorithms for solving the dynamics of multibody systems. Mass matrix factorization and inversion techniques and the O(N) class of forward dynamics algorithms developed using a spatial operator algebra stand out as important breakthrough on this front. Techniques such as these provide the efficient algorithms and methods for the application and implementation of such multibody dynamics models. However, these methods are limited only to tree-topology multibody systems. Closed-chain topology systems require different techniques that are not as efficient or as broad as those for tree-topology systems. The closed-chain forward dynamics approach consists of treating the closed-chain topology as a tree-topology system subject to additional closure constraints. The resulting forward dynamics solution consists of: (a) ignoring the closure constraints and using the O(N) algorithm to solve for the free unconstrained accelerations for the system; (b) using the tree-topology solution to compute a correction force to enforce the closure constraints; and (c) correcting the unconstrained accelerations with correction accelerations resulting from the correction forces. This constraint-embedding technique shows how to use direct embedding to eliminate local closure-loops in the system and effectively convert the system back to a tree-topology system. At this point, standard tree-topology techniques can be brought to bear on the problem. The approach uses a spatial operator algebra approach to formulating the equations of motion. The operators are block-partitioned around the local body subgroups to convert them into aggregate bodies. Mass matrix operator factorization and inversion techniques are applied to the reformulated tree-topology system. Thus in essence, the new technique allows conversion of a system with
Simbody: multibody dynamics for biomedical research.
Sherman, Michael A; Seth, Ajay; Delp, Scott L
Multibody software designed for mechanical engineering has been successfully employed in biomedical research for many years. For real time operation some biomedical researchers have also adapted game physics engines. However, these tools were built for other purposes and do not fully address the needs of biomedical researchers using them to analyze the dynamics of biological structures and make clinically meaningful recommendations. We are addressing this problem through the development of an open source, extensible, high performance toolkit including a multibody mechanics library aimed at the needs of biomedical researchers. The resulting code, Simbody, supports research in a variety of fields including neuromuscular, prosthetic, and biomolecular simulation, and related research such as biologically-inspired design and control of humanoid robots and avatars. Simbody is the dynamics engine behind OpenSim, a widely used biomechanics simulation application. This article reviews issues that arise uniquely in biomedical research, and reports on the architecture, theory, and computational methods Simbody uses to address them. By addressing these needs explicitly Simbody provides a better match to the needs of researchers than can be obtained by adaptation of mechanical engineering or gaming codes. Simbody is a community resource, free for any purpose. We encourage wide adoption and invite contributions to the code base at https://simtk.org/home/simbody.
Constraint Embedding for Multibody System Dynamics
Jain, Abhinandan
2009-01-01
This paper describes a constraint embedding approach for the handling of local closure constraints in multibody system dynamics. The approach uses spatial operator techniques to eliminate local-loop constraints from the system and effectively convert the system into tree-topology systems. This approach allows the direct derivation of recursive O(N) techniques for solving the system dynamics and avoiding the expensive steps that would otherwise be required for handling the closedchain dynamics. The approach is very effective for systems where the constraints are confined to small-subgraphs within the system topology. The paper provides background on the spatial operator O(N) algorithms, the extensions for handling embedded constraints, and concludes with some examples of such constraints.
Nonlinear dynamic analysis of flexible multibody systems
Bauchau, Olivier A.; Kang, Nam Kook
1991-01-01
Two approaches are developed to analyze the dynamic behavior of flexible multibody systems. In the first approach each body is modeled with a modal methodology in a local non-inertial frame of reference, whereas in the second approach, each body is modeled with a finite element methodology in the inertial frame. In both cases, the interaction among the various elastic bodies is represented by constraint equations. The two approaches were compared for accuracy and efficiency: the first approach is preferable when the nonlinearities are not too strong but it becomes cumbersome and expensive to use when many modes must be used. The second approach is more general and easier to implement but could result in high computation costs for a large system. The constraints should be enforced in a time derivative fashion for better accuracy and stability.
Flexible joints in structural and multibody dynamics
Directory of Open Access Journals (Sweden)
O. A. Bauchau
2013-02-01
Full Text Available Flexible joints, sometimes called bushing elements or force elements, are found in all structural and multibody dynamics codes. In their simplest form, flexible joints simply consist of sets of three linear and three torsional springs placed between two nodes of the model. For infinitesimal deformations, the selection of the lumped spring constants is an easy task, which can be based on a numerical simulation of the joint or on experimental measurements. If the joint undergoes finite deformations, identification of its stiffness characteristics is not so simple, specially if the joint is itself a complex system. When finite deformations occur, the definition of deformation measures becomes a critical issue. This paper proposes a family of tensorial deformation measures suitable for elastic bodies of finite dimension. These families are generated by two parameters that can be used to modify the constitutive behavior of the joint, while maintaining the tensorial nature of the deformation measures. Numerical results demonstrate the objectivity of the deformations measures, a feature that is not shared by the deformations measures presently used in the literature. The impact of the choice of the two parameters on the constitutive behavior of the flexible joint is also investigated.
Validation of flexible multibody dynamics beam formulations using benchmark problems
Bauchau, O.A.; Wu, Genyong; Betsch, P.; Cardona, A.; Gerstmayr, J.; Jonker, Jan B.; Masarati, P.; Sonneville, V.
2016-01-01
As the need to model flexibility arose in multibody dynamics, the floating frame of reference formulation was developed, but this approach can yield inaccurate results when elastic displacements becomes large. While the use of three-dimensional finite element formulations overcomes this problem, the
System Theory Aspects of Multi-Body Dynamics.
1978-08-18
systems are described from a system theory point of view. Various system theory concepts and research topics which have applicability to this class of...systems are identified and briefly described. The subject of multi-body dynamics is presented in a vector space setting and is related to system theory concepts. (Author)
Multibody system dynamics and mechatronics. Plenary lecture
Energy Technology Data Exchange (ETDEWEB)
Hiller, M.H.; Hirsch, K. [Duisburg-Essen Univ., Duisburg (Germany). Faculty of Engineering
2006-02-15
Mechatronics as an interdisciplinary combination of domains of mechanical engineering, electrical engineering, electronics, and computer science has developed in industry and universities since the eighties of the last century, and it is meanwhile fully established in many technical areas. The main focus of the mechatronic approach is to extend and to complete the design process of mechanical and more general engineering systems by incorporating from the very beginning sensors and controllers - which includes also the required information processing - and thus being able to generate partly intelligent products. The components and modules of such systems originate from mechanical engineering, from electrical engineering or from other engineering domains. Methods for describing and designing these components and modules are based in the fields of applied mechanics, electrical engineering, system theory, control and automation theory, and information processing. In particular, in mechatronic systems like robots, manipulation systems, machine tools, or all kinds of vehicles, the multibody systems approach offers a powerful tool to model the mechanical properties of the system in an appropriate manner. In this paper, methodologies for the development of formalisms and software for modeling and simulation of multibody and mechatronic systems will be presented and illustrated by examples from automotive systems and robotics. (orig.)
Rigid multibody system dynamics with uncertain rigid bodies
Energy Technology Data Exchange (ETDEWEB)
Batou, A., E-mail: anas.batou@univ-paris-est.fr; Soize, C., E-mail: christian.soize@univ-paris-est.fr [Universite Paris-Est, Laboratoire Modelisation et Simulation Multi Echelle, MSME UMR 8208 CNRS (France)
2012-03-15
This paper is devoted to the construction of a probabilistic model of uncertain rigid bodies for multibody system dynamics. We first construct a stochastic model of an uncertain rigid body by replacing the mass, the center of mass, and the tensor of inertia by random variables. The prior probability distributions of the stochastic model are constructed using the maximum entropy principle under the constraints defined by the available information. The generators of independent realizations corresponding to the prior probability distribution of these random quantities are further developed. Then several uncertain rigid bodies can be linked to each other in order to calculate the random response of a multibody dynamical system. An application is proposed to illustrate the theoretical development.
Comparative multibody dynamics analysis of falls from playground climbing frames
Forero Rueda, Manuel A.; Gilchrist, M. D.
2009-01-01
This paper shows the utility of multibody dynamics in evaluating changes in injury related parameters of the head and lower limbs of children following falls from playground climbing frames. A particular fall case was used as a starting point to analyze the influence of surface properties, posture of the body at impact, and intermediate collisions against the climbing frame before impacting the ground. Simulations were made using the 6-year-old pedestrian MADYMO rigid body model and scaled he...
Dynamic analysis of multibody system immersed in a fluid medium
International Nuclear Information System (INIS)
Wu, R.W.; Liu, L.K.; Levy, S.
1977-01-01
This paper is concerned primarily with the development and evaluation of an analysis method for the reponse prediction of immersed systems to seismic and other dynamic excitations. For immersed multibody systems, the hydrodynamic interaction causes coupled motion among the solid bodies. Also, under intense external excitations, impact between bodies may occur. The complex character of such systems inhibit the use of conventional analytical solutions in closed form. Therefore, approximate numerical schemes have been devised. For an incompressible, inviscid fluid, the hydrodynamic forces exerted by the fluid on solid bodies are determined to be linearly proportional to the acceleration of the vibrating solid bodies; i.e., the presence of the fluid only affects the inertia of the solid body system. A finite element computer program has been developed for computing this hydrodynamic (or added) mass effect. This program can be used to determine the hydrodynamic mass of a two-dimensional fluid field with solid bodies of arbitrary geometry. Triangular elements and linear pressure interpolation function are used to discretize the fluid region. The component element method is used to determine the dynamic response of the multibody system to externally applied mechanical loading or support excitation. The present analysis method for predicting the dynamic response of submerged multibody system is quite general and pertains to any number of solid bodies. However in this paper, its application is demonstrated only for 4 and 25 body systems. (Auth.)
On the constraints violation in forward dynamics of multibody systems
Energy Technology Data Exchange (ETDEWEB)
Marques, Filipe [University of Minho, Department of Mechanical Engineering (Portugal); Souto, António P. [University of Minho, Department of Textile Engineering (Portugal); Flores, Paulo, E-mail: pflores@dem.uminho.pt [University of Minho, Department of Mechanical Engineering (Portugal)
2017-04-15
It is known that the dynamic equations of motion for constrained mechanical multibody systems are frequently formulated using the Newton–Euler’s approach, which is augmented with the acceleration constraint equations. This formulation results in the establishment of a mixed set of partial differential and algebraic equations, which are solved in order to predict the dynamic behavior of general multibody systems. The classical solution of the equations of motion is highly prone to constraints violation because the position and velocity constraint equations are not fulfilled. In this work, a general and comprehensive methodology to eliminate the constraints violation at the position and velocity levels is offered. The basic idea of the described approach is to add corrective terms to the position and velocity vectors with the intent to satisfy the corresponding kinematic constraint equations. These corrective terms are evaluated as a function of the Moore–Penrose generalized inverse of the Jacobian matrix and of the kinematic constraint equations. The described methodology is embedded in the standard method to solve the equations of motion based on the technique of Lagrange multipliers. Finally, the effectiveness of the described methodology is demonstrated through the dynamic modeling and simulation of different planar and spatial multibody systems. The outcomes in terms of constraints violation at the position and velocity levels, conservation of the total energy and computational efficiency are analyzed and compared with those obtained with the standard Lagrange multipliers method, the Baumgarte stabilization method, the augmented Lagrangian formulation, the index-1 augmented Lagrangian, and the coordinate partitioning method.
Linked-List-Based Multibody Dynamics (MBDyn) Engine
MacLean, John; Brain, Thomas; Wuiocho, Leslie; Huynh, An; Ghosh, Tushar
2012-01-01
This new release of MBDyn is a software engine that calculates the dynamics states of kinematic, rigid, or flexible multibody systems. An MBDyn multibody system may consist of multiple groups of articulated chains, trees, or closed-loop topologies. Transient topologies are handled through conservation of energy and momentum. The solution for rigid-body systems is exact, and several configurable levels of nonlinear term fidelity are available for flexible dynamics systems. The algorithms have been optimized for efficiency and can be used for both non-real-time (NRT) and real-time (RT) simulations. Interfaces are currently compatible with NASA's Trick Simulation Environment. This new release represents a significant advance in capability and ease of use. The two most significant new additions are an application programming interface (API) that clarifies and simplifies use of MBDyn, and a link-list infrastructure that allows a single MBDyn instance to propagate an arbitrary number of interacting groups of multibody top ologies. MBDyn calculates state and state derivative vectors for integration using an external integration routine. A Trickcompatible interface is provided for initialization, data logging, integration, and input/output.
Roller-chain Drives Mechanics using Multibody Dynamics Tools
DEFF Research Database (Denmark)
Ambrosio, Jorge A. C.; Hansen, John Michael
1999-01-01
An integrated model for the simulation of roller-chain drives based on a multibody dynamics methodology is presented here in order to describeits complex dynamic behavior. The chain is modeled by masses lumped at the roller locations and connected by translational spring-damper elements in order ...... engagement on the sprockets responsible for the polygonal effect is thoroughly analyzed and the induced impulsive forces developed during that action are treated by a strategy where kinematic constraints between sprockets and rollers are added and deleted....
System Reduction in Nonlinear Multibody Dynamics of Wind Turbines
DEFF Research Database (Denmark)
Holm-Jørgensen, Kristian; Nielsen, Søren R.K.; Rubak, Rune
2007-01-01
In this paper the system reduction in nonlinear multibody dynamics of wind turbines is investigated for various updating schemes of the moving frame of reference. In one case, the moving frame of reference is updated to a stiff body, relative to which the elastic deformations are fixed at one end....... In the other case, the stiff body motion is defined as the chord line connecting the end points of the beam, and the elastic deformations are simply supported at the end points. The system reduction is performed by discretizing the spatial motion into a set of rigid body modes and linear elastic eigenmodes...
General background and approach to multibody dynamics for space applications
Santini, Paolo; Gasbarri, Paolo
2009-06-01
Multibody dynamics for space applications is dictated by space environment such as space-varying gravity forces, orbital and attitude perturbations, control forces if any. Several methods and formulations devoted to the modeling of flexible bodies undergoing large overall motions were developed in recent years. Most of these different formulations were aimed to face one of the main problems concerning the analysis of spacecraft dynamics namely the reduction of computer simulation time. By virtue of this, the use of symbolic manipulation, recursive formulation and parallel processing algorithms were proposed. All these approaches fall into two categories, the one based on Newton/Euler methods and the one based on Lagrangian methods; both of them have their advantages and disadvantages although in general, Newtonian approaches lend to a better understanding of the physics of problems and in particular of the magnitude of the reactions and of the corresponding structural stresses. Another important issue which must be addressed carefully in multibody space dynamics is relevant to a correct choice of kinematics variables. In fact, when dealing with flexible multibody system the resulting equations include two different types of state variables, the ones associated with large (rigid) displacements and the ones associated with elastic deformations. These two sets of variables have generally two different time scales if we think of the attitude motion of a satellite whose period of oscillation, due to the gravity gradient effects, is of the same order of magnitude as the orbital period, which is much bigger than the one associated with the structural vibration of the satellite itself. Therefore, the numerical integration of the equations of the system represents a challenging problem. This was the abstract and some of the arguments that Professor Paolo Santini intended to present for the Breakwell Lecture; unfortunately a deadly disease attacked him and shortly took him
Validation of flexible multibody dynamics beam formulations using benchmark problems
Energy Technology Data Exchange (ETDEWEB)
Bauchau, Olivier A., E-mail: obauchau@umd.edu [University of Maryland (United States); Betsch, Peter [Karlsruhe Institute of Technology (Germany); Cardona, Alberto [CIMEC (UNL/Conicet) (Argentina); Gerstmayr, Johannes [Leopold-Franzens Universität Innsbruck (Austria); Jonker, Ben [University of Twente (Netherlands); Masarati, Pierangelo [Politecnico di Milano (Italy); Sonneville, Valentin [Université de Liège (Belgium)
2016-05-15
As the need to model flexibility arose in multibody dynamics, the floating frame of reference formulation was developed, but this approach can yield inaccurate results when elastic displacements becomes large. While the use of three-dimensional finite element formulations overcomes this problem, the associated computational cost is overwhelming. Consequently, beam models, which are one-dimensional approximations of three-dimensional elasticity, have become the workhorse of many flexible multibody dynamics codes. Numerous beam formulations have been proposed, such as the geometrically exact beam formulation or the absolute nodal coordinate formulation, to name just two. New solution strategies have been investigated as well, including the intrinsic beam formulation or the DAE approach. This paper provides a systematic comparison of these various approaches, which will be assessed by comparing their predictions for four benchmark problems. The first problem is the Princeton beam experiment, a study of the static large displacement and rotation behavior of a simple cantilevered beam under a gravity tip load. The second problem, the four-bar mechanism, focuses on a flexible mechanism involving beams and revolute joints. The third problem investigates the behavior of a beam bent in its plane of greatest flexural rigidity, resulting in lateral buckling when a critical value of the transverse load is reached. The last problem investigates the dynamic stability of a rotating shaft. The predictions of eight independent codes are compared for these four benchmark problems and are found to be in close agreement with each other and with experimental measurements, when available.
Dynamics of Multibody Systems Near Lagrangian Points
Wong, Brian
This thesis examines the dynamics of a physically connected multi-spacecraft system in the vicinity of the Lagrangian points of a Circular Restricted Three-Body System. The spacecraft system is arranged in a wheel-spoke configuration with smaller and less massive satellites connected to a central hub using truss/beams or tether connectors. The kinematics of the system is first defined, and the kinetic, gravitational potential energy and elastic potential energy of the system are derived. The Assumed Modes Method is used to discretize the continuous variables of the system, and a general set of ordinary differential equations describing the dynamics of the connectors and the central hub are obtained using the Lagrangian method. The flexible body dynamics of the tethered and truss connected systems are examined using numerical simulations. The results show that these systems experienced only small elastic deflections when they are naturally librating or rotating at moderate angular velocities, and these deflections have relatively small effect on the attitude dynamics of the systems. Based on these results, it is determined that the connectors can be modeled as rigid when only the attitude dynamics of the system is of interest. The equations of motion of rigid satellites stationed at the Lagrangian points are linearized, and the stability conditions of the satellite are obtained from the linear equations. The required conditions are shown to be similar to those of geocentric satellites. Study of the linear equations also revealed the resonant conditions of rigid Lagrangian point satellites, when a librational natural frequency of the satellite matches the frequency of its station-keeping orbit leading to large attitude motions. For tethered satellites, the linear analysis shows that the tethers are in stable equilibrium when they lie along a line joining the two primary celestial bodies of the Three-Body System. Numerical simulations are used to study the long term
Dynamic multibody modeling for tethered space elevators
Williams, Paul
2009-08-01
This paper presents a fundamental modeling strategy for dealing with powered and propelled bodies moving along space tethers. The tether is divided into a large number of discrete masses, which are connected by viscoelastic springs. The tether is subject to the full range of forces expected in Earth orbit in a relatively simple manner. Two different models of the elevator dynamics are presented. In order to capture the effect of the elevator moving along the tether, the elevator dynamics are included as a separate body in both models. One model treats the elevator's motion dynamically, where propulsive and friction forces are applied to the elevator body. The second model treats the elevator's motion kinematically, where the distance along the tether is determined by adjusting the lengths of tether on either side of the elevator. The tether model is used to determine optimal configurations for the space elevator. A modal analysis of two different configurations is presented which show that the fundamental mode of oscillation is a pendular one around the anchor point with a period on the order of 160 h for the in-plane motion, and 24 h for the out-of-plane motion. Numerical simulation results of the effects of the elevator moving along the cable are presented for different travel velocities and different elevator masses.
System Reduction in Multibody Dynamics of Wind Turbines
DEFF Research Database (Denmark)
Holm-Jørgensen, Kristian; Nielsen, Søren R.K.
2009-01-01
Abstract A system reduction scheme is devised related to a multibody formulation from which the dynamic response of a wind turbine is determined. In this formulation each substructure is described in its own frame of reference, which is moving freely in the vicinity of the moving substructure....... The Ritz bases spanning the reduced system comprises of rigid body modes and some dynamic low-frequency elastic eigenmodes compatible to the kinematic constraints of the related substructure. The high-frequency elastic modes are presumed to cause merely quasi-static displacements, and thus are included...... in the expansion via a quasi-static correction. The results show that by using the derived reduction scheme it is only necessary with 2 dynamical modes for the blade substructure when the remaining modes are treated as quasi-static. Moreover, it is shown that it has little to none effect if the gyroscopic...
Comparative multibody dynamics analysis of falls from playground climbing frames.
Forero Rueda, M A; Gilchrist, M D
2009-10-30
This paper shows the utility of multibody dynamics in evaluating changes in injury related parameters of the head and lower limbs of children following falls from playground climbing frames. A particular fall case was used as a starting point to analyze the influence of surface properties, posture of the body at impact, and intermediate collisions against the climbing frame before impacting the ground. Simulations were made using the 6-year-old pedestrian MADYMO rigid body model and scaled head contact characteristics. Energy absorbing surfaces were shown to reduce injury severity parameters by up to 30-80% of those of rigid surfaces, depending on impact posture and surface. Collisions against components of a climbing frame during a fall can increase injury severity of the final impact of the head with the ground by more than 90%. Negligible changes are associated with lower limb injury risks when different surfacing materials are used. Computer reconstructions of actual falls that are intended to quantify the severity of physical injuries rely on accurate knowledge of initial conditions prior to falling, intermediate kinematics of the fall and the orientation of the body when it impacts against the ground. Multibody modelling proved to be a valuable tool to analyze the quality of eyewitness information and analyze the relative injury risk associated with changes in components influencing fall injuries from playground climbing frames. Such simulations can also support forensic investigations by evaluating alternative hypotheses for the sequence of kinematic motion of falls which result in known injuries.
Evaluation of constraint stabilization procedures for multibody dynamical systems
Park, K. C.; Chiou, J. C.
1987-01-01
Comparative numerical studies of four constraint treatment techniques for the simulation of general multibody dynamic systems are presented, and results are presented for the example of a classical crank mechanism and for a simplified version of the seven-link manipulator deployment problem. The staggered stabilization technique (Park, 1986) is found to yield improved accuracy and robustness over Baumgarte's (1972) technique, the singular decomposition technique (Walton and Steeves, 1969), and the penalty technique (Lotstedt, 1979). Furthermore, the staggered stabilization technique offers software modularity, and the only data each solution module needs to exchange with the other is a set of vectors plus a common module to generate the gradient matrix of the constraints, B.
Dynamics of underactuated multibody systems modeling, control and optimal design
Seifried, Robert
2014-01-01
Underactuated multibody systems are intriguing mechatronic systems, as they possess fewer control inputs than degrees of freedom. Some examples are modern light-weight flexible robots and articulated manipulators with passive joints. This book investigates such underactuated multibody systems from an integrated perspective. This includes all major steps from the modeling of rigid and flexible multibody systems, through nonlinear control theory, to optimal system design. The underlying theories and techniques from these different fields are presented using a self-contained and unified approach and notation system. Subsequently, the book focuses on applications to large multibody systems with multiple degrees of freedom, which require a combination of symbolical and numerical procedures. Finally, an integrated, optimization-based design procedure is proposed, whereby both structural and control design are considered concurrently. Each chapter is supplemented by illustrated examples.
Directory of Open Access Journals (Sweden)
Sol Ha
2016-01-01
Full Text Available This paper suggests an event-based scenario manager capable of creating and editing a scenario for shipbuilding process simulation based on multibody dynamics. To configure various situation in shipyards and easily connect with multibody dynamics, the proposed method has two main concepts: an Actor and an Action List. The Actor represents the anatomic unit of action in the multibody dynamics and can be connected to a specific component of the dynamics kernel such as the body and joint. The user can make a scenario up by combining the actors. The Action List contains information for arranging and executing the actors. Since the shipbuilding process is a kind of event-based sequence, all simulation models were configured using Discrete EVent System Specification (DEVS formalism. The proposed method was applied to simulations of various operations in shipyards such as lifting and erection of a block and heavy load lifting operation using multiple cranes.
Structure-preserving integrators in nonlinear structural dynamics and flexible multibody dynamics
2016-01-01
This book focuses on structure-preserving numerical methods for flexible multibody dynamics, including nonlinear elastodynamics and geometrically exact models for beams and shells. It also deals with the newly emerging class of variational integrators as well as Lie-group integrators. It discusses two alternative approaches to the discretization in space of nonlinear beams and shells. Firstly, geometrically exact formulations, which are typically used in the finite element community and, secondly, the absolute nodal coordinate formulation, which is popular in the multibody dynamics community. Concerning the discretization in time, the energy-momentum method and its energy-decaying variants are discussed. It also addresses a number of issues that have arisen in the wake of the structure-preserving discretization in space. Among them are the parameterization of finite rotations, the incorporation of algebraic constraints and the computer implementation of the various numerical methods. The practical application...
Evolution of the DeNOC-based dynamic modelling for multibody systems
Directory of Open Access Journals (Sweden)
S. K. Saha
2013-01-01
Full Text Available Dynamic modelling of a multibody system plays very essential role in its analyses. As a result, several methods for dynamic modelling have evolved over the years that allow one to analyse multibody systems in a very efficient manner. One such method of dynamic modelling is based on the concept of the Decoupled Natural Orthogonal Complement (DeNOC matrices. The DeNOC-based methodology for dynamics modelling, since its introduction in 1995, has been applied to a variety of multibody systems such as serial, parallel, general closed-loop, flexible, legged, cam-follower, and space robots. The methodology has also proven useful for modelling of proteins and hyper-degree-of-freedom systems like ropes, chains, etc. This paper captures the evolution of the DeNOC-based dynamic modelling applied to different type of systems, and its benefits over other existing methodologies. It is shown that the DeNOC-based modelling provides deeper understanding of the dynamics of a multibody system. The power of the DeNOC-based modelling has been illustrated using several numerical examples.
Advances in Chimera Grid Tools for Multi-Body Dynamics Simulations and Script Creation
Chan, William M.
2004-01-01
This viewgraph presentation contains information about (1) Framework for multi-body dynamics - Geometry Manipulation Protocol (GMP), (2) Simulation procedure using Chimera Grid Tools (CGT) and OVERFLOW-2 (3) Further recent developments in Chimera Grid Tools OVERGRID, Grid modules, Script library and (4) Future work.
DEFF Research Database (Denmark)
Damkjær, Jesper; Erleben, Kenny
2009-01-01
and a simultaneous descend in the tandem traversal. The data structure design and traversal are highly specialized for exploiting the parallel threads in the NVIDIA GPUs. As proof-of-concept we demonstrate a GPU implementation for a multibody dynamics simulation, showing an approximate speedup factor of up to 8...
Flight Loads Prediction of High Aspect Ratio Wing Aircraft Using Multibody Dynamics
Directory of Open Access Journals (Sweden)
Michele Castellani
2016-01-01
Full Text Available A framework based on multibody dynamics has been developed for the static and dynamic aeroelastic analyses of flexible high aspect ratio wing aircraft subject to structural geometric nonlinearities. Multibody dynamics allows kinematic nonlinearities and nonlinear relationships in the forces definition and is an efficient and promising methodology to model high aspect ratio wings, which are known to be prone to structural nonlinear effects because of the high deflections in flight. The multibody dynamics framework developed employs quasi-steady aerodynamics strip theory and discretizes the wing as a series of rigid bodies interconnected by beam elements, representative of the stiffness distribution, which can undergo arbitrarily large displacements and rotations. The method is applied to a flexible high aspect ratio wing commercial aircraft and both trim and gust response analyses are performed in order to calculate flight loads. These results are then compared to those obtained with the standard linear aeroelastic approach provided by the Finite Element Solver Nastran. Nonlinear effects come into play mainly because of the need of taking into account the large deflections of the wing for flight loads computation and of considering the aerodynamic forces as follower forces.
Simulating coupled dynamics of a rigid-flexible multibody system and compressible fluid
Hu, Wei; Tian, Qiang; Hu, HaiYan
2018-04-01
As a subsequent work of previous studies of authors, a new parallel computation approach is proposed to simulate the coupled dynamics of a rigid-flexible multibody system and compressible fluid. In this approach, the smoothed particle hydrodynamics (SPH) method is used to model the compressible fluid, the natural coordinate formulation (NCF) and absolute nodal coordinate formulation (ANCF) are used to model the rigid and flexible bodies, respectively. In order to model the compressible fluid properly and efficiently via SPH method, three measures are taken as follows. The first is to use the Riemann solver to cope with the fluid compressibility, the second is to define virtual particles of SPH to model the dynamic interaction between the fluid and the multibody system, and the third is to impose the boundary conditions of periodical inflow and outflow to reduce the number of SPH particles involved in the computation process. Afterwards, a parallel computation strategy is proposed based on the graphics processing unit (GPU) to detect the neighboring SPH particles and to solve the dynamic equations of SPH particles in order to improve the computation efficiency. Meanwhile, the generalized-alpha algorithm is used to solve the dynamic equations of the multibody system. Finally, four case studies are given to validate the proposed parallel computation approach.
A Component Mode Synthesis Algorithm for Multibody Dynamics of Wind Turbines
DEFF Research Database (Denmark)
Holm-Jørgensen, Kristian; Nielsen, Søren R.K.
2009-01-01
A system reduction scheme related to a multibody formulation of wind turbine dynamics is devised. Each substructure is described in its own frame of reference, which is moving freely in the vicinity of the moving substructure, in principle without any constraints to the rigid body part of the mot......A system reduction scheme related to a multibody formulation of wind turbine dynamics is devised. Each substructure is described in its own frame of reference, which is moving freely in the vicinity of the moving substructure, in principle without any constraints to the rigid body part...... of the motion of the substructure. The system reduction is based on a component mode synthesis method, where the response of the internal degrees of freedom of the substructure is described as the quasi-static response induced by the boundary degrees of freedom via the constraint modes superimposed...
Directory of Open Access Journals (Sweden)
Polach P.
2008-11-01
Full Text Available Vertical dynamic properties of the ŠKODA 21 Tr low-floor trolleybus were investigated on an artificial test track when driving with a real vehicle and when simulating driving with a multibody model along a virtual test track. Driving along the artificial test track was aimed to determine vertical dynamic properties of the real trolleybus and on the basis of them to verify computer trolleybus models. Time histories and extreme values of the air springs relative deflections are the monitored quantities. Due to differences of the experiments and the computer simulations results the influences of the characteristics of the spring-damper structural elements of the axles suspension and the radial characteristics of the tires used in the trolleybus multibody model on the extreme values of the monitored quantities are evaluated.
Experimental validation of flexible multibody dynamics beam formulations
Energy Technology Data Exchange (ETDEWEB)
Bauchau, Olivier A., E-mail: olivier.bauchau@sjtu.edu.cn; Han, Shilei [University of Michigan-Shanghai Jiao Tong University Joint Institute (China); Mikkola, Aki; Matikainen, Marko K. [Lappeenranta University of Technology, Department of Mechanical Engineering (Finland); Gruber, Peter [Austrian Center of Competence in Mechatronics GmbH (Austria)
2015-08-15
In this paper, the accuracies of the geometrically exact beam and absolute nodal coordinate formulations are studied by comparing their predictions against an experimental data set referred to as the “Princeton beam experiment.” The experiment deals with a cantilevered beam experiencing coupled flap, lag, and twist deformations. In the absolute nodal coordinate formulation, two different beam elements are used. The first is based on a shear deformable approach in which the element kinematics is described using two nodes. The second is based on a recently proposed approach featuring three nodes. The numerical results for the geometrically exact beam formulation and the recently proposed three-node absolute nodal coordinate formulation agree well with the experimental data. The two-node beam element predictions are similar to those of linear beam theory. This study suggests that a careful and thorough evaluation of beam elements must be carried out to assess their ability to deal with the three-dimensional deformations typically found in flexible multibody systems.
Masticatory biomechanics in the rabbit: a multi-body dynamics analysis.
Watson, Peter J; Gröning, Flora; Curtis, Neil; Fitton, Laura C; Herrel, Anthony; McCormack, Steven W; Fagan, Michael J
2014-10-06
Multi-body dynamics is a powerful engineering tool which is becoming increasingly popular for the simulation and analysis of skull biomechanics. This paper presents the first application of multi-body dynamics to analyse the biomechanics of the rabbit skull. A model has been constructed through the combination of manual dissection and three-dimensional imaging techniques (magnetic resonance imaging and micro-computed tomography). Individual muscles are represented with multiple layers, thus more accurately modelling muscle fibres with complex lines of action. Model validity was sought through comparing experimentally measured maximum incisor bite forces with those predicted by the model. Simulations of molar biting highlighted the ability of the masticatory system to alter recruitment of two muscle groups, in order to generate shearing or crushing movements. Molar shearing is capable of processing a food bolus in all three orthogonal directions, whereas molar crushing and incisor biting are predominately directed vertically. Simulations also show that the masticatory system is adapted to process foods through several cycles with low muscle activations, presumably in order to prevent rapidly fatiguing fast fibres during repeated chewing cycles. Our study demonstrates the usefulness of a validated multi-body dynamics model for investigating feeding biomechanics in the rabbit, and shows the potential for complementing and eventually reducing in vivo experiments.
Online Kinematic and Dynamic-State Estimation for Constrained Multibody Systems Based on IMUs
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José Luis Torres-Moreno
2016-03-01
Full Text Available This article addresses the problems of online estimations of kinematic and dynamic states of a mechanism from a sequence of noisy measurements. In particular, we focus on a planar four-bar linkage equipped with inertial measurement units (IMUs. Firstly, we describe how the position, velocity, and acceleration of all parts of the mechanism can be derived from IMU signals by means of multibody kinematics. Next, we propose the novel idea of integrating the generic multibody dynamic equations into two variants of Kalman filtering, i.e., the extended Kalman filter (EKF and the unscented Kalman filter (UKF, in a way that enables us to handle closed-loop, constrained mechanisms, whose state space variables are not independent and would normally prevent the direct use of such estimators. The proposal in this work is to apply those estimators over the manifolds of allowed positions and velocities, by means of estimating a subset of independent coordinates only. The proposed techniques are experimentally validated on a testbed equipped with encoders as a means of establishing the ground-truth. Estimators are run online in real-time, a feature not matched by any previous procedure of those reported in the literature on multibody dynamics.
Online Kinematic and Dynamic-State Estimation for Constrained Multibody Systems Based on IMUs
Torres-Moreno, José Luis; Blanco-Claraco, José Luis; Giménez-Fernández, Antonio; Sanjurjo, Emilio; Naya, Miguel Ángel
2016-01-01
This article addresses the problems of online estimations of kinematic and dynamic states of a mechanism from a sequence of noisy measurements. In particular, we focus on a planar four-bar linkage equipped with inertial measurement units (IMUs). Firstly, we describe how the position, velocity, and acceleration of all parts of the mechanism can be derived from IMU signals by means of multibody kinematics. Next, we propose the novel idea of integrating the generic multibody dynamic equations into two variants of Kalman filtering, i.e., the extended Kalman filter (EKF) and the unscented Kalman filter (UKF), in a way that enables us to handle closed-loop, constrained mechanisms, whose state space variables are not independent and would normally prevent the direct use of such estimators. The proposal in this work is to apply those estimators over the manifolds of allowed positions and velocities, by means of estimating a subset of independent coordinates only. The proposed techniques are experimentally validated on a testbed equipped with encoders as a means of establishing the ground-truth. Estimators are run online in real-time, a feature not matched by any previous procedure of those reported in the literature on multibody dynamics. PMID:26959027
Partition method and experimental validation for impact dynamics of flexible multibody system
Wang, J. Y.; Liu, Z. Y.; Hong, J. Z.
2018-06-01
The impact problem of a flexible multibody system is a non-smooth, high-transient, and strong-nonlinear dynamic process with variable boundary. How to model the contact/impact process accurately and efficiently is one of the main difficulties in many engineering applications. The numerical approaches being used widely in impact analysis are mainly from two fields: multibody system dynamics (MBS) and computational solid mechanics (CSM). Approaches based on MBS provide a more efficient yet less accurate analysis of the contact/impact problems, while approaches based on CSM are well suited for particularly high accuracy needs, yet require very high computational effort. To bridge the gap between accuracy and efficiency in the dynamic simulation of a flexible multibody system with contacts/impacts, a partition method is presented considering that the contact body is divided into two parts, an impact region and a non-impact region. The impact region is modeled using the finite element method to guarantee the local accuracy, while the non-impact region is modeled using the modal reduction approach to raise the global efficiency. A three-dimensional rod-plate impact experiment is designed and performed to validate the numerical results. The principle for how to partition the contact bodies is proposed: the maximum radius of the impact region can be estimated by an analytical method, and the modal truncation orders of the non-impact region can be estimated by the highest frequency of the signal measured. The simulation results using the presented method are in good agreement with the experimental results. It shows that this method is an effective formulation considering both accuracy and efficiency. Moreover, a more complicated multibody impact problem of a crank slider mechanism is investigated to strengthen this conclusion.
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Gerardo Peláez
2018-06-01
Full Text Available Input shaping is an Optimal Control feedforward strategy whose ability to define how and when a flexible dynamical system defined by Ordinary Differential Equations (ODEs and computer controlled would move into its operative space, without command induced unwanted dynamics, has been exhaustively demonstrated. This work examines the issue of Embedded Internet of Things (IoT Input Shaping with regard to real time control of multibody oscillatory systems whose dynamics are better described by differential algebraic equations (DAEs. An overhead crane hanging a double link multibody payload has been appointed as a benchmark case; it is a multibody, multimode system. This might be worst scenario to implement Input Shaping. The reasons can be found in the wide array of constraints that arise. Firstly, the reliability of the multibody model was tested on a Functional Mock-Up Interface (FMI with the two link payload suspended from the trolley by comparing the experimental video tapping signals in time domain faced with the signals extracted from the multibody model. The FFTs of the simulated and the experimental signal contain the same frequency harmonics only with somewhat different power due to the real world light damping in the joints. The application of this approach may be extended to other cases i.e., the usefulness of mobile hydraulic cranes is limited because the payload is supported by an overhead cable under tension that allows oscillation to occur during crane motion. If the payload size is not negligible small when compared with the cable length may introduce an additional oscillatory mode that creates a multibody double pendulum. To give the insight into the double pendulum dynamics by Lagrangian methods two slender rods as payloads are analyzed dealing with the overhead crane and a composite revolute-revolute joint is proposed to model the cable of the hydraulic crane, both assumptions facilitates an affordable analysis. This allows
Peláez, Gerardo; Vaugan, Joshua; Izquierdo, Pablo; Rubio, Higinio; García-Prada, Juan Carlos
2018-06-04
Input shaping is an Optimal Control feedforward strategy whose ability to define how and when a flexible dynamical system defined by Ordinary Differential Equations (ODEs) and computer controlled would move into its operative space, without command induced unwanted dynamics, has been exhaustively demonstrated. This work examines the issue of Embedded Internet of Things (IoT) Input Shaping with regard to real time control of multibody oscillatory systems whose dynamics are better described by differential algebraic equations (DAEs). An overhead crane hanging a double link multibody payload has been appointed as a benchmark case; it is a multibody, multimode system. This might be worst scenario to implement Input Shaping. The reasons can be found in the wide array of constraints that arise. Firstly, the reliability of the multibody model was tested on a Functional Mock-Up Interface (FMI) with the two link payload suspended from the trolley by comparing the experimental video tapping signals in time domain faced with the signals extracted from the multibody model. The FFTs of the simulated and the experimental signal contain the same frequency harmonics only with somewhat different power due to the real world light damping in the joints. The application of this approach may be extended to other cases i.e., the usefulness of mobile hydraulic cranes is limited because the payload is supported by an overhead cable under tension that allows oscillation to occur during crane motion. If the payload size is not negligible small when compared with the cable length may introduce an additional oscillatory mode that creates a multibody double pendulum. To give the insight into the double pendulum dynamics by Lagrangian methods two slender rods as payloads are analyzed dealing with the overhead crane and a composite revolute-revolute joint is proposed to model the cable of the hydraulic crane, both assumptions facilitates an affordable analysis. This allows developing a general
Schilder, J.; Ellenbroek, M.; de Boer, A.
2017-12-01
In this work, the floating frame of reference formulation is used to create a flexible multibody model of slender offshore structures such as pipelines and risers. It is shown that due to the chain-like topology of the considered structures, the equation of motion can be expressed in terms of absolute interface coordinates. In the presented form, kinematic constraint equations are satisfied explicitly and the Lagrange multipliers are eliminated from the equations. Hence, the structures can be conveniently coupled to finite element or multibody models of for example seabed and vessel. The chain-like topology enables the efficient use of recursive solution procedures for both transient dynamic analysis and equilibrium analysis. For this, the transfer matrix method is used. In order to improve the convergence of the equilibrium analysis, the analytical solution of an ideal catenary is used as an initial configuration, reducing the number of required iterations.
Meng, Luming; Sheong, Fu Kit; Zeng, Xiangze; Zhu, Lizhe; Huang, Xuhui
2017-07-01
Constructing Markov state models from large-scale molecular dynamics simulation trajectories is a promising approach to dissect the kinetic mechanisms of complex chemical and biological processes. Combined with transition path theory, Markov state models can be applied to identify all pathways connecting any conformational states of interest. However, the identified pathways can be too complex to comprehend, especially for multi-body processes where numerous parallel pathways with comparable flux probability often coexist. Here, we have developed a path lumping method to group these parallel pathways into metastable path channels for analysis. We define the similarity between two pathways as the intercrossing flux between them and then apply the spectral clustering algorithm to lump these pathways into groups. We demonstrate the power of our method by applying it to two systems: a 2D-potential consisting of four metastable energy channels and the hydrophobic collapse process of two hydrophobic molecules. In both cases, our algorithm successfully reveals the metastable path channels. We expect this path lumping algorithm to be a promising tool for revealing unprecedented insights into the kinetic mechanisms of complex multi-body processes.
Multibody dynamic analysis using a rotation-free shell element with corotational frame
Shi, Jiabei; Liu, Zhuyong; Hong, Jiazhen
2018-03-01
Rotation-free shell formulation is a simple and effective method to model a shell with large deformation. Moreover, it can be compatible with the existing theories of finite element method. However, a rotation-free shell is seldom employed in multibody systems. Using a derivative of rigid body motion, an efficient nonlinear shell model is proposed based on the rotation-free shell element and corotational frame. The bending and membrane strains of the shell have been simplified by isolating deformational displacements from the detailed description of rigid body motion. The consistent stiffness matrix can be obtained easily in this form of shell model. To model the multibody system consisting of the presented shells, joint kinematic constraints including translational and rotational constraints are deduced in the context of geometric nonlinear rotation-free element. A simple node-to-surface contact discretization and penalty method are adopted for contacts between shells. A series of analyses for multibody system dynamics are presented to validate the proposed formulation. Furthermore, the deployment of a large scaled solar array is presented to verify the comprehensive performance of the nonlinear shell model.
Biomechanical Analysis and Evaluation Technology Using Human Multi-Body Dynamic Model
Energy Technology Data Exchange (ETDEWEB)
Kim, Yoon Hyuk; Shin, June Ho; Khurelbaatar, Tsolmonbaatar [Kyung Hee University, Yongin (Korea, Republic of)
2011-10-15
This paper presents the biomechanical analysis and evaluation technology of musculoskeletal system by multi-body human dynamic model and 3-D motion capture data. First, medical image based geometric model and material properties of tissue were used to develop the human dynamic model and 3-D motion capture data based motion analysis techniques were develop to quantify the in-vivo joint kinematics, joint moment, joint force, and muscle force. Walking and push-up motion was investigated using the developed model. The present model and technologies would be useful to apply the biomechanical analysis and evaluation of human activities.
Applied dynamics with applications to multibody and mechatronic systems
Moon, Francis C
1998-01-01
Applied Dynamics provides a modern and thorough examination of dynamics with specific emphasis on physical examples and applications such as: robotic systems, magnetic bearings, aerospace dynamics, and microelectromagnetic machines. Also includes the development of the method of virtual velocities based on the principle of virtual power
Evolution of Flexible Multibody Dynamics for Simulation Applications Supporting Human Spaceflight
Huynh, An; Brain, Thomas A.; MacLean, John R.; Quiocho, Leslie J.
2016-01-01
During the course of transition from the Space Shuttle and International Space Station programs to the Orion and Journey to Mars exploration programs, a generic flexible multibody dynamics formulation and associated software implementation has evolved to meet an ever changing set of requirements at the NASA Johnson Space Center (JSC). Challenging problems related to large transitional topologies and robotic free-flyer vehicle capture/ release, contact dynamics, and exploration missions concept evaluation through simulation (e.g., asteroid surface operations) have driven this continued development. Coupled with this need is the requirement to oftentimes support human spaceflight operations in real-time. Moreover, it has been desirable to allow even more rapid prototyping of on-orbit manipulator and spacecraft systems, to support less complex infrastructure software for massively integrated simulations, to yield further computational efficiencies, and to take advantage of recent advances and availability of multi-core computing platforms. Since engineering analysis, procedures development, and crew familiarity/training for human spaceflight is fundamental to JSC's charter, there is also a strong desire to share and reuse models in both the non-realtime and real-time domains, with the goal of retaining as much multibody dynamics fidelity as possible. Three specific enhancements are reviewed here: (1) linked list organization to address large transitional topologies, (2) body level model order reduction, and (3) parallel formulation/implementation. This paper provides a detailed overview of these primary updates to JSC's flexible multibody dynamics algorithms as well as a comparison of numerical results to previous formulations and associated software.
Butler, Jason E.; Shaqfeh, Eric S. G.
2005-01-01
Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.
Multibody Dynamic Stress Simulation of Rigid-Flexible Shovel Crawler Shoes
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Samuel Frimpong
2016-06-01
Full Text Available Electric shovels are used in surface mining operations to achieve economic production capacities. The capital investments and operating costs associated with the shovels deployed in the Athabasca oil sands formation are high due to the abrasive conditions. The shovel crawler shoes interact with sharp and abrasive sand particles, and, thus, are subjected to high transient dynamic stresses. These high stresses cause wear and tear leading to crack initiation, propagation and premature fatigue failure. The objective of this paper is to develop a model to characterize the crawler stresses and deformation for the P&H 4100C BOSS during propel and loading using rigid-flexible multi-body dynamic theory. A 3-D virtual prototype model of the rigid-flexible crawler track assembly and its interactions with oil sand formation is simulated to capture the model dynamics within multibody dynamics software MSC ADAMS. The modal and stress shapes and modal loads due to machine weight for each flexible crawler shoes are generated from finite element analysis (FEA. The modal coordinates from the simulation are combined with mode and stress shapes using modal superposition method to calculate real-time stresses and deformation of flexible crawler shoes. The results show a maximum von Mises stress value of 170 MPa occurring in the driving crawler shoe during the propel motion. This study provides a foundation for the subsequent fatigue life analysis of crawler shoes for extending crawler service life.
DEFF Research Database (Denmark)
Wagner, Falko Jens
1999-01-01
Multibody Systems is one area, in which methods for solving DAEs are of special interst. This chapter is about multibody systems, why they result in DAE systems and what kind of problems that can arise when dealing with multibody systems and formulating their corresponding DAE system....
International Nuclear Information System (INIS)
Wu, Jianing; Yan, Shaoze; Zuo, Ming J.
2016-01-01
Mechanism reliability is defined as the ability of a certain mechanism to maintain output accuracy under specified conditions. Mechanism reliability is generally assessed by the classical direct probability method (DPM) derived from the first order second moment (FOSM) method. The DPM relies strongly on the analytical form of the dynamic solution so it is not applicable to multi-body mechanisms that have only numerical solutions. In this paper, an indirect probability model (IPM) is proposed for mechanism reliability evaluation of multi-body mechanisms. IPM combines the dynamic equation, degradation function and Kaplan–Meier estimator to evaluate mechanism reliability comprehensively. Furthermore, to reduce the amount of computation in practical applications, the IPM is simplified into the indirect probability step model (IPSM). A case study of a crank–slider mechanism with clearance is investigated. Results show that relative errors between the theoretical and experimental results of mechanism reliability are less than 5%, demonstrating the effectiveness of the proposed method. - Highlights: • An indirect probability model (IPM) is proposed for mechanism reliability evaluation. • The dynamic equation, degradation function and Kaplan–Meier estimator are used. • Then the simplified form of indirect probability model is proposed. • The experimental results agree well with the predicted results.
A Non-smooth Newton Method for Multibody Dynamics
International Nuclear Information System (INIS)
Erleben, K.; Ortiz, R.
2008-01-01
In this paper we deal with the simulation of rigid bodies. Rigid body dynamics have become very important for simulating rigid body motion in interactive applications, such as computer games or virtual reality. We present a novel way of computing contact forces using a Newton method. The contact problem is reformulated as a system of non-linear and non-smooth equations, and we solve this system using a non-smooth version of Newton's method. One of the main contribution of this paper is the reformulation of the complementarity problems, used to model impacts, as a system of equations that can be solved using traditional methods.
Daneshjou, Kamran; Alibakhshi, Reza
2018-01-01
In the current manuscript, the process of spacecraft docking, as one of the main risky operations in an on-orbit servicing mission, is modeled based on unconstrained multibody dynamics. The spring-damper buffering device is utilized here in the docking probe-cone system for micro-satellites. Owing to the impact occurs inevitably during docking process and the motion characteristics of multibody systems are remarkably affected by this phenomenon, a continuous contact force model needs to be considered. Spring-damper buffering device, keeping the spacecraft stable in an orbit when impact occurs, connects a base (cylinder) inserted in the chaser satellite and the end of docking probe. Furthermore, by considering a revolute joint equipped with torsional shock absorber, between base and chaser satellite, the docking probe can experience both translational and rotational motions simultaneously. Although spacecraft docking process accompanied by the buffering mechanisms may be modeled by constrained multibody dynamics, this paper deals with a simple and efficient formulation to eliminate the surplus generalized coordinates and solve the impact docking problem based on unconstrained Lagrangian mechanics. By an example problem, first, model verification is accomplished by comparing the computed results with those recently reported in the literature. Second, according to a new alternative validation approach, which is based on constrained multibody problem, the accuracy of presented model can be also evaluated. This proposed verification approach can be applied to indirectly solve the constrained multibody problems by minimum required effort. The time history of impact force, the influence of system flexibility and physical interaction between shock absorber and penetration depth caused by impact are the issues followed in this paper. Third, the MATLAB/SIMULINK multibody dynamic analysis software will be applied to build impact docking model to validate computed results and
A Coupled Helicopter Rotor/Fuselage Dynamics Model Using Finite Element Multi-body
Directory of Open Access Journals (Sweden)
Cheng Qi-you
2016-01-01
Full Text Available To develop a coupled rotor/flexible fuselage model for vibration reduction studies, the equation of coupled rotor-fuselage is set up based on the theory of multi-body dynamics, and the dynamic analysis model is established with the software MSC.ADMAS and MSC.NASTRAN. The frequencies and vibration acceleration responses of the system are calculated with the model of coupled rotor-fuselage, and the results are compared with those of uncoupled modeling method. Analysis results showed that compared with uncoupled model, the dynamic characteristic obtained by the model of coupled rotor-fuselage are some different. The intrinsic frequency of rotor is increased with the increase of rotational velocities. The results also show that the flying speed has obvious influence on the vibration acceleration responses of the fuselage. The vibration acceleration response in the vertical direction is much higher at the low speed and high speed flight conditions.
Directory of Open Access Journals (Sweden)
Patrick Piprek
2018-02-01
Full Text Available This paper presents an approach to model a ski jumper as a multi-body system for an optimal control application. The modeling is based on the constrained Newton-Euler-Equations. Within this paper the complete multi-body modeling methodology as well as the musculoskeletal modeling is considered. For the musculoskeletal modeling and its incorporation in the optimization model, we choose a nonlinear dynamic inversion control approach. This approach uses the muscle models as nonlinear reference models and links them to the ski jumper movement by a control law. This strategy yields a linearized input-output behavior, which makes the optimal control problem easier to solve. The resulting model of the ski jumper can then be used for trajectory optimization whose results are compared to literature jumps. Ultimately, this enables the jumper to get a very detailed feedback of the flight. To achieve the maximal jump length, exact positioning of his body with respect to the air can be displayed.
Model Reduction in Co-Rotated Multi-Body Dynamics Based on the Dual Craig-Bampton Method
Weerathunge Kadawathagedara, S.T.; Rixen, D.J.
2011-01-01
A new reduction method for dynamical analsis of multi-body systems is presented in this paper. It fundamentally differs from the ones previously published in the way kinematical constraints are handled. Our approach is based on component mode synthesis, but the specificity of articulated mechanism,
Research on The Construction of Flexible Multi-body Dynamics Model based on Virtual Components
Dong, Z. H.; Ye, X.; Yang, F.
2018-05-01
Focus on the harsh operation condition of space manipulator, which cannot afford relative large collision momentum, this paper proposes a new concept and technology, called soft-contact technology. In order to solve the problem of collision dynamics of flexible multi-body system caused by this technology, this paper also proposes the concepts of virtual components and virtual hinges, and constructs flexible dynamic model based on virtual components, and also studies on its solutions. On this basis, this paper uses NX to carry out model and comparison simulation for space manipulator in 3 different modes. The results show that using the model of multi-rigid body + flexible body hinge + controllable damping can make effective control on amplitude for the force and torque caused by target satellite collision.
Dynamic Behavior of Wind Turbine by a Mixed Flexible-Rigid Multi-Body Model
Wang, Jianhong; Qin, Datong; Ding, Yi
A mixed flexible-rigid multi-body model is presented to study the dynamic behavior of a horizontal axis wind turbine. The special attention is given to flexible body: flexible rotor is modeled by a newly developed blade finite element, support bearing elasticities, variations in the number of teeth in contact as well as contact tooth's elasticities are mainly flexible components in the power train. The couple conditions between different subsystems are established by constraint equations. The wind turbine model is generated by coupling models of rotor, power train and generator with constraint equations together. Based on this model, an eigenproblem analysis is carried out to show the mode shape of rotor and power train at a few natural frequencies. The dynamic responses and contact forces among gears under constant wind speed and fixed pitch angle are analyzed.
Directory of Open Access Journals (Sweden)
Hai-gen Yang
2015-09-01
Full Text Available The complex mechanical systems such as high-speed trains, multiple launch rocket system, self-propelled artillery, and industrial robots are becoming increasingly larger in scale and more complicated in structure. Designing these products often requires complex model design, multibody system dynamics calculation, and analysis of large amounts of data repeatedly. In recent 20 years, the transfer matrix method of multibody system has been widely applied in engineering fields and welcomed at home and in abroad for the following features: without global dynamic equations of the system, low orders of involved system matrices, high computational efficiency, and high programming. In order to realize the rapid and visual simulation for complex mechanical system virtual design using transfer matrix method of multibody system, a virtual design software named MSTMMSim is designed and implemented. In the MSTMMSim, the transfer matrix method of multibody system is used as the solver for dynamic modeling and calculation; the Open CASCADE is used for solid geometry modeling. Various auxiliary analytical tools such as curve plot and animation display are provided in the post-processor to analyze and process the simulation results. Two numerical examples are given to verify the validity and accuracy of the software, and a multiple launch rocket system engineering example is given at the end of this article to show that the software provides a powerful platform for complex mechanical systems simulation and virtual design.
International Nuclear Information System (INIS)
Leyendecker, Sigrid; Betsch, Peter; Steinmann, Paul
2008-01-01
In the present work, the unified framework for the computational treatment of rigid bodies and nonlinear beams developed by Betsch and Steinmann (Multibody Syst. Dyn. 8, 367-391, 2002) is extended to the realm of nonlinear shells. In particular, a specific constrained formulation of shells is proposed which leads to the semi-discrete equations of motion characterized by a set of differential-algebraic equations (DAEs). The DAEs provide a uniform description for rigid bodies, semi-discrete beams and shells and, consequently, flexible multibody systems. The constraints may be divided into two classes: (i) internal constraints which are intimately connected with the assumption of rigidity of the bodies, and (ii) external constraints related to the presence of joints in a multibody framework. The present approach thus circumvents the use of rotational variables throughout the whole time discretization, facilitating the design of energy-momentum methods for flexible multibody dynamics. After the discretization has been completed a size-reduction of the discrete system is performed by eliminating the constraint forces. Numerical examples dealing with a spatial slider-crank mechanism and with intersecting shells illustrate the performance of the proposed method
Yew, Alvin G.; Chai, Dean J.; Olney, David J.
2010-01-01
The goal of NASA's Magnetospheric MultiScale (MMS) mission is to understand magnetic reconnection with sensor measurements from four spinning satellites flown in a tight tetrahedron formation. Four of the six electric field sensors on each satellite are located at the end of 60- meter wire booms to increase measurement sensitivity in the spin plane and to minimize motion coupling from perturbations on the main body. A propulsion burn however, might induce boom oscillations that could impact science measurements if oscillations do not damp to values on the order of 0.1 degree in a timely fashion. Large damping time constants could also adversely affect flight dynamics and attitude control performance. In this paper, we will discuss the implementation of a high resolution method for calculating the boom's intrinsic damping, which was used in multi-body dynamics simulations. In summary, experimental data was obtained with a scaled-down boom, which was suspended as a pendulum in vacuum. Optical techniques were designed to accurately measure the natural decay of angular position and subsequently, data processing algorithms resulted in excellent spatial and temporal resolutions. This method was repeated in a parametric study for various lengths, root tensions and vacuum levels. For all data sets, regression models for damping were applied, including: nonlinear viscous, frequency-independent hysteretic, coulomb and some combination of them. Our data analysis and dynamics models have shown that the intrinsic damping for the baseline boom is insufficient, thereby forcing project management to explore mitigation strategies.
Directory of Open Access Journals (Sweden)
Pål Johan From
2012-04-01
Full Text Available This paper presents the explicit dynamic equations of multibody mechanical systems. This is the second paper on this topic. In the first paper the dynamics of a single rigid body from the Boltzmann--Hamel equations were derived. In this paper these results are extended to also include multibody systems. We show that when quasi-velocities are used, the part of the dynamic equations that appear from the partial derivatives of the system kinematics are identical to the single rigid body case, but in addition we get terms that come from the partial derivatives of the inertia matrix, which are not present in the single rigid body case. We present for the first time the complete and correct derivation of multibody systems based on the Boltzmann--Hamel formulation of the dynamics in Lagrangian form where local position and velocity variables are used in the derivation to obtain the singularity-free dynamic equations. The final equations are written in global variables for both position and velocity. The main motivation of these papers is to allow practitioners not familiar with differential geometry to implement the dynamic equations of rigid bodies without the presence of singularities. Presenting the explicit dynamic equations also allows for more insight into the dynamic structure of the system. Another motivation is to correct some errors commonly found in the literature. Unfortunately, the formulation of the Boltzmann-Hamel equations used here are presented incorrectly. This has been corrected by the authors, but we present here, for the first time, the detailed mathematical details on how to arrive at the correct equations. We also show through examples that using the equations presented here, the dynamics of a single rigid body is reduced to the standard equations on a Lagrangian form, for example Euler's equations for rotational motion and Euler--Lagrange equations for free motion.
Directory of Open Access Journals (Sweden)
William I. Sellers
2017-07-01
Full Text Available The running ability of Tyrannosaurus rex has been intensively studied due to its relevance to interpretations of feeding behaviour and the biomechanics of scaling in giant predatory dinosaurs. Different studies using differing methodologies have produced a very wide range of top speed estimates and there is therefore a need to develop techniques that can improve these predictions. Here we present a new approach that combines two separate biomechanical techniques (multibody dynamic analysis and skeletal stress analysis to demonstrate that true running gaits would probably lead to unacceptably high skeletal loads in T. rex. Combining these two approaches reduces the high-level of uncertainty in previous predictions associated with unknown soft tissue parameters in dinosaurs, and demonstrates that the relatively long limb segments of T. rex—long argued to indicate competent running ability—would actually have mechanically limited this species to walking gaits. Being limited to walking speeds contradicts arguments of high-speed pursuit predation for the largest bipedal dinosaurs like T. rex, and demonstrates the power of multiphysics approaches for locomotor reconstructions of extinct animals.
A joint-space numerical model of metabolic energy expenditure for human multibody dynamic system.
Kim, Joo H; Roberts, Dustyn
2015-09-01
Metabolic energy expenditure (MEE) is a critical performance measure of human motion. In this study, a general joint-space numerical model of MEE is derived by integrating the laws of thermodynamics and principles of multibody system dynamics, which can evaluate MEE without the limitations inherent in experimental measurements (phase delays, steady state and task restrictions, and limited range of motion) or muscle-space models (complexities and indeterminacies from excessive DOFs, contacts and wrapping interactions, and reliance on in vitro parameters). Muscle energetic components are mapped to the joint space, in which the MEE model is formulated. A constrained multi-objective optimization algorithm is established to estimate the model parameters from experimental walking data also used for initial validation. The joint-space parameters estimated directly from active subjects provide reliable MEE estimates with a mean absolute error of 3.6 ± 3.6% relative to validation values, which can be used to evaluate MEE for complex non-periodic tasks that may not be experimentally verifiable. This model also enables real-time calculations of instantaneous MEE rate as a function of time for transient evaluations. Although experimental measurements may not be completely replaced by model evaluations, predicted quantities can be used as strong complements to increase reliability of the results and yield unique insights for various applications. Copyright © 2015 John Wiley & Sons, Ltd.
Energy Technology Data Exchange (ETDEWEB)
Papadopoulos, Alessandro Vittorio, E-mail: alessandro.papadopoulos@control.lth.se [Lund University, Department of Automatic Control (Sweden); Leva, Alberto, E-mail: alberto.leva@polimi.it [Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria (Italy)
2015-06-15
The presence of different time scales in a dynamic model significantly hampers the efficiency of its simulation. In multibody systems the fact is particularly relevant, as the mentioned time scales may be very different, due, for example, to the coexistence of mechanical components controled by electronic drive units, and may also appear in conjunction with significant nonlinearities. This paper proposes a systematic technique, based on the principles of dynamic decoupling, to partition a model based on the time scales that are relevant for the particular simulation studies to be performed and as transparently as possible for the user. In accordance with said purpose, peculiar to the technique is its neat separation into two parts: a structural analysis of the model, which is general with respect to any possible simulation scenario, and a subsequent decoupled integration, which can conversely be (easily) tailored to the study at hand. Also, since the technique does not aim at reducing but rather at partitioning the model, the state space and the physical interpretation of the dynamic variables are inherently preserved. Moreover, the proposed analysis allows us to define some novel indices relative to the separability of the system, thereby extending the idea of “stiffness” in a way that is particularly keen to its use for the improvement of simulation efficiency, be the envisaged integration scheme monolithic, parallel, or even based on cosimulation. Finally, thanks to the way the analysis phase is conceived, the technique is naturally applicable to both linear and nonlinear models. The paper contains a methodological presentation of the proposed technique, which is related to alternatives available in the literature so as to evidence the peculiarities just sketched, and some application examples illustrating the achieved advantages and motivating the major design choice from an operational viewpoint.
Huang, Juyang
2002-08-01
Experimental evidences have indicated that cholesterol may adapt highly regular lateral distributions (i.e., superlattices) in a phospholipid bilayer. We investigated the formations of superlattices at cholesterol mole fraction of 0.154, 0.25, 0.40, and 0.5 using Monte Carlo simulation. We found that in general, conventional pairwise-additive interactions cannot produce superlattices. Instead, a multibody (nonpairwise) interaction is required. Cholesterol superlattice formation reveals that although the overall interaction between cholesterol and phospholipids is favorable, it contains two large opposing components: an interaction favoring cholesterol-phospholipid mixing and an unfavorable acyl chain multibody interaction that increases nonlinearly with the number of cholesterol contacts. The magnitudes of interactions are in the order of kT. The physical origins of these interactions can be explained by our umbrella model. They most likely come from the requirement for polar phospholipid headgroups to cover the nonpolar cholesterol to avoid the exposure of cholesterol to water and from the sharp decreasing of acyl chain conformation entropy due to cholesterol contact. This study together with our previous work demonstrate that the driving force of cholesterol-phospholipid mixing is a hydrophobic interaction, and multibody interactions dominate others over a wide range of cholesterol concentration.
Constraint treatment techniques and parallel algorithms for multibody dynamic analysis. Ph.D. Thesis
Chiou, Jin-Chern
1990-01-01
Computational procedures for kinematic and dynamic analysis of three-dimensional multibody dynamic (MBD) systems are developed from the differential-algebraic equations (DAE's) viewpoint. Constraint violations during the time integration process are minimized and penalty constraint stabilization techniques and partitioning schemes are developed. The governing equations of motion, a two-stage staggered explicit-implicit numerical algorithm, are treated which takes advantage of a partitioned solution procedure. A robust and parallelizable integration algorithm is developed. This algorithm uses a two-stage staggered central difference algorithm to integrate the translational coordinates and the angular velocities. The angular orientations of bodies in MBD systems are then obtained by using an implicit algorithm via the kinematic relationship between Euler parameters and angular velocities. It is shown that the combination of the present solution procedures yields a computationally more accurate solution. To speed up the computational procedures, parallel implementation of the present constraint treatment techniques, the two-stage staggered explicit-implicit numerical algorithm was efficiently carried out. The DAE's and the constraint treatment techniques were transformed into arrowhead matrices to which Schur complement form was derived. By fully exploiting the sparse matrix structural analysis techniques, a parallel preconditioned conjugate gradient numerical algorithm is used to solve the systems equations written in Schur complement form. A software testbed was designed and implemented in both sequential and parallel computers. This testbed was used to demonstrate the robustness and efficiency of the constraint treatment techniques, the accuracy of the two-stage staggered explicit-implicit numerical algorithm, and the speed up of the Schur-complement-based parallel preconditioned conjugate gradient algorithm on a parallel computer.
International Nuclear Information System (INIS)
Tanabe, M; Wakui, H; Sogabe, M; Matsumoto, N; Tanabe, Y
2010-01-01
A combined multibody and finite element approach is given to solve the dynamic interaction of a Shinkansen train (high-speed train in Japan) and the railway structure including post-derailment during an earthquake effectively. The motion of the train is expressed in multibody dynamics. Efficient mechanical models to express interactions between wheel and track structure including post-derailment are given. Rail and track elements expressed in multibody dynamics and FEM are given to solve contact problems between wheel and long railway components effectively. The motion of a railway structure is modeled with various finite elements and rail and track elements. The computer program has been developed for the dynamic interaction analysis of a Shinkansen train and railway structure including post derailment during an earthquake. Numerical examples are demonstrated.
Directory of Open Access Journals (Sweden)
Gangli Chen
2013-01-01
Full Text Available The dynamic test precision of the strapdown inertial measurement unit (SIMU is the basis of estimating accurate motion of various vehicles such as warships, airplanes, spacecrafts, and missiles. So, it is paid great attention in the above fields to increase the dynamic precision of SIMU by decreasing the vibration of the vehicles acting on the SIMU. In this paper, based on the transfer matrix method for multibody system (MSTMM, the multibody system dynamics model of laser gyro strapdown inertial measurement unit (LGSIMU is developed; the overall transfer equation of the system is deduced automatically. The computational results show that the frequency response function of the LGSIMU got by the proposed method and Newton-Euler method have good agreements. Further, the vibration reduction performance and the attitude error responses under harmonic and random excitations are analyzed. The proposed method provides a powerful technique for studying dynamics of LGSIMU because of using MSTMM and its following features: without the global dynamics equations of the system, high programming, low order of system matrix, and high computational speed.
Schilder, Jurnan Paul; Ellenbroek, Marcellinus Hermannus Maria; de Boer, A.
2017-01-01
In this work, the floating frame of reference formulation is used to create a flexible multibody model of slender offshore structures such as pipelines and risers. It is shown that due to the chain-like topology of the considered structures, the equation of motion can be expressed in terms of
Virlez, Geoffrey; Bruls, Olivier; Tromme, Emmanuel; Duysinx, Pierre
2012-01-01
Defects in kinematic joints can sometimes highly influence the simulation response of the whole multibody system within which these joints are included. For instance, the clearance, the friction, the lubrication and the flexibility affect the transient behaviour, reduce the component life and produce noise and vibration for classical joints such as prismatic, cylindric or universal joint. In this work, a new 3D cylindrical joint model which accounts for the clearance, the misalignment and the...
Parallel Evolutionary Optimization of Multibody Systems with Application to Railway Dynamics
Energy Technology Data Exchange (ETDEWEB)
Eberhard, Peter [University of Erlangen-Nuremberg, Institute of Applied Mechanics (Germany)], E-mail: eberhard@ltm.uni-erlangen.de; Dignath, Florian [University of Stuttgart, Institute B of Mechanics (Germany)], E-mail: fd@mechb.uni-stuttgart.de; Kuebler, Lars [University of Erlangen-Nuremberg, Institute of Applied Mechanics (Germany)], E-mail: kuebler@ltm.uni-erlangen.de
2003-03-15
The optimization of multibody systems usually requires many costly criteria computations since the equations of motion must be evaluated by numerical time integration for each considered design. For actively controlled or flexible multibody systems additional difficulties arise as the criteria may contain non-differentiable points or many local minima. Therefore, in this paper a stochastic evolution strategy is used in combination with parallel computing in order to reduce the computation times whilst keeping the inherent robustness. For the parallelization a master-slave approach is used in a heterogeneous workstation/PC cluster. The pool-of-tasks concept is applied in order to deal with the frequently changing workloads of different machines in the cluster. In order to analyze the performance of the parallel optimization method, the suspension of an ICE passenger coach, modeled as an elastic multibody system, is optimized simultaneously with regard to several criteria including vibration damping and a criterion related to safety against derailment. The iterative and interactive nature of a typical optimization process for technical systems is emphasized.
Parallel Evolutionary Optimization of Multibody Systems with Application to Railway Dynamics
International Nuclear Information System (INIS)
Eberhard, Peter; Dignath, Florian; Kuebler, Lars
2003-01-01
The optimization of multibody systems usually requires many costly criteria computations since the equations of motion must be evaluated by numerical time integration for each considered design. For actively controlled or flexible multibody systems additional difficulties arise as the criteria may contain non-differentiable points or many local minima. Therefore, in this paper a stochastic evolution strategy is used in combination with parallel computing in order to reduce the computation times whilst keeping the inherent robustness. For the parallelization a master-slave approach is used in a heterogeneous workstation/PC cluster. The pool-of-tasks concept is applied in order to deal with the frequently changing workloads of different machines in the cluster. In order to analyze the performance of the parallel optimization method, the suspension of an ICE passenger coach, modeled as an elastic multibody system, is optimized simultaneously with regard to several criteria including vibration damping and a criterion related to safety against derailment. The iterative and interactive nature of a typical optimization process for technical systems is emphasized
Rong, Bao; Rui, Xiaoting; Lu, Kun; Tao, Ling; Wang, Guoping; Ni, Xiaojun
2018-05-01
In this paper, an efficient method of dynamics modeling and vibration control design of a linear hybrid multibody system (MS) is studied based on the transfer matrix method. The natural vibration characteristics of a linear hybrid MS are solved by using low-order transfer equations. Then, by constructing the brand-new body dynamics equation, augmented operator and augmented eigenvector, the orthogonality of augmented eigenvector of a linear hybrid MS is satisfied, and its state space model expressed in each independent model space is obtained easily. According to this dynamics model, a robust independent modal space-fuzzy controller is designed for vibration control of a general MS, and the genetic optimization of some critical control parameters of fuzzy tuners is also presented. Two illustrative examples are performed, which results show that this method is computationally efficient and with perfect control performance.
Pamadi, Bandu N.; Toniolo, Matthew D.; Tartabini, Paul V.; Roithmayr, Carlos M.; Albertson, Cindy W.; Karlgaard, Christopher D.
2016-01-01
The objective of this report is to develop and implement a physics based method for analysis and simulation of multi-body dynamics including launch vehicle stage separation. The constraint force equation (CFE) methodology discussed in this report provides such a framework for modeling constraint forces and moments acting at joints when the vehicles are still connected. Several stand-alone test cases involving various types of joints were developed to validate the CFE methodology. The results were compared with ADAMS(Registered Trademark) and Autolev, two different industry standard benchmark codes for multi-body dynamic analysis and simulations. However, these two codes are not designed for aerospace flight trajectory simulations. After this validation exercise, the CFE algorithm was implemented in Program to Optimize Simulated Trajectories II (POST2) to provide a capability to simulate end-to-end trajectories of launch vehicles including stage separation. The POST2/CFE methodology was applied to the STS-1 Space Shuttle solid rocket booster (SRB) separation and Hyper-X Research Vehicle (HXRV) separation from the Pegasus booster as a further test and validation for its application to launch vehicle stage separation problems. Finally, to demonstrate end-to-end simulation capability, POST2/CFE was applied to the ascent, orbit insertion, and booster return of a reusable two-stage-to-orbit (TSTO) vehicle concept. With these validation exercises, POST2/CFE software can be used for performing conceptual level end-to-end simulations, including launch vehicle stage separation, for problems similar to those discussed in this report.
Nonlinear model order reduction for flexible multibody dynamics: a modal derivatives approach
Energy Technology Data Exchange (ETDEWEB)
Wu, Long, E-mail: L.Wu-1@tudelft.nl [Delft University of Technology, Faculty of Mechanical, Maritime and Materials Engineering (Netherlands); Tiso, Paolo, E-mail: ptiso@ethz.ch [ETH Zürich, Institute for Mechanical Systems (Switzerland)
2016-04-15
An effective reduction technique is presented for flexible multibody systems, for which the elastic deflection could not be considered small. We consider here the planar beam systems undergoing large elastic rotations, in the floating frame description. The proposed method enriches the classical linear reduction basis with modal derivatives stemming from the derivative of the eigenvalue problem. Furthermore, the Craig–Bampton method is applied to couple the different reduced components. Based on the linear projection, the configuration-dependent internal force can be expressed as cubic polynomials in the reduced coordinates. Coefficients of these polynomials can be precomputed for efficient runtime evaluation. The numerical results show that the modal derivatives are essential for the correct approximation of the nonlinear elastic deflection with respect to the body reference. The proposed reduction method constitutes a natural and effective extension of the classical linear modal reduction in the floating frame.
Application of stabilization techniques in the dynamic analysis of multibody systems
Directory of Open Access Journals (Sweden)
Hajžman M.
2007-11-01
Full Text Available This paper is intended to the discussion of possible methods for the solution of the motion equations of constrained multibody systems. They can be formulated in the form of differential-algebraic equations and their numerical solution brings the problems of constraint violation and numerical stability. Therefore special methods were proposed to handle these problems. Various approaches for the numerical solution of equations are briefly reviewed and the application of the Baumgarte’s stabilization method on testing examples is shown. The paper was motivated by the effort to find the suitable solution methods for the equations of motion in the form of differentialalgebraic equations using the MATLAB standard computational system.
Directory of Open Access Journals (Sweden)
Wenguang Yang
2016-01-01
Full Text Available This paper proposes an improved rigid multibody model for the dynamic analysis of the planetary gearbox in a wind turbine. The improvements mainly include choosing the inertia frame as the reference frame of the carrier, the ring, and the sun and adding a new degree of freedom for each planet. An element assembly method is introduced to build the model, and a time-varying mesh stiffness model is presented. A planetary gear study case is employed to verify the validity of the improved model. Comparisons between the improvement model and the traditional model show that the natural characteristics are very close; the improved model can obtain the right equivalent moment of inertia of the planetary gear in the transient simulation, and all the rotation speeds satisfy the transmission relationships well; harmonic resonance and resonance modulation phenomena can be found in their vibration signals. The improved model is applied in a multistage gearbox dynamics analysis to reveal the prospects of the model. Modal analysis and transient analysis with and without time-varying mesh stiffness considered are conducted. The rotation speeds from the transient analysis are consistent with the theory, and resonance modulation can be found in the vibration signals.
Energy Technology Data Exchange (ETDEWEB)
Gross, Volker [ZF Friedrichshafen AG, Friedrichshafen (Germany)
2011-07-01
The legal regulations and the customers' requirements as regards vehicle comfort are growing more and more stringent. This also includes the transmission systems, as they are expected not so show any obvious acoustic or dynamic weaknesses. Modern simulation methods permit evaluation and optimization of structure-borne and airborne noise in the early stage of development. Especially the FE method is a well-established technique for the simulation of structure-borne sound. With regard to complex transmissions, multibody simulations (MBS) can provide valuable insights for a realistic evaluation of the dynamic behaviour of a transmission. This is demonstrated using a truck transmission as an example. (orig.)
Efficiency Analysis of a Wave Power Generation System by Using Multibody Dynamics
International Nuclear Information System (INIS)
Kim, Min Soo; Sohn, Jeong Hyun; Kim, Jung Hee; Sung, Yong Jun
2016-01-01
The energy absorption efficiency of a wave power generation system is calculated as the ratio of the wave power to the power of the system. Because absorption efficiency depends on the dynamic behavior of the wave power generation system, a dynamic analysis of the wave power generation system is required to estimate the energy absorption efficiency of the system. In this study, a dynamic analysis of the wave power generation system under wave loads is performed to estimate the energy absorption efficiency. RecurDyn is employed to carry out the dynamic analysis of the system, and the Morison equation is used for the wave load model. According to the results, the lower the wave height and the shorter the period, the higher is the absorption efficiency of the system
Efficiency Analysis of a Wave Power Generation System by Using Multibody Dynamics
Energy Technology Data Exchange (ETDEWEB)
Kim, Min Soo; Sohn, Jeong Hyun [Pukyong National Univ., Busan (Korea, Republic of); Kim, Jung Hee; Sung, Yong Jun [INGINE Inc., Seoul (Korea, Republic of)
2016-06-15
The energy absorption efficiency of a wave power generation system is calculated as the ratio of the wave power to the power of the system. Because absorption efficiency depends on the dynamic behavior of the wave power generation system, a dynamic analysis of the wave power generation system is required to estimate the energy absorption efficiency of the system. In this study, a dynamic analysis of the wave power generation system under wave loads is performed to estimate the energy absorption efficiency. RecurDyn is employed to carry out the dynamic analysis of the system, and the Morison equation is used for the wave load model. According to the results, the lower the wave height and the shorter the period, the higher is the absorption efficiency of the system.
Constrained Multi-Body Dynamics for Modular Underwater Robots — Theory and Experiments
DEFF Research Database (Denmark)
Nielsen, Mikkel Cornelius; Eidsvik, Ole Alexander; Blanke, Mogens
2018-01-01
This paper investigates the problem of modelling a system of interconnected underwater robots with highly coupled dynamics. The objective is to develop a mathematical description of the system that captures its most significant dynamics. The proposed modelling method is based on active constraint...... on a BlueROV vehicle to determine the model parameters. The applicability of the modelling approach is assessed by comparing experimental data to simulations of an equivalent model synthesised using the proposed theory....
Toledo Fuentes, A.; Kipfmueller, M.; José Prieto, M. A.
2017-10-01
Mobile manipulators are becoming a key instrument to increase the flexibility in industrial processes. Some of their requirements include handling of objects with different weights and sizes and their “fast” transportation, without jeopardizing production workers and machines. The compensation of forces affecting the system dynamic is therefore needed to avoid unwanted oscillations and tilting by sudden accelerations and decelerations. One general solution may be the implementation of external positioning elements to active stabilize the system. To accomplish the approach, the dynamic behavior of a robotic arm and a mobile platform was investigated to develop the stabilization mechanism using multibody simulations. The methodology used was divided into two phases for each subsystem: their natural frequencies and modal shapes were obtained using experimental modal analyses. Then, based on these experimental results, multibody simulation models (MBS) were set up and its dynamical parameters adjusted. Their modal shapes together with their obtained natural frequencies allowed a quantitative and qualitative analysis. In summary, the MBS models were successfully validated with the real subsystems, with a maximal percentage error of 15%. These models will serve as the basis for future steps in the design of the external actuators and its control strategy using a co-simulation tool.
A multi-body dynamics approach to a cable simulator for kites
Breukels, J.; Ockels, W.J.
2007-01-01
For the purpose of ultimately building a fully dynamic simulation of kites, an investigation is launched into a viable model of the cable with which the kite is attached to the ground. In the model proposed in this paper, only the slow modes of motion are taken into account due to the fact that only
Numerical simulation of track settlement using a multibody dynamic software a holistic approach
DEFF Research Database (Denmark)
Tejada, Alejandro de Miguel; Lau, A.; Santos, Ilmar
2017-01-01
that it is necessary to intensify the frequency and the amount of maintenance works in the critical track sections, resulting in increased costs for the infrastructure manager. The fundamental idea of this work is to create and implement a novel methodology to analyse the train/track dynamic interaction and its...
Gain in computational efficiency by vectorization in the dynamic simulation of multi-body systems
Amirouche, F. M. L.; Shareef, N. H.
1991-01-01
An improved technique for the identification and extraction of the exact quantities associated with the degrees of freedom at the element as well as the flexible body level is presented. It is implemented in the dynamic equations of motions based on the recursive formulation of Kane et al. (1987) and presented in a matrix form, integrating the concepts of strain energy, the finite-element approach, modal analysis, and reduction of equations. This technique eliminates the CPU intensive matrix multiplication operations in the code's hot spots for the dynamic simulation of the interconnected rigid and flexible bodies. A study of a simple robot with flexible links is presented by comparing the execution times on a scalar machine and a vector-processor with and without vector options. Performance figures demonstrating the substantial gains achieved by the technique are plotted.
DEFF Research Database (Denmark)
Estupinan, Edgar Alberto; Santos, Ilmar
2009-01-01
elements are supported by fluid film bearings, where the hydrodynamic interaction forces are described by the Reynolds equation. The system of nonlinear equations is numerically solved for three different restrictive conditions of the motion of the crank, where the third case takes into account lateral...... and tilting oscillations of the extremity of the crankshaft. The numerical results of the behaviour of the journal bearings for each case are presented giving some insights into design parameters such as, maximum oil film pressure, minimum oil film thickness, maximum vibration levels and dynamic reaction...
Polymer friction Molecular Dynamics
DEFF Research Database (Denmark)
Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.
We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....
Molecular dynamics for fermions
International Nuclear Information System (INIS)
Feldmeier, H.; Schnack, J.
2000-02-01
The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)
The nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
Hoover, W.G.
1992-03-01
MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments
Molecular dynamics simulations
International Nuclear Information System (INIS)
Alder, B.J.
1985-07-01
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs
Physical essence of the multibody contact-sliding at atomic scale
Han, Xuesong
2014-01-01
Investigation the multibody contact-sliding occurred at atomic discrete contact spot will play an important role in determine the origin of tribology behavior and evaluates the micro-mechanical property of nanomaterials and thus optimizing the design of surface texture. This paper carries out large scale parallel molecular dynamics simulation on contact-sliding at atomic scale to uncover the special physical essence. The research shows that some kind of force field exists between nanodot pair and the interaction can be expressed by the linear combination of exponential function while the effective interaction distance limited in 1 angstrom for nanodot with several tens of nanometer diameter. The variation tendency about the interaction force between nanodot array is almost the same between nanodot pairs and thus the interaction between two nanodot array can be characterized by parallel mechanical spring. Multibody effect which dominates the interaction between atoms or molecules will gradually diminish with the increasing of length scales.
Molecular dynamics of bacteriorhodopsin.
Lupo, J A; Pachter, R
1997-02-01
A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.
Molecular photoionization dynamics
International Nuclear Information System (INIS)
Dehmer, J.L.
1982-01-01
This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed
Physical adsorption and molecular dynamics
International Nuclear Information System (INIS)
Cohan, N.V.
1981-01-01
Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt
International Nuclear Information System (INIS)
Amengonu, Yawo H; Kakad, Yogendra P
2014-01-01
Quasivelocity techniques were applied to derive the dynamics of a Differential Wheeled Mobile Robot (DWMR) in the companion paper. The present paper formulates a control system design for trajectory tracking of this class of robots. The method develops a feedback linearization technique for the nonlinear system using dynamic extension algorithm. The effectiveness of the nonlinear controller is illustrated with simulation example
Downer, Janice Diane
1990-01-01
The dynamic analysis of three dimensional elastic beams which experience large rotational and large deformational motions are examined. The beam motion is modeled using an inertial reference for the translational displacements and a body-fixed reference for the rotational quantities. Finite strain rod theories are then defined in conjunction with the beam kinematic description which accounts for the effects of stretching, bending, torsion, and transverse shear deformations. A convected coordinate representation of the Cauchy stress tensor and a conjugate strain definition is introduced to model the beam deformation. To treat the beam dynamics, a two-stage modification of the central difference algorithm is presented to integrate the translational coordinates and the angular velocity vector. The angular orientation is then obtained from the application of an implicit integration algorithm to the Euler parameter/angular velocity kinematical relation. The combined developments of the objective internal force computation with the dynamic solution procedures result in the computational preservation of total energy for undamped systems. The present methodology is also extended to model the dynamics of deployment/retrieval of the flexible members. A moving spatial grid corresponding to the configuration of a deployed rigid beam is employed as a reference for the dynamic variables. A transient integration scheme which accurately accounts for the deforming spatial grid is derived from a space-time finite element discretization of a Hamiltonian variational statement. The computational results of this general deforming finite element beam formulation are compared to reported results for a planar inverse-spaghetti problem.
Energy Technology Data Exchange (ETDEWEB)
Fu, Yao, E-mail: Yao.Fu@colorado.edu; Song, Jeong-Hoon, E-mail: JH.Song@colorado.edu
2015-08-01
Heat flux expressions are derived for multibody potential systems by extending the original Hardy's methodology and modifying Admal & Tadmor's formulas. The continuum thermomechanical quantities obtained from these two approaches are easy to compute from molecular dynamics (MD) results, and have been tested for a constant heat flux model in two distinctive systems: crystalline iron and polyethylene (PE) polymer. The convergence criteria and affecting parameters, i.e. spatial and temporal window size, and specific forms of localization function are found to be different between the two systems. The conservation of mass, momentum, and energy are discussed and validated within this atomistic–continuum bridging.
International Nuclear Information System (INIS)
Fu, Yao; Song, Jeong-Hoon
2015-01-01
Heat flux expressions are derived for multibody potential systems by extending the original Hardy's methodology and modifying Admal & Tadmor's formulas. The continuum thermomechanical quantities obtained from these two approaches are easy to compute from molecular dynamics (MD) results, and have been tested for a constant heat flux model in two distinctive systems: crystalline iron and polyethylene (PE) polymer. The convergence criteria and affecting parameters, i.e. spatial and temporal window size, and specific forms of localization function are found to be different between the two systems. The conservation of mass, momentum, and energy are discussed and validated within this atomistic–continuum bridging
International Nuclear Information System (INIS)
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-01-01
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 wave packet calculations that provide insights into energy flow between the vibrational modes of the molecule
A new version of transfer matrix method for multibody systems
Energy Technology Data Exchange (ETDEWEB)
Rui, Xiaoting, E-mail: ruixt@163.net [Nanjing University of Science and Technology, Institute of Launch Dynamics (China); Bestle, Dieter, E-mail: bestle@b-tu.de [Brandenburg University of Technology, Engineering Mechanics and Vehicle Dynamics (Germany); Zhang, Jianshu, E-mail: zhangdracpa@sina.com; Zhou, Qinbo, E-mail: zqb912-new@163.com [Nanjing University of Science and Technology, Institute of Launch Dynamics (China)
2016-10-15
In order to avoid the global dynamics equations and increase the computational efficiency for multibody system dynamics (MSD), the transfer matrix method of multibody system (MSTMM) has been developed and applied very widely in research and engineering in recent 20 years. It differs from ordinary methods in multibody system dynamics with respect to the feature that there is no need for a global dynamics equation, and it uses low-order matrices for high computational efficiency. For linear systems, MSTMM is exact even if continuous elements like beams are involved. The discrete time MSTMM, however, has to use local linearization. In order to release the method from such approximations, a new version of MSTMM is presented in this paper where translational and angular accelerations, on the one hand, and internal forces and moments, on the other hand, are used as state variables. Already linear relationships among these quantities are utilized, which results in new element transfer matrices and algorithms making the study of multibody systems as simple as the study of single bodies. The proposed approach also allows combining MSTMM with any general numerical integration procedure. Some numerical examples of MSD are given to demonstrate the proposed method.
Thomas-Fermi molecular dynamics
International Nuclear Information System (INIS)
Clerouin, J.; Pollock, E.L.; Zerah, G.
1992-01-01
A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated
Symmetry of quantum molecular dynamics
International Nuclear Information System (INIS)
Burenin, A.V.
2002-01-01
The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru
Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics
International Nuclear Information System (INIS)
Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.
1992-09-01
Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs
Molecular dynamics for dense matter
International Nuclear Information System (INIS)
Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)
Molecular dynamics for dense matter
Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi
2012-08-01
We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.
NMR investigations of molecular dynamics
Palmer, Arthur
2011-03-01
NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.
Introduction to Molecular Dynamics and Accelerated Molecular Dynamics
International Nuclear Information System (INIS)
Perez, Danny
2012-01-01
We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.
Rheology via nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference
Linking rigid multibody systems via controllable thin fluid films
DEFF Research Database (Denmark)
Estupinan, Edgar Alberto; Santos, Ilmar
2009-01-01
, this paper gives a theoretical contribution to the combined fields of fluid–structure interaction and vibration control. The methodology is applied to a reciprocating linear compressor, where the dynamics of the mechanical components are described with help of multibody dynamics. The crank is linked......This work deals with the mathematical modelling of multibody systems interconnected via thin fluid films. The dynamics of the fluid films can be actively controlled by means of different types of actuators, allowing significant vibration reduction of the system components. In this framework...... to the rotor via a thin fluid film, where the hydrodynamic pressure is described by the Reynolds equation, which is modified to accommodate the controllable lubrication conditions. The fluid film forces are coupled to the set of nonlinear equations that describes the dynamics of the reciprocating linear...
Laser Controlled Molecular Orientation Dynamics
International Nuclear Information System (INIS)
Atabek, O.
2004-01-01
Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation
Molecular dynamics study of silver
International Nuclear Information System (INIS)
Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.
1995-03-01
We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs
Active vibration control of spatial flexible multibody systems
Energy Technology Data Exchange (ETDEWEB)
Neto, Maria Augusta, E-mail: augusta.neto@dem.uc.pt [Universidade de Coimbra (Polo II), Departamento de Engenharia Mecanica, Faculdade de Ciencia e Tecnologia (Portugal); Ambrosio, Jorge A. C., E-mail: jorge@dem.ist.utl.pt [Instituto Superior Tecnico, Instituto de Engenharia Mecanica (Portugal); Roseiro, Luis M., E-mail: lroseiro@isec.pt [Instituto Superior de Engenharia de Coimbra, Departamento de Engenharia Mecanica (Portugal); Amaro, A., E-mail: ana.amaro@dem.uc.pt [Universidade de Coimbra (Polo II), Departamento de Engenharia Mecanica, Faculdade de Ciencia e Tecnologia (Portugal); Vasques, C. M. A., E-mail: cvasques@inegi.up.pt [Universidade do Porto, INEGI-Instituto de Engenharia Mecanica e Gestao Industrial (Portugal)
2013-06-15
In this work a flexible multibody dynamics formulation of complex models including elastic components made of composite materials is extended to include piezoelectric sensors and actuators. The only limitation for the deformation of a structural member is that they must remain elastic and linear when described in a coordinate frame fixed to a material point or region of its domain. The flexible finite-element model of each flexible body is obtained referring the flexible body nodal coordinates to the body fixed frame and using a diagonalized mass description of the inertia in the mass matrix and on the gyroscopic force vector. The modal superposition technique is used to reduce the number of generalized coordinates to a reasonable dimension for complex shaped structural models of flexible bodies. The active vibration control of the flexible multibody components is implemented using an asymmetric collocated piezoelectric sensor/actuator pair. An electromechanically coupled model is taken into account to properly consider the surface-bonded piezoelectric transducers and their effects on the time and spatial response of the flexible multibody components. The electromechanical effects are introduced in the flexible multibody equations of motion by the use of beam and plate/shell elements, developed to this purpose. A comparative study between the classical control strategies, constant gain and amplitude velocity feedback, and optimal control strategy, linear quadratic regulator (LQR), is performed in order to investigate their effectiveness to suppress vibrations in structures with piezoelectric sensing and actuating patches.
Flexible Multibody Systems Models Using Composite Materials Components
International Nuclear Information System (INIS)
Neto, Maria Augusta; Ambr'osio, Jorge A. C.; Leal, Rog'erio Pereira
2004-01-01
The use of a multibody methodology to describe the large motion of complex systems that experience structural deformations enables to represent the complete system motion, the relative kinematics between the components involved, the deformation of the structural members and the inertia coupling between the large rigid body motion and the system elastodynamics. In this work, the flexible multibody dynamics formulations of complex models are extended to include elastic components made of composite materials, which may be laminated and anisotropic. The deformation of any structural member must be elastic and linear, when described in a coordinate frame fixed to one or more material points of its domain, regardless of the complexity of its geometry. To achieve the proposed flexible multibody formulation, a finite element model for each flexible body is used. For the beam composite material elements, the sections properties are found using an asymptotic procedure that involves a two-dimensional finite element analysis of their cross-section. The equations of motion of the flexible multibody system are solved using an augmented Lagrangian formulation and the accelerations and velocities are integrated in time using a multi-step multi-order integration algorithm based on the Gear method
Active vibration control of spatial flexible multibody systems
International Nuclear Information System (INIS)
Neto, Maria Augusta; Ambrósio, Jorge A. C.; Roseiro, Luis M.; Amaro, A.; Vasques, C. M. A.
2013-01-01
In this work a flexible multibody dynamics formulation of complex models including elastic components made of composite materials is extended to include piezoelectric sensors and actuators. The only limitation for the deformation of a structural member is that they must remain elastic and linear when described in a coordinate frame fixed to a material point or region of its domain. The flexible finite-element model of each flexible body is obtained referring the flexible body nodal coordinates to the body fixed frame and using a diagonalized mass description of the inertia in the mass matrix and on the gyroscopic force vector. The modal superposition technique is used to reduce the number of generalized coordinates to a reasonable dimension for complex shaped structural models of flexible bodies. The active vibration control of the flexible multibody components is implemented using an asymmetric collocated piezoelectric sensor/actuator pair. An electromechanically coupled model is taken into account to properly consider the surface-bonded piezoelectric transducers and their effects on the time and spatial response of the flexible multibody components. The electromechanical effects are introduced in the flexible multibody equations of motion by the use of beam and plate/shell elements, developed to this purpose. A comparative study between the classical control strategies, constant gain and amplitude velocity feedback, and optimal control strategy, linear quadratic regulator (LQR), is performed in order to investigate their effectiveness to suppress vibrations in structures with piezoelectric sensing and actuating patches.
Molecular potentials and relaxation dynamics
International Nuclear Information System (INIS)
Karo, A.M.
1981-01-01
The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy
Modeling Multibody Systems with Uncertainties. Part I: Theoretical and Computational Aspects
International Nuclear Information System (INIS)
Sandu, Adrian; Sandu, Corina; Ahmadian, Mehdi
2006-01-01
This study explores the use of generalized polynomial chaos theory for modeling complex nonlinear multibody dynamic systems in the presence of parametric and external uncertainty. The polynomial chaos framework has been chosen because it offers an efficient computational approach for the large, nonlinear multibody models of engineering systems of interest, where the number of uncertain parameters is relatively small, while the magnitude of uncertainties can be very large (e.g., vehicle-soil interaction). The proposed methodology allows the quantification of uncertainty distributions in both time and frequency domains, and enables the simulations of multibody systems to produce results with 'error bars'. The first part of this study presents the theoretical and computational aspects of the polynomial chaos methodology. Both unconstrained and constrained formulations of multibody dynamics are considered. Direct stochastic collocation is proposed as less expensive alternative to the traditional Galerkin approach. It is established that stochastic collocation is equivalent to a stochastic response surface approach. We show that multi-dimensional basis functions are constructed as tensor products of one-dimensional basis functions and discuss the treatment of polynomial and trigonometric nonlinearities. Parametric uncertainties are modeled by finite-support probability densities. Stochastic forcings are discretized using truncated Karhunen-Loeve expansions. The companion paper 'Modeling Multibody Dynamic Systems With Uncertainties. Part II: Numerical Applications' illustrates the use of the proposed methodology on a selected set of test problems. The overall conclusion is that despite its limitations, polynomial chaos is a powerful approach for the simulation of multibody systems with uncertainties
A concurrent multiscale micromorphic molecular dynamics
International Nuclear Information System (INIS)
Li, Shaofan; Tong, Qi
2015-01-01
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation
Color molecular dynamics for dense matter
International Nuclear Information System (INIS)
Maruyama, Toshiki; Hatsuda, Tetsuo
2000-01-01
We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)
Molecular dynamics of liquid crystals
Sarman, Sten
1997-02-01
We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.
Theoretical Concepts in Molecular Photodissociation Dynamics
DEFF Research Database (Denmark)
Henriksen, Niels Engholm
1995-01-01
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...
International Nuclear Information System (INIS)
Pi Ting; Zhang Yunqing; Chen Liping
2012-01-01
Design sensitivity analysis of flexible multibody systems is important in optimizing the performance of mechanical systems. The choice of coordinates to describe the motion of multibody systems has a great influence on the efficiency and accuracy of both the dynamic and sensitivity analysis. In the flexible multibody system dynamics, both the floating frame of reference formulation (FFRF) and absolute nodal coordinate formulation (ANCF) are frequently utilized to describe flexibility, however, only the former has been used in design sensitivity analysis. In this article, ANCF, which has been recently developed and focuses on modeling of beams and plates in large deformation problems, is extended into design sensitivity analysis of flexible multibody systems. The Motion equations of a constrained flexible multibody system are expressed as a set of index-3 differential algebraic equations (DAEs), in which the element elastic forces are defined using nonlinear strain-displacement relations. Both the direct differentiation method and adjoint variable method are performed to do sensitivity analysis and the related dynamic and sensitivity equations are integrated with HHT-I3 algorithm. In this paper, a new method to deduce system sensitivity equations is proposed. With this approach, the system sensitivity equations are constructed by assembling the element sensitivity equations with the help of invariant matrices, which results in the advantage that the complex symbolic differentiation of the dynamic equations is avoided when the flexible multibody system model is changed. Besides that, the dynamic and sensitivity equations formed with the proposed method can be efficiently integrated using HHT-I3 method, which makes the efficiency of the direct differentiation method comparable to that of the adjoint variable method when the number of design variables is not extremely large. All these improvements greatly enhance the application value of the direct differentiation
Modeling multibody systems with uncertainties. Part II: Numerical applications
International Nuclear Information System (INIS)
Sandu, Corina; Sandu, Adrian; Ahmadian, Mehdi
2006-01-01
This study applies generalized polynomial chaos theory to model complex nonlinear multibody dynamic systems operating in the presence of parametric and external uncertainty. Theoretical and computational aspects of this methodology are discussed in the companion paper 'Modeling Multibody Dynamic Systems With Uncertainties. Part I: Theoretical and Computational Aspects .In this paper we illustrate the methodology on selected test cases. The combined effects of parametric and forcing uncertainties are studied for a quarter car model. The uncertainty distributions in the system response in both time and frequency domains are validated against Monte-Carlo simulations. Results indicate that polynomial chaos is more efficient than Monte Carlo and more accurate than statistical linearization. The results of the direct collocation approach are similar to the ones obtained with the Galerkin approach. A stochastic terrain model is constructed using a truncated Karhunen-Loeve expansion. The application of polynomial chaos to differential-algebraic systems is illustrated using the constrained pendulum problem. Limitations of the polynomial chaos approach are studied on two different test problems, one with multiple attractor points, and the second with a chaotic evolution and a nonlinear attractor set. The overall conclusion is that, despite its limitations, generalized polynomial chaos is a powerful approach for the simulation of multibody dynamic systems with uncertainties
Modeling multibody systems with uncertainties. Part II: Numerical applications
Energy Technology Data Exchange (ETDEWEB)
Sandu, Corina, E-mail: csandu@vt.edu; Sandu, Adrian; Ahmadian, Mehdi [Virginia Polytechnic Institute and State University, Mechanical Engineering Department (United States)
2006-04-15
This study applies generalized polynomial chaos theory to model complex nonlinear multibody dynamic systems operating in the presence of parametric and external uncertainty. Theoretical and computational aspects of this methodology are discussed in the companion paper 'Modeling Multibody Dynamic Systems With Uncertainties. Part I: Theoretical and Computational Aspects .In this paper we illustrate the methodology on selected test cases. The combined effects of parametric and forcing uncertainties are studied for a quarter car model. The uncertainty distributions in the system response in both time and frequency domains are validated against Monte-Carlo simulations. Results indicate that polynomial chaos is more efficient than Monte Carlo and more accurate than statistical linearization. The results of the direct collocation approach are similar to the ones obtained with the Galerkin approach. A stochastic terrain model is constructed using a truncated Karhunen-Loeve expansion. The application of polynomial chaos to differential-algebraic systems is illustrated using the constrained pendulum problem. Limitations of the polynomial chaos approach are studied on two different test problems, one with multiple attractor points, and the second with a chaotic evolution and a nonlinear attractor set. The overall conclusion is that, despite its limitations, generalized polynomial chaos is a powerful approach for the simulation of multibody dynamic systems with uncertainties.
Molecular dynamics for irradiation driven chemistry
DEFF Research Database (Denmark)
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-01-01
A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...
Thermally driven molecular linear motors - A molecular dynamics study
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence
2009-01-01
We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...
DEFF Research Database (Denmark)
Chen, Shanshin; Tortorelli, Daniel A.; Hansen, John Michael
1999-01-01
of ordinary diffferential equations is employed to avoid the instabilities associated with the direct integrations of differential-algebraic equations. To extend the unconditional stability of the implicit Newmark method to nonlinear dynamic systems, a discrete energy balance is enforced. This constraint......Advances in computer hardware and improved algorithms for multibody dynamics over the past decade have generated widespread interest in real-time simulations of multibody mechanics systems. At the heart of the widely used algorithms for multibody dynamics are a choice of coordinates which define...... the kinmatics of the system, and a choice of time integrations algorithms. The current approach uses a non-dissipative implict Newmark method to integrate the equations of motion defined in terms of the independent joint coordinates of the system. The reduction of the equations of motion to a minimal set...
Omar, Mohamed A
2014-01-01
Initial transient oscillations inhibited in the dynamic simulations responses of multibody systems can lead to inaccurate results, unrealistic load prediction, or simulation failure. These transients could result from incompatible initial conditions, initial constraints violation, and inadequate kinematic assembly. Performing static equilibrium analysis before the dynamic simulation can eliminate these transients and lead to stable simulation. Most exiting multibody formulations determine the static equilibrium position by minimizing the system potential energy. This paper presents a new general purpose approach for solving the static equilibrium in large-scale articulated multibody. The proposed approach introduces an energy drainage mechanism based on Baumgarte constraint stabilization approach to determine the static equilibrium position. The spatial algebra operator is used to express the kinematic and dynamic equations of the closed-loop multibody system. The proposed multibody system formulation utilizes the joint coordinates and modal elastic coordinates as the system generalized coordinates. The recursive nonlinear equations of motion are formulated using the Cartesian coordinates and the joint coordinates to form an augmented set of differential algebraic equations. Then system connectivity matrix is derived from the system topological relations and used to project the Cartesian quantities into the joint subspace leading to minimum set of differential equations.
A Molecular Dynamics Study of Lunasin | Singh | South African ...
African Journals Online (AJOL)
A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...
Chirality in molecular collision dynamics
Lombardi, Andrea; Palazzetti, Federico
2018-02-01
Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.
Molecular dynamics for reactions of heterogeneous catalysis
Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.
1991-01-01
An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.
molecular dynamics simulations and quantum chemical calculations
African Journals Online (AJOL)
ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu
2011-01-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We
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
Visualizing Energy on Target: Molecular Dynamics Simulations
2017-12-01
ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target
Molecular ions, Rydberg spectroscopy and dynamics
International Nuclear Information System (INIS)
Jungen, Ch.
2015-01-01
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering
Pattern recognition in molecular dynamics. [FORTRAN
Energy Technology Data Exchange (ETDEWEB)
Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)
1977-07-01
An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.
Molecular ions, Rydberg spectroscopy and dynamics
Energy Technology Data Exchange (ETDEWEB)
Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)
2015-01-22
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.
Lattice dynamics and molecular dynamics simulation of complex materials
International Nuclear Information System (INIS)
Chaplot, S.L.
1997-01-01
In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)
Energy Technology Data Exchange (ETDEWEB)
Han, Jong-Boo; Song, Hajun; Kim, Sung-Soo [Chungnam Nat’l Univ., Daejeon (Korea, Republic of)
2017-06-15
Flexible multibody simulations are widely used in the industry to design mechanical systems. In flexible multibody dynamics, deformation coordinates are described either relatively in the body reference frame that is floating in the space or in the inertial reference frame. Moreover, these deformation coordinates are generated based on the discretization of the body according to the finite element approach. Therefore, the formulation of the flexible multibody system always deals with a huge number of degrees of freedom and the numerical solution methods require a substantial amount of computational time. Parallel computational methods are a solution for efficient computation. However, most of the parallel computational methods are focused on the efficient solution of large-sized linear equations. For multibody analysis, we need to develop an efficient formulation that could be suitable for parallel computation. In this paper, we developed a subsystem synthesis method for a flexible multibody system and proposed efficient parallel computational schemes based on the OpenMP API in order to achieve efficient computation. Simulations of a rotating blade system, which consists of three identical blades, were carried out with two different parallel computational schemes. Actual CPU times were measured to investigate the efficiency of the proposed parallel schemes.
Wavelet Analysis for Molecular Dynamics
2015-06-01
Our method takes as input the topology and sparsity of the bonding structure of a molecular system, and returns a hierarchical set of system-specific...problems, such as modeling crack initiation and propagation, or interfacial phenomena. In the present work, we introduce a wavelet-based approach to extend...Several functional forms are common for angle poten- tials complicating not only implementation but also choice of approximation. In all cases, the
Dynamics and Thermodynamics of Molecular Machines
DEFF Research Database (Denmark)
Golubeva, Natalia
2014-01-01
to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...
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...
Molecular dynamics and diffusion a compilation
Fisher, David
2013-01-01
The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...
Molecular Dynamics Studies of Nanofluidic Devices
DEFF Research Database (Denmark)
Zambrano Rodriguez, Harvey Alexander
of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...
Energy Technology Data Exchange (ETDEWEB)
Fijany, A. [Jet Propulsion Lab., Pasadena, CA (United States); Coley, T.R. [Virtual Chemistry, Inc., San Diego, CA (United States); Cagin, T.; Goddard, W.A. III [California Institute of Technology, Pasadena, CA (United States)
1997-12-31
Successful molecular dynamics (MD) simulation of large systems (> million atoms) for long times (> nanoseconds) requires the integration of constrained equations of motion (CEOM). Constraints are used to eliminate high frequency degrees of freedom (DOF) and to allow the use of rigid bodies. Solving the CEOM allows for larger integration time-steps and helps focus the simulation on the important collective dynamics of chemical, biological, and materials systems. We explore advances in multibody dynamics which have resulted in O(N) algorithms for propagating the CEOM. However, because of their strictly sequential nature, the computational time required by these algorithms does not scale down with increased numbers of processors. We then present the new constraint force algorithm for solving the CEOM and show that this algorithm is fully parallelizable, leading to a computational cost of O(N/P+IogP) for N DOF on P processors.
Molecular dynamics modeling of polymer flammability
International Nuclear Information System (INIS)
Nyden, M.R.; Brown, J.E.; Lomakin, S.M.
1992-01-01
Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)
First-principles molecular dynamics for metals
International Nuclear Information System (INIS)
Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.
1989-01-01
A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases
Scalable Molecular Dynamics for Large Biomolecular Systems
Directory of Open Access Journals (Sweden)
Robert K. Brunner
2000-01-01
Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.
Theory and application of quantum molecular dynamics
Zeng Hui Zhang, John
1999-01-01
This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli
Nonadiabatic electron wavepacket dynamics behind molecular autoionization
Matsuoka, Takahide; Takatsuka, Kazuo
2018-01-01
A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.
Ultrafast molecular dynamics illuminated with synchrotron radiation
International Nuclear Information System (INIS)
Bozek, John D.; Miron, Catalin
2015-01-01
Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.
Dynamic signature of molecular association in methanol
International Nuclear Information System (INIS)
Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.
2016-01-01
Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.
DEFF Research Database (Denmark)
Hansen, Michael R.; Hansen, John Michael
1998-01-01
A point contact joint has been developed and implemented in a joint coordinate based planar multibody dynamics analysis program that also supports revolute and translational joints. Further, a segment library for the definition of the contours of the point contact joints has been integrated...
Molecular dynamics simulation of impact test
International Nuclear Information System (INIS)
Akahoshi, Y.; Schmauder, S.; Ludwig, M.
1998-01-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Ab Initio molecular dynamics with excited electrons
Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.
1994-01-01
A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.
Molecular dynamics simulations of RNA motifs
Czech Academy of Sciences Publication Activity Database
Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.
2002-01-01
Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics
Molecular dynamics simulation of impact test
Energy Technology Data Exchange (ETDEWEB)
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular dynamics simulation of a phospholipid membrane
Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.
We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in
Molecular dynamics simulations and quantum chemical calculations ...
African Journals Online (AJOL)
Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...
Nanotribology investigations with classical molecular dynamics
Solhjoo, Soheil
2017-01-01
This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:
Catalysis and communication in dynamic molecular networks
Fanlo Virgos, Hugo
2015-01-01
The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity
Reaction dynamics in polyatomic molecular systems
Energy Technology Data Exchange (ETDEWEB)
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
International Nuclear Information System (INIS)
Jolly, B.; Rizk, M.; Moran, R.
2005-01-01
The Air Force SEEK EAGLE Office (AFSEO) provided independent aerodynamic data, which was key in the separation analysis for the X-37 Approach and Landing Test Vehicle (ALTV). To ensure the best aerodynamic B-52H interference database would be generated for the analysis, NASA contracted both NASA Johnson Space Center (JSC) and the AFSEO via the 412th Flight Test Squadron (Edwards AFB CA) to run independent Computational Fluid Dynamics (CFD) studies. These data were then compared to the existing database from Boeing to establish confidence and determine areas of uncertainty. NASA requested CFD data from the AFSEO primarily for static and carriage solutions of the X-37 at various positions under the B-52H. In addition, several dynamic simulations of X-37 trajectories used rate feedback control to deflect the control surfaces to stabilize the X-37. The AFSEO CFD team calculated 140 static, unsteady solutions and 9 dynamic time-accurate trajectory simulations between April 2003 and June 2004 to support the NASA X-37 ALTV program. The computational models used structured adjacent and overlapping grids with the total computational domain consisting of 25 million points in 315 grids. The rate-control autopilot commanded both yaw and roll in four control surfaces; pitch commands were preset. The results show significant increase in stability of the X-37 trajectory from the B-52H. (author)
Kinetics from Replica Exchange Molecular Dynamics Simulations.
Stelzl, Lukas S; Hummer, Gerhard
2017-08-08
Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.
Dynamical quenching of tunneling in molecular magnets
Energy Technology Data Exchange (ETDEWEB)
José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)
2015-12-15
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.
Dynamical quenching of tunneling in molecular magnets
International Nuclear Information System (INIS)
José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.
2015-01-01
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation
Orthonormal Wavelet Bases for Quantum Molecular Dynamics
International Nuclear Information System (INIS)
Tymczak, C.; Wang, X.
1997-01-01
We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society
Excited-state molecular photoionization dynamics
International Nuclear Information System (INIS)
Pratt, S.T.
1995-01-01
This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)
Towards the molecular bases of polymerase dynamics
International Nuclear Information System (INIS)
Chela Flores, J.
1991-03-01
One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs
Electron-nuclear dynamics of molecular systems
International Nuclear Information System (INIS)
Diz, A.; Oehrn, Y.
1994-01-01
The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions
Molecular quantum dynamics. From theory to applications
International Nuclear Information System (INIS)
Gatti, Fabien
2014-01-01
An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the
Molecular quantum dynamics. From theory to applications
Energy Technology Data Exchange (ETDEWEB)
Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253
2014-09-01
An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible
Molecular Dynamics with Helical Periodic Boundary Conditions
Czech Academy of Sciences Publication Activity Database
Kessler, Jiří; Bouř, Petr
2014-01-01
Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014
Molecular dynamics simulation of a chemical reaction
International Nuclear Information System (INIS)
Gorecki, J.; Gryko, J.
1988-06-01
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
Nonequilibrium molecular dynamics theory, algorithms and applications
Todd, Billy D
2017-01-01
Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...
Extended Lagrangian Excited State Molecular Dynamics.
Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N
2018-02-13
An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).
Coulomb interactions via local dynamics: a molecular-dynamics algorithm
International Nuclear Information System (INIS)
Pasichnyk, Igor; Duenweg, Burkhard
2004-01-01
We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented
Molecular dynamics studies of superionic conductors
International Nuclear Information System (INIS)
Rahman, A.; Vashishta, P.
1983-01-01
Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables
Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...
Indian Academy of Sciences (India)
Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.
Molecular Dynamics: New Frontier in Personalized Medicine.
Sneha, P; Doss, C George Priya
2016-01-01
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.
Parallelization of quantum molecular dynamics simulation code
International Nuclear Information System (INIS)
Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu
1998-02-01
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)
Lipid Configurations from Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek
2018-01-01
of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...
Molecular dynamics studies of actinide nitrides
International Nuclear Information System (INIS)
Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo
2004-01-01
The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)
Viscosity calculations at molecular dynamics simulations
International Nuclear Information System (INIS)
Kirova, E M; Norman, G E
2015-01-01
Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)
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 of surfactant protein C
DEFF Research Database (Denmark)
Ramírez, Eunice; Santana, Alberto; Cruz, Anthony
2006-01-01
Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...
Molecular dynamics in high electric fields
International Nuclear Information System (INIS)
Apostol, M.; Cune, L.C.
2016-01-01
Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.
Hard real-time multibody simulations using ARM-based embedded systems
Energy Technology Data Exchange (ETDEWEB)
Pastorino, Roland, E-mail: roland.pastorino@kuleuven.be, E-mail: rpastorino@udc.es; Cosco, Francesco, E-mail: francesco.cosco@kuleuven.be; Naets, Frank, E-mail: frank.naets@kuleuven.be; Desmet, Wim, E-mail: wim.desmet@kuleuven.be [KU Leuven, PMA division, Department of Mechanical Engineering (Belgium); Cuadrado, Javier, E-mail: javicuad@cdf.udc.es [Universidad de La Coruña, Laboratorio de Ingeniería Mecánica (Spain)
2016-05-15
The real-time simulation of multibody models on embedded systems is of particular interest for controllers and observers such as model predictive controllers and state observers, which rely on a dynamic model of the process and are customarily executed in electronic control units. This work first identifies the software techniques and tools required to easily write efficient code for multibody models to be simulated on ARM-based embedded systems. Automatic Programming and Source Code Translation are the two techniques that were chosen to generate source code for multibody models in different programming languages. Automatic Programming is used to generate procedural code in an intermediate representation from an object-oriented library and Source Code Translation is used to translate the intermediate representation automatically to an interpreted language or to a compiled language for efficiency purposes. An implementation of these techniques is proposed. It is based on a Python template engine and AST tree walkers for Source Code Generation and on a model-driven translator for the Source Code Translation. The code is translated from a metalanguage to any of the following four programming languages: Python-Numpy, Matlab, C++-Armadillo, C++-Eigen. Two examples of multibody models were simulated: a four-bar linkage with multiple loops and a 3D vehicle steering system. The code for these examples has been generated and executed on two ARM-based single-board computers. Using compiled languages, both models could be simulated faster than real-time despite the low resources and performance of these embedded systems. Finally, the real-time performance of both models was evaluated when executed in hard real-time on Xenomai for both embedded systems. This work shows through measurements that Automatic Programming and Source Code Translation are valuable techniques to develop real-time multibody models to be used in embedded observers and controllers.
Hard real-time multibody simulations using ARM-based embedded systems
International Nuclear Information System (INIS)
Pastorino, Roland; Cosco, Francesco; Naets, Frank; Desmet, Wim; Cuadrado, Javier
2016-01-01
The real-time simulation of multibody models on embedded systems is of particular interest for controllers and observers such as model predictive controllers and state observers, which rely on a dynamic model of the process and are customarily executed in electronic control units. This work first identifies the software techniques and tools required to easily write efficient code for multibody models to be simulated on ARM-based embedded systems. Automatic Programming and Source Code Translation are the two techniques that were chosen to generate source code for multibody models in different programming languages. Automatic Programming is used to generate procedural code in an intermediate representation from an object-oriented library and Source Code Translation is used to translate the intermediate representation automatically to an interpreted language or to a compiled language for efficiency purposes. An implementation of these techniques is proposed. It is based on a Python template engine and AST tree walkers for Source Code Generation and on a model-driven translator for the Source Code Translation. The code is translated from a metalanguage to any of the following four programming languages: Python-Numpy, Matlab, C++-Armadillo, C++-Eigen. Two examples of multibody models were simulated: a four-bar linkage with multiple loops and a 3D vehicle steering system. The code for these examples has been generated and executed on two ARM-based single-board computers. Using compiled languages, both models could be simulated faster than real-time despite the low resources and performance of these embedded systems. Finally, the real-time performance of both models was evaluated when executed in hard real-time on Xenomai for both embedded systems. This work shows through measurements that Automatic Programming and Source Code Translation are valuable techniques to develop real-time multibody models to be used in embedded observers and controllers.
Classical molecular dynamics simulation of nuclear fuels
International Nuclear Information System (INIS)
Devanathan, R.; Krack, M.; Bertolus, M.
2015-01-01
Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)
The 2011 Dynamics of Molecular Collisions Conference
Energy Technology Data Exchange (ETDEWEB)
Nesbitt, David J. [JILA, NIST
2011-07-11
The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor
Applications of Lie Group Theory to the Modeling and Control of Multibody Systems
International Nuclear Information System (INIS)
Mladenova, Clementina D.
1999-01-01
This paper reviews our research activities concerning the modeling and control of rigid and elastic joint multibody mechanical systems, including some investigations into nonholonomic systems. Bearing in mind the different parameterizations of the rotation group in three-dimensional space SO(3), and the fact that the properties of the parameterization more or less influence the efficiency of the dynamics model, here the so-called vector parameter is used for parallel considerations of rigid body motion and of rigid and elastic joint multibody mechanical systems. Besides the fundamental role of this study, the vector-parameter approach is efficient in its computational aspect and quite convenient for real time simulation and control. The consideration of the mechanical system on the configuration space of pure vector parameters with a group structure opens the possibilities for the Lie group theory to be applied in problems of dynamics and control
Molecular structures and intramolecular dynamics of pentahalides
Ischenko, A. A.
2017-03-01
This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp; Tchipev, Nikola
2012-01-01
We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm
Hydration dynamics in water clusters via quantum molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of
Molecular dynamics simulation of laser shock phenomena
Energy Technology Data Exchange (ETDEWEB)
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)
Molecular dynamic simulation study of molten cesium
Directory of Open Access Journals (Sweden)
Yeganegi Saeid
2017-01-01
Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.
Nonequilibrium molecular dynamics: The first 25 years
International Nuclear Information System (INIS)
Hoover, W.G.
1992-08-01
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments
Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Cedrix J. Dongmo Foumthuim
2018-01-01
Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
Armen, Roger S; Chen, Jianhan; Brooks, Charles L
2009-10-13
Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.
A molecular dynamics simulation study of chloroform
Tironi, Ilario G.; van Gunsteren, Wilfred F.
Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.
Molecular beam studies of reaction dynamics
International Nuclear Information System (INIS)
Lee, Yuan T.
1991-03-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation
A molecular dynamics approach to barrodiffusion
Cooley, James; Marciante, Mathieu; Murillo, Michael
2016-10-01
Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin
Molecular beam studies of reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Approximation of quantum observables by molecular dynamics simulations
Sandberg, Mattias
2016-01-01
In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.
Approximation of quantum observables by molecular dynamics simulations
Sandberg, Mattias
2016-01-06
In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.
Three-dimensional formulation of rigid-flexible multibody systems with flexible beam elements
International Nuclear Information System (INIS)
Garcia-Vallejo, D.; Mayo, J.; Escalona, J. L.; Dominguez, J.
2008-01-01
Multibody systems generally contain solids with appreciable deformations and which decisively influence the dynamics of the system. These solids have to be modeled by means of special formulations for flexible solids. At the same time, other solids are of such a high stiffness that they may be considered rigid, which simplifies their modeling. For these reasons, for a rigid-flexible multibody system, two types of formulations coexist in the equations of the system. Among the different possibilities provided in the literature on the material, the formulation in natural coordinates and the formulation in absolute nodal coordinates are utilized in this paper to model the rigid and flexible solids, respectively. This paper contains a mixed formulation based on the possibility of sharing coordinates between a rigid solid and a flexible solid. The global mass matrix of the system is shown to be constant and, in addition, many of the constraint equations obtained upon utilizing these formulations are linear and can be eliminated
Attitude coordination of multi-HUG formation based on multibody system theory
Xue, Dong-yang; Wu, Zhi-liang; Qi, Er-mai; Wang, Yan-hui; Wang, Shu-xin
2017-04-01
Application of multiple hybrid underwater gliders (HUGs) is a promising method for large scale, long-term ocean survey. Attitude coordination has become a requisite for task execution of multi-HUG formation. In this paper, a multibody model is presented for attitude coordination among agents in the HUG formation. The HUG formation is regarded as a multi-rigid body system. The interaction between agents in the formation is described by artificial potential field (APF) approach. Attitude control torque is composed of a conservative torque generated by orientation potential field and a dissipative term related with angular velocity. Dynamic modeling of the multibody system is presented to analyze the dynamic process of the HUG formation. Numerical calculation is carried out to simulate attitude synchronization with two kinds of formation topologies. Results show that attitude synchronization can be fulfilled based on the multibody method described in this paper. It is also indicated that different topologies affect attitude control quality with respect to energy consumption and adjusting time. Low level topology should be adopted during formation control scheme design to achieve a better control effect.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)
2015-06-28
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
International Nuclear Information System (INIS)
Gottwald, Fabian; Karsten, Sven; 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 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
Thermal transpiration: A molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)
2014-12-09
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Investigating Ebola virus pathogenicity using molecular dynamics.
Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N
2017-08-11
Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.
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…
Molecular beam studies of adsorption dynamics
International Nuclear Information System (INIS)
Arumainayagam, C.R.; McMaster, M.C.; Madix, R.J.
1991-01-01
We have investigated the trapping dynamics of C 1 -C 3 alkanes and Xe on Pt(111) using supersonic molecular beams and a direct technique to measure trapping probabilities. We have extended a one-dimensional model based on classical mechanics to include trapping and have found semiquantitative agreement with experimental results for the dependence of the initial trapping probability on incident translational energy at normal incidence. Our measurements of the initial trapping probability as a function of incident translational energy at normal incidence are in agreement with previous mean translational energy measurements for Xe and CH 4 desorbing near the surface normal, in accordance with detailed balance. However, the angular dependence of the initial trapping probability shows deviations from normal energy scaling, demonstrating the importance of parallel momentum in the trapping process and the inadequacy of one-dimensional models. The dependence of the initial trapping probability of Xe on incident translational energy and angle is quite well fit by three-dimensional stochastic classical trajectory calculations utilizing a Morse potential. Angular distributions of the scattered molecules indicate that the trapping probability is not a sensitive function of surface temperature. The trapping probability increases with surface coverage in quantitative agreement with a modified Kisliuk model which incorporates enhanced trapping onto the monolayer. We have also used the direct technique to study trapping onto a saturated monolayer state to investigate the dynamics of extrinsic precursor adsorption and find that the initial trapping probability onto the monolayer is higher than on the clean surface. The initial trapping probability onto the monolayer scales with total energy, indicating a highly corrugated interaction potential
Shen, Wenqing; Kumari, Niru; Gibson, Gary; Jeon, Yoocharn; Henze, Dick; Silverthorn, Sarah; Bash, Cullen; Kumar, Satish
2018-02-01
Non-volatile memory is a promising alternative to present memory technologies. Oxygen vacancy diffusion has been widely accepted as one of the reasons for the resistive switching mechanism of transition-metal-oxide based resistive random access memory. In this study, molecular dynamics simulation is applied to investigate the diffusion coefficient and activation energy of oxygen in amorphous hafnia. Two sets of empirical potential, Charge-Optimized Many-Body (COMB) and Morse-BKS (MBKS), were considered to investigate the structural and diffusion properties at different temperatures. COMB predicts the activation energy of 0.53 eV for the temperature range of 1000-2000 K, while MBKS predicts 2.2 eV at high temperature (1600-2000 K) and 0.36 eV at low temperature (1000-1600 K). Structural changes and appearance of nano-crystalline phases with increasing temperature might affect the activation energy of oxygen diffusion predicted by MBKS, which is evident from the change in coordination number distribution and radial distribution function. None of the potentials make predictions that are fully consistent with density functional theory simulations of both the structure and diffusion properties of HfO2. This suggests the necessity of developing a better multi-body potential that considers charge exchange.
Folding very short peptides using molecular dynamics.
Directory of Open Access Journals (Sweden)
Bosco K Ho
2006-04-01
Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.
Molecular dynamics studies of displacement cascades
International Nuclear Information System (INIS)
Averback, R.S.; Hsieh, Horngming; Diaz de la Rubia, T.
1990-02-01
Molecular-dynamics simulations of cascades in Cu and Ni with primary-knock-on energies up to 5 keV and lattice temperatures in the range 0 K--700 K are described. Interatomic forces were represented by either the Gibson II (Cu) or Johnson-Erginsoy (Ni) potentials in most of this work, although some simulations using ''Embedded Atom Method'' potentials, e.g., for threshold events in Ni 3 Al, are also presented. The results indicate that the primary state of damage produced by displacement cascades is controlled by two phenomena, replacement collision sequences during the collisional phase of the cascade and local melting during the thermal spike. As expected, the collisional phase is rather similar in Cu and Ni, however, the thermal spike is of longer duration and has a more pronounced influence in Cu than Ni. When the ambient temperature of the lattice is increased, the melt zones are observed to both increase in size and cool more slowly. This has the effect of reducing defect production and enhancing atomic mixing and disordering. The implications of these results for defect production, cascade collapse, atomic disordering will be discussed. 34 refs., 7 figs., 2 tabs
A molecular dynamics simulation code ISIS
International Nuclear Information System (INIS)
Kambayashi, Shaw
1992-06-01
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)
Spin-diffusions and diffusive molecular dynamics
Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon
2017-12-01
Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.
Modeling shockwave deformation via molecular dynamics
International Nuclear Information System (INIS)
Holian, B.L.
1987-01-01
Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too
Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics
Directory of Open Access Journals (Sweden)
Lin Lin
2013-12-01
Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.
Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions
Czech Academy of Sciences Publication Activity Database
Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel
2016-01-01
Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016
Molecular dynamics using quasielastic neutron scattering
Mitra, S
2003-01-01
Quasielastic neutron scattering (QENS) technique is well suited to study the molecular motions (rotations and translations) in solids or liquids. It offers a unique possibility of analysing spatial dimensions of atomic or molecular processes in their development over time. We describe here some of the systems studied using the QENS spectrometer, designed, developed and commissioned at Dhruva reactor in Trombay. We have studied a variety of systems to investigate the molecular motion, for example, simple molecular solids, molecules adsorbed in confined medium like porous systems or zeolites, monolayer-protected nano-sized metal clusters, water in Portland cement as it cures with time, etc. (author)
Integrating Multibody Simulation and CFD: toward Complex Multidisciplinary Design Optimization
Pieri, Stefano; Poloni, Carlo; Mühlmeier, Martin
This paper describes the use of integrated multidisciplinary analysis and optimization of a race car model on a predefined circuit. The objective is the definition of the most efficient geometric configuration that can guarantee the lowest lap time. In order to carry out this study it has been necessary to interface the design optimization software modeFRONTIER with the following softwares: CATIA v5, a three dimensional CAD software, used for the definition of the parametric geometry; A.D.A.M.S./Motorsport, a multi-body dynamic simulation software; IcemCFD, a mesh generator, for the automatic generation of the CFD grid; CFX, a Navier-Stokes code, for the fluid-dynamic forces prediction. The process integration gives the possibility to compute, for each geometrical configuration, a set of aerodynamic coefficients that are then used in the multiboby simulation for the computation of the lap time. Finally an automatic optimization procedure is started and the lap-time minimized. The whole process is executed on a Linux cluster running CFD simulations in parallel.
Criteria of benchmark selection for efficient flexible multibody system formalisms
Directory of Open Access Journals (Sweden)
Valášek M.
2007-10-01
Full Text Available The paper deals with the selection process of benchmarks for testing and comparing efficient flexible multibody formalisms. The existing benchmarks are briefly summarized. The purposes for benchmark selection are investigated. The result of this analysis is the formulation of the criteria of benchmark selection for flexible multibody formalisms. Based on them the initial set of suitable benchmarks is described. Besides that the evaluation measures are revised and extended.
Crystal structure and pair potentials: A molecular-dynamics study
Energy Technology Data Exchange (ETDEWEB)
Parrinello, M.; Rahman, A.
1980-10-06
With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.
Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation
National Research Council Canada - National Science Library
Johnston, K
1998-01-01
.... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...
Molecular Dynamics and Bioactivity of a Novel Mutated Human ...
African Journals Online (AJOL)
Keywords: Parathyroid hormone, Mutation prediction, Molecular dynamics, RANKL/OPG, UAMS-32P cell. Tropical .... PTH1R were used as MD simulation starting points. A full-atom ... Values of RMSD, Rg, and potential energy evaluation ...
Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting
National Research Council Canada - National Science Library
Low, Tammy K
2006-01-01
.... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...
A molecular dynamics calculation of solid phase of malonic acid ...
Indian Academy of Sciences (India)
Sathya S R R Perumal
Keywords. Hydrogen bond chain; elastic constants; molecular dynamics. 1. Introduction ... theory - a probabilistic model to determine the hydro- gen bonds within the .... compares poorly with the experimental value of 108.5. Similarly β and γ ...
Molecular dynamics and Monte Carlo calculations in statistical mechanics
International Nuclear Information System (INIS)
Wood, W.W.; Erpenbeck, J.J.
1976-01-01
Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references
Next generation extended Lagrangian first principles molecular dynamics.
Niklasson, Anders M N
2017-08-07
Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.
Dynamical analysis of highly excited molecular spectra
Energy Technology Data Exchange (ETDEWEB)
Kellman, M.E. [Univ. of Oregon, Eugene (United States)
1993-12-01
The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.
Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter
DEFF Research Database (Denmark)
Toxvaerd, Søren
2001-01-01
Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...
A fermionic molecular dynamics technique to model nuclear matter
International Nuclear Information System (INIS)
Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.
2009-01-01
Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)
Current-driven dynamics in molecular-scale devices
International Nuclear Information System (INIS)
Seideman, Tamar
2003-01-01
We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)
Molecular Dynamic Modeling and Simulation for Polymers
National Research Council Canada - National Science Library
Harrell, Anthony
2003-01-01
... the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity...
Molecular dynamics of a proguanil derivative
African Journals Online (AJOL)
pc
Proguanil is a prophylactic antimalarial drug t .... presence of resistance to individual component. ... This is the mathematical ... predicting equilibrium structures of molecular systems ..... for the modeling and subsequent development of.
Visualizing functional motions of membrane transporters with molecular dynamics simulations.
Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad
2013-01-29
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.
Pseudorotational dynamics of small molecular species
International Nuclear Information System (INIS)
Hagelberg, F.
2002-01-01
The electron nuclear dynamics (END) theory was designed to provide a full description of the dynamic development of the electronic system. It is independent of any potential energy surface constructions. The dynamic behavior of molecules close to the threshold of dissociation was the objective of this study. Thus, simulations based on END theory were performed with the aim to extend the current understanding of the dynamic features of pseudorotational into a non-adiabatic regime. Electron dynamics of triatomic species (H 3 + and Li 3 + ) in terms of electronic angular momentum expectation values were characterized. Finally, it is shown that the expansion coefficients which carry the information about the excitation content of the electronic system at any stage of the motional process can be calculated. (nevyjel)
Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes
Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes
2007-01-01
This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the
Energy conservation in molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren; Heilmann, Ole; Dyre, J. C.
2012-01-01
Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...
Invariant molecular-dynamics approach to structural phase transitions
International Nuclear Information System (INIS)
Wentzcovitch, R.M.
1991-01-01
Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics
Ab initio molecular dynamics in a finite homogeneous electric field.
Umari, P; Pasquarello, Alfredo
2002-10-07
We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.
Classical and quantum molecular dynamics in NMR spectra
Szymański, Sławomir
2018-01-01
The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...
Dynamics of molecular superrotors in an external magnetic field
Korobenko, Aleksey; Milner, Valery
2015-08-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.
Dynamics of molecular superrotors in an external magnetic field
International Nuclear Information System (INIS)
Korobenko, Aleksey; Milner, Valery
2015-01-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)
Molecular dynamics with deterministic and stochastic numerical methods
Leimkuhler, Ben
2015-01-01
This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...
Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation
Institute of Scientific and Technical Information of China (English)
Chengzhen Sun; Bofeng Bai
2017-01-01
Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.
First principles molecular dynamics without self-consistent field optimization
International Nuclear Information System (INIS)
Souvatzis, Petros; Niklasson, Anders M. N.
2014-01-01
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations
Next Generation Extended Lagrangian Quantum-based Molecular Dynamics
Negre, Christian
2017-06-01
A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.
Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C
2013-11-07
Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.
Molecular dynamics study of atomic displacements in disordered solid alloys
Puzyrev, Yevgeniy S.
The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.
Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics
International Nuclear Information System (INIS)
Sanz-Navarro, Carlos F.
2002-01-01
The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)
Dynamic molecular oxygen production in cometary comae
Yao, Yunxi; Giapis, Konstantinos P.
2017-05-01
Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2-. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.
Cawkwell, M J; Niklasson, Anders M N
2012-10-07
Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.
Femtochemistry and femtobiology ultrafast dynamics in molecular science
Douhal, Abderrazzak
2002-01-01
This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol
AceCloud: Molecular Dynamics Simulations in the Cloud.
Harvey, M J; De Fabritiis, G
2015-05-26
We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.
State-to-state dynamics of molecular energy transfer
Energy Technology Data Exchange (ETDEWEB)
Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)
1993-12-01
The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.
Chain networking revealed by molecular dynamics simulation
Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing
Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)
Multiple time step integrators in ab initio molecular dynamics
International Nuclear Information System (INIS)
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-01-01
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp
2012-06-01
We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.
Plastic dislocation motion via nonequilibrium molecular and continuum dynamics
International Nuclear Information System (INIS)
Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.
1980-01-01
The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition
Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties
Czech Academy of Sciences Publication Activity Database
Fojtíková, J.; Kalvoda, L.; Sedlák, Petr
2015-01-01
Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf
Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation
International Nuclear Information System (INIS)
Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.
1991-01-01
We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus
Theory of multiexciton dynamics in molecular chains
Wang, Luxia; May, Volkhard
2016-11-01
Ultrafast and strong optical excitation of a molecular system is considered which is formed by a regular one-dimensional arrangement of identical molecules. As it is typical for zinc chlorine-type molecules the transition energy from the ground state to the first excited singlet state is assumed to be smaller than the energy difference between the first excited state and the following one. This enables the creation of many excitons without their immediate quenching due to exciton-exciton annihilation. As a first step into the field of dense Frenkel-exciton systems the present approach stays at a mean-field type of description and ignores vibrational contributions. The resulting nonlinear kinetic equations mix Rabi-type oscillations with those caused by energy transfer and suggest an excitation-dependent narrowing of the exciton band. The indication of this effect in the framework of a two-color pump-probe experiment and of the detection of photon emission is discussed.
Molecular dynamics studies of superionic conductors
International Nuclear Information System (INIS)
Rahman, A.
1979-01-01
Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard
Photoionization dynamics of excited molecular states
International Nuclear Information System (INIS)
Dehmer, J.L.; O'Halloran, M.A.; Tomkins, F.S.; Dehmer, P.M.; Pratt, S.T.
1987-01-01
Resonance Enhanced Multiphoton Ionization (REMPI) utilizes tunable dye lasers to ionize an atom or molecule by first preparing an excited state by multiphoton absorption and then ionizing that state before it can decay. This process is highly selective with respect to both the initial and resonant intermediate states of the target, and it can be extremely sensitive. In addition, the products of the REMPI process can be detected as needed by analyzing the resulting electrons, ions, fluorescence, or by additional REMPI. This points to a number of opportunities for exploring excited state physics and chemistry at the quantum-state-specific level. Here we will first give a brief overview of the large variety of experimental approaches to excited state phenomena made possible by REMPI. Then we will examine in more detail, recent studies of the three photon resonant, four photon (3 + 1) ionization of H 2 via the C 'PI/sup u/ state. Strong non-Franck-Condon behavior in the photoelectron spectra of this nominally simple Rydberg state has led to the examination of a variety of dynamical mechanisms. Of these, the role of doubly excited autoionizing states now seems decisive. Progress on photoelectron studies of autoionizing states in H 2 , excited in a (2 + 1) REMPI process via the E, F 1 Σ/sub g/ + will also be briefly discussed. 26 refs., 7 figs
Dynamical photo-induced electronic properties of molecular junctions
Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.
2018-03-01
Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.
Accelerating convergence of molecular dynamics-based structural relaxation
DEFF Research Database (Denmark)
Christensen, Asbjørn
2005-01-01
We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...
Molecular dynamics of the structure and thermodynamics of dusty ...
African Journals Online (AJOL)
The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...
A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS
AHLSTROM, P; BERENDSEN, HJC
1993-01-01
Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)
Structure of hydrogenated amorphous silicon from ab initio molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))
1991-09-15
We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.
Ab initio molecular dynamics simulation of laser melting of silicon
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1996-01-01
The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting
Microsecond atomic-scale molecular dynamics simulations of polyimides
Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.
2013-01-01
We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long
Molecular dynamics study of the silica-water-SDA interactions
Szyja, B.M.; Jansen, A.P.J.; Verstraelen, T.; Santen, van R.A.
2009-01-01
In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species
Molecular dynamics simulations of ballistic He penetration into W fuzz
Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.
2016-01-01
Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
Directory of Open Access Journals (Sweden)
Renata De Paris
2015-01-01
Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.
Toluene model for molecular dynamics simulations in the ranges 298
Fioroni, M.; Vogt, D.
2004-01-01
An all-atom model for toluene is presented in the framework of classical molecular dynamics (MD). The model has been parametrized under the GROMOS96 force field to reproduce the physicochemical properties of the neat liquid. Four new atom types have been introduced, distinguishing between carbons
Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics
Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de
1997-01-01
The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.
Molecular dynamics simulations and free energy profile of ...
Indian Academy of Sciences (India)
aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.
Molecular dynamics simulations of lipid vesicle fusion in atomic detail
Knecht, Volker; Marrink, Siewert-Jan
The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic
Molecular dynamic analysis of the structure of dendrimers
Energy Technology Data Exchange (ETDEWEB)
Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it
2004-01-01
We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.
Molecular dynamic analysis of the structure of dendrimers
International Nuclear Information System (INIS)
Canetta, E.; Maino, G.
2004-01-01
We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques
Molecular dynamics study on the relaxation properties of bilayered ...
Indian Academy of Sciences (India)
2017-08-31
Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...
Metal cluster fission: jellium model and Molecular dynamics simulations
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia
2004-01-01
Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...
Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...
Indian Academy of Sciences (India)
Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...
Free energy from molecular dynamics with multiple constraints
den Otter, Wouter K.; Briels, Willem J.
2000-01-01
In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to
Molecular dynamics simulations on PGLa using NMR orientational constraints
Energy Technology Data Exchange (ETDEWEB)
Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)
2015-11-15
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
Multiscale equation-free algorithms for molecular dynamics
Abi Mansour, Andrew
Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...
Reaction dynamics of molecular hydrogen on silicon surfaces
DEFF Research Database (Denmark)
Bratu, P.; Brenig, W.; Gross, A.
1996-01-01
of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...
Implementation of surface hopping molecular dynamics using semiempirical methods
International Nuclear Information System (INIS)
Fabiano, E.; Keal, T.W.; Thiel, W.
2008-01-01
A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.
Li, Jianwei; Nowak, Piotr; Otto, Sijbren
2013-06-26
Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.
Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms
Directory of Open Access Journals (Sweden)
Dirk-Sören Lühmann
2015-08-01
Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.
Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.
Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N
2015-04-21
Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik; Szepessy, Anders
2010-01-01
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik
2010-03-17
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
Molecular electron recollision dynamics in intense circularly polarized laser pulses
Bandrauk, André D.; Yuan, Kai-Jun
2018-04-01
Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
2014-01-01
Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585
Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.
Cooke, Ben; Schmidler, Scott C
2008-10-28
We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.
Orbital free molecular dynamics; Approche sans orbitale des plasmas denses
Energy Technology Data Exchange (ETDEWEB)
Lambert, F
2007-08-15
The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)
A multibody motorcycle model with rigid-ring tyres: formulation and validation
Leonelli, Luca; Mancinelli, Nicolò
2015-06-01
The aim of this paper is the development and validation of a three-dimensional multibody motorcycle model including a rigid-ring tyre model, taking into account both the slopes and elevation of the road surface. In order to achieve accurate assessment of ride and handling performances of a road racing motorcycle, a tyre model capable of reproducing the dynamic response to actual road excitation is required. While a number of vehicle models with such feature are available for car application, the extension to the motorcycle modelling has not been addressed yet. To do so, a novel parametrisation for the general motorcycle kinematics is proposed, using a mixed reference point and relative coordinates approach. The resulting description, developed in terms of dependent coordinates, makes it possible to include the rigid-ring kinematics as well as road elevation and slopes, without affecting computational efficiency. The equations of motion for the whole multibody system are derived symbolically and the constraint equations arising from the dependent coordinate formulation are handled using the position and velocity vector projection technique. The resulting system of equations is integrated in time domain using a standard ordinary differential equation (ODE) algorithm. Finally, the model is validated with respect to experimentally measured data in both time and frequency domains.
Analysis of Large Flexible Body Deformation in Multibody Systems Using Absolute Coordinates
Energy Technology Data Exchange (ETDEWEB)
Dombrowski, Stefan von [Institute of Robotics and Mechatronics, German Aerospace Center (DLR) (Germany)], E-mail: stefan.von.dombrowski@dlr.de
2002-11-15
To consider large deformation problems in multibody system simulations a finite element approach, called absolute nodal coordinate.formulation,has been proposed. In this formulation absolute nodal coordinates and their material derivatives are applied to represent both deformation and rigid body motion. The choice of nodal variables allows a fully nonlinear representation of rigid body motion and can provide the exact rigid body inertia in the case of large rotations. The methodology is especially suited for but not limited to modeling of beams, cables and shells in multibody dynamics.This paper summarizes the absolute nodal coordinate formulation for a 3D Euler-Bernoulli beam model, in particular the definition of nodal variables, corresponding generalized elastic and inertia forces and equations of motion. The element stiffness matrix is a nonlinear function of the nodal variables even in the case of linearized strain/displacement relations. Nonlinear strain/displacement relations can be calculated from the global displacements using quadrature formulae.Computational examples are given which demonstrate the capabilities of the applied methodology. Consequences of the choice of shape.functions on the representation of internal forces are discussed. Linearized strain/displacement modeling is compared to the nonlinear approach and significant advantages of the latter, when using the absolute nodal coordinate formulation, are outlined.
Analysis of Large Flexible Body Deformation in Multibody Systems Using Absolute Coordinates
International Nuclear Information System (INIS)
Dombrowski, Stefan von
2002-01-01
To consider large deformation problems in multibody system simulations a finite element approach, called absolute nodal coordinate.formulation,has been proposed. In this formulation absolute nodal coordinates and their material derivatives are applied to represent both deformation and rigid body motion. The choice of nodal variables allows a fully nonlinear representation of rigid body motion and can provide the exact rigid body inertia in the case of large rotations. The methodology is especially suited for but not limited to modeling of beams, cables and shells in multibody dynamics.This paper summarizes the absolute nodal coordinate formulation for a 3D Euler-Bernoulli beam model, in particular the definition of nodal variables, corresponding generalized elastic and inertia forces and equations of motion. The element stiffness matrix is a nonlinear function of the nodal variables even in the case of linearized strain/displacement relations. Nonlinear strain/displacement relations can be calculated from the global displacements using quadrature formulae.Computational examples are given which demonstrate the capabilities of the applied methodology. Consequences of the choice of shape.functions on the representation of internal forces are discussed. Linearized strain/displacement modeling is compared to the nonlinear approach and significant advantages of the latter, when using the absolute nodal coordinate formulation, are outlined
MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Molecular dynamics of TBP and DBP studied by neutron transmission
International Nuclear Information System (INIS)
Salles Filho, J.B.V.; Refinetti, M.E.; Fulfaro, R.; Vinhas, L.A.
1984-04-01
Differences between the properties of TBP and DBP, concerning the uranium extraction processes, may be related to certain characteristics of the molecular dynamics of each compound. In order to investigate the dynamical behaviour of hydrogen in these molecules, neutron transmission of TBP and DBP has been measured as a function of neutron wavelenght in the range 4.0 - 6.0 A, at room temperature. Scattering cross sections per hydrogen atom have been obtained. From the comparison with results previously obtained for n-butanol, similar dynamical behaviour of butyl radicals in these compounds could be observed. This similarity indicates that the presence of two or three butyl radicals in butylphosphate molecules does not exert influence in the hydrogen motion of methyl and methylene groups. This suggests that the different chemical behaviour between TBP and DBP is related to the dynamics of the hydrogen directly bound to the DBP phosphate group.(Author) [pt
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
International Nuclear Information System (INIS)
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-01-01
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study
National Research Council Canada - National Science Library
Isaev, Olexandr; Kholod, Yana; Gorb, Leonid; Qasim, Mohammad; Fredrickson, Herb; Leszczynski, Jerzy
2006-01-01
.... In the present study molecular structure, electrostatic potential, vibrational spectrum and dynamics of thermal decomposition of CL-20 have been investigated by static and dynamic methods of ab...
Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories
Directory of Open Access Journals (Sweden)
Jenny Farmer
2017-11-01
Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.
Czech Academy of Sciences Publication Activity Database
Chocholoušová, Jana; Feig, M.
2006-01-01
Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006
Coalescence of silver unidimensional structures by molecular dynamics simulation
International Nuclear Information System (INIS)
Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.
2007-01-01
The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)
Microscopic study of nuclear 'pasta' by quantum molecular dynamics
International Nuclear Information System (INIS)
Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu
2002-01-01
Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. and be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape. We also observe intermediate phases, which has complicated nuclear shapes. Geometrical structures of matter are analyzed with Minkowski functionals, and it is found out that intermediate phases can be characterized as ones with negative Euler characteristic. Our result suggests the existence of these kinds of phases in addition to the simple 'pasta' phases in neutron star crusts. (author)
Nonlinear dynamics of zigzag molecular chains (in Russian)
DEFF Research Database (Denmark)
Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth
1999-01-01
models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...
The chaos and order in nuclear molecular dynamics
International Nuclear Information System (INIS)
Srokowski, T.
1995-01-01
The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or 12 C, 16 O and 20 Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs
Statistical ensembles and molecular dynamics studies of anisotropic solids. II
International Nuclear Information System (INIS)
Ray, J.R.; Rahman, A.
1985-01-01
We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities
Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ
DEFF Research Database (Denmark)
Euro, Liliya; Haapanen, Outi; Róg, Tomasz
2017-01-01
of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...
Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates
Energy Technology Data Exchange (ETDEWEB)
Zhang Junfang [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia); Rivero, Mayela [CSIRO Petroleum, PO Box 1130, Bentley, Western Australia, 6102 (Australia); Choi, S K [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia)
2007-02-14
We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 A. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.
Fermionic molecular dynamics for ground states and collisions of nuclei
International Nuclear Information System (INIS)
Feldmeier, H.; Bieler, K.; Schnack, J.
1994-08-01
The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)
Fermionic molecular dynamics for colliding and decaying nuclei
International Nuclear Information System (INIS)
Feldmeier, H.; Schnack, J.
1993-11-01
Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)
Molecular Dynamics Simulations of displacement cascades in metallic systems
International Nuclear Information System (INIS)
Doan, N.V.; Tietze, H.
1995-01-01
We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)
Optical spectra and lattice dynamics of molecular crystals
Zhizhin, GN
1995-01-01
The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.
Enhancing protein adsorption simulations by using accelerated molecular dynamics.
Directory of Open Access Journals (Sweden)
Christian Mücksch
Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.
Stereochemical errors and their implications for molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Freddolino Peter L
2011-05-01
Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.
Ultrafast dissociation: An unexpected tool for probing molecular dynamics
International Nuclear Information System (INIS)
Morin, Paul; Miron, Catalin
2012-01-01
Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.
Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite
Yoon, Seyoon; Monteiro, Paulo J.M.
2013-01-01
The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current
High-temperature annealing of graphite: A molecular dynamics study
Petersen, Andrew; Gillette, Victor
2018-05-01
A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
Energy Technology Data Exchange (ETDEWEB)
Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche
1997-09-01
Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.
Incorporation of quantum statistical features in molecular dynamics
International Nuclear Information System (INIS)
Ohnishi, Akira; Randrup, J.
1995-01-01
We formulate a method for incorporating quantum fluctuations into molecular-dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous transitions to occur between the wave packets which are not energy eigenstates. The ensuing diffusive evolution in the space of the wave packet parameters exhibits appealing physical properties, including relaxation towards quantum-statistical equilibrium. (author)
Molecular Dynamics Simulations of Tensile Behavior of Copper
Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.
2014-01-01
Molecular dynamics simulations on tensile deformation of initially defect free single crystal copper nanowire oriented in {100} has been carried out at 10 K under adiabatic and isothermal loading conditions. The tensile behaviour was characterized by sharp rise in stress in elastic regime followed by sudden drop at the point of dislocation nucleation. The important finding is that the variation in dislocation density is correlated with the observed stress-strain response. Several interesting ...
Automated processing of data generated by molecular dynamics
International Nuclear Information System (INIS)
Lobato Hoyos, Ivan; Rojas Tapia, Justo; Instituto Peruano de Energia Nuclear, Lima
2008-01-01
A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane
Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping
2012-01-01
We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present new results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition...
Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties
International Nuclear Information System (INIS)
Swygenhoven, H. van; Caro, A.
1997-01-01
Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young's modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs
Accelerating Molecular Dynamic Simulation on Graphics Processing Units
Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.
2009-01-01
We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. PMID:19191337
Molecular dynamics simulation of cascade damage in gold
International Nuclear Information System (INIS)
Alonso, E.; Caturla, M.J.; Tang, M.; Huang, H.; Diaz de la Rubia, T.
1997-01-01
High-energy cascades have been simulated in gold using molecular dynamics with a modified embedded atom method potential. The results show that both vacancy and interstitial clusters form with high probability as a result of intracascade processes. The formation of clusters has been interpreted in terms of the high pressures generated in the core of the cascade during the early stages. The authors provide evidence that correlation between interstitial and vacancy clustering exists
Thermal conductivity of ZnTe investigated by molecular dynamics
International Nuclear Information System (INIS)
Wang Hanfu; Chu Weiguo
2009-01-01
The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.
Fragmentation dynamics of molecular hydrogen in strong ultrashort laser pulses
International Nuclear Information System (INIS)
Rudenko, A; Feuerstein, B; Zrost, K; Jesus, V L B de; Ergler, T; Dimopoulou, C; Schroeter, C D; Moshammer, R; Ullrich, J
2005-01-01
We present the results of a systematic experimental study of dissociation and Coulomb explosion of molecular hydrogen induced by intense ultrashort (7-25 fs) laser pulses. Using coincident recoil-ion momentum spectroscopy we can distinguish the contributions from dissociation and double ionization even if they result in the same kinetic energies of the fragments. The dynamics of all fragmentation channels drastically depends on the pulse duration, and for 7 fs pulses becomes extremely sensitive to the pulse shape
Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation
DEFF Research Database (Denmark)
Pedersen, U.R.; Peters, Günther H.j.; Westh, P.
2007-01-01
The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...
Molecular dynamics simulation of bubble nucleation in explosive boiling
International Nuclear Information System (INIS)
Zou Yu; Chinese Academy of Sciences, Beijing; Huai Xiulan; Liang Shiqiang
2009-01-01
Molecular dynamics (MD) simulation is carried out for the bubble nucleation of liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. The results indicate that the initial equilibrium temperature of liquid and molecular cluster size affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of bubble nucleation, the potential energy of the system slowly increases. In the bubble nucleation of explosive boiling, the lower the initial equilibrium temperature, the larger the size of the molecular cluster, and the more the heat transferred into the system of the simulation cell, causing the increase potential energy in a larger range. (authors)
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
International Nuclear Information System (INIS)
Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid
2015-01-01
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields
Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics
Directory of Open Access Journals (Sweden)
Wei Zhang
2017-07-01
Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.
Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations
International Nuclear Information System (INIS)
Kim, Woongkee; Kaviany, Massoud; Shim, J. H.
2014-01-01
It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments
Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets
Lehmann, Kevin K.
2003-03-01
Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.
Excitation dynamics and relaxation in a molecular heterodimer
International Nuclear Information System (INIS)
Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.
2012-01-01
Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.
Molecular dynamics simulations of solutions at constant chemical potential
Perego, C.; Salvalaglio, M.; Parrinello, M.
2015-04-01
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.
Non-Adiabatic Molecular Dynamics Methods for Materials Discovery
Energy Technology Data Exchange (ETDEWEB)
Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)
2017-04-04
The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.
Electron-nuclear corellations for photoinduced dynamics in molecular dimers
Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.
2003-03-01
Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).
A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations
van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J
2012-01-01
Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,
A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations
van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.
2012-01-01
Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.
2012-01-01
In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...
Hu, Hao; Liu, Haiyan
2013-05-30
Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.
DEFF Research Database (Denmark)
Papaleo, Elena
2015-01-01
that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....
Molecular dynamics investigation of tracer diffusion in a simple liquid
International Nuclear Information System (INIS)
Ould-Kaddour, F.; Barrat, J.L.
1991-05-01
Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs
Molecular dynamics of coalescence and collisions of silver nanoparticles
Energy Technology Data Exchange (ETDEWEB)
Guevara-Chapa, Enrique, E-mail: enrique_guevara@hotmail.com [Universidad Autónoma de Nuevo León, Facultad de Ciencias Físico Matemáticas (Mexico); Mejía-Rosales, Sergio [Universidad Autónoma de Nuevo León, Center for Innovation, Research and Development in Engineering and Technology (CIIDIT), and CICFIM-Facultad de Ciencias Físico Matemáticas (Mexico)
2014-12-15
We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy.
Molecular dynamics simulations of lysozyme in water/sugar solutions
Energy Technology Data Exchange (ETDEWEB)
Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)
2008-04-18
Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.
Molecular dynamics of coalescence and collisions of silver nanoparticles
International Nuclear Information System (INIS)
Guevara-Chapa, Enrique; Mejía-Rosales, Sergio
2014-01-01
We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy
Liquid-vapor coexistence by molecular dynamics simulation
International Nuclear Information System (INIS)
Baranyai, Andras; Cummings, Peter T.
2000-01-01
We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics
The classical and quantum dynamics of molecular spins on graphene
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2016-02-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.
Machine learning molecular dynamics for the simulation of infrared spectra.
Gastegger, Michael; Behler, Jörg; Marquetand, Philipp
2017-10-01
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.
Directory of Open Access Journals (Sweden)
Elena ePapaleo
2015-05-01
Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
Accelerated molecular dynamics methods: introduction and recent developments
International Nuclear Information System (INIS)
Uberuaga, Blas Pedro; Voter, Arthur F.; Perez, Danny; Shim, Y.; Amar, J.G.
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) (10, 19, 23) to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what
Accelerated molecular dynamics methods: introduction and recent developments
Energy Technology Data Exchange (ETDEWEB)
Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what
Planar reorientation maneuvers of space multibody systems using internal controls
Reyhanoglu, Mahmut; Mcclamroch, N. H.
1992-01-01
In this paper a reorientation maneuvering strategy for an interconnection of planar rigid bodies in space is developed. It is assumed that there are no exogeneous torques, and torques generated by joint motors are used as means of control so that the total angular momentum of the multibody system is a constant, assumed to be zero in this paper. The maneuver strategy uses the nonintegrability of the expression for the angular momentum. We demonstrate that large-angle maneuvers can be designed to achieve an arbitrary reorientation of the multibody system with respect to an inertial frame. The theoretical background for carrying out the required maneuvers is briefly summarized. Specifications and computer simulations of a specific reorientation maneuver, and the corresponding control strategies, are described.
Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics
Energy Technology Data Exchange (ETDEWEB)
Yu H. G.; Muckerman, J.T.
2012-05-29
The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.
Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics
Energy Technology Data Exchange (ETDEWEB)
Yu, H.G.; Muckerman, J.T.
2010-06-01
The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.
Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen
1999-06-01
Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.
Validating clustering of molecular dynamics simulations using polymer models
Directory of Open Access Journals (Sweden)
Phillips Joshua L
2011-11-01
Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our
DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS
JUFFER, AH; BERENDSEN, HJC
1993-01-01
A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the
Risselada, H. Jelger; Marrink, Siewert J.
2009-01-01
The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high
Marrink, SJ; Mark, AE
2003-01-01
Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at
Czech Academy of Sciences Publication Activity Database
Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.
2004-01-01
Roč. 70, č. 6 (2004), 0611031-0611034 ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant - others:NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004
Physical properties of Cu nanoparticles: A molecular dynamics study
International Nuclear Information System (INIS)
Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.
2014-01-01
Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index
Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems
Stanton, L. G.; Glosli, J. N.; Murillo, M. S.
2018-04-01
Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.
Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors
Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery
2015-05-01
Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.
Directory of Open Access Journals (Sweden)
Daisuke Nishiura
2017-06-01
Full Text Available Simulation of a large number of deformable bodies is often difficult because complex high-level modeling is required to address both multi-body contact and viscoelastic deformation. This necessitates the combined use of a discrete element method (DEM and a finite element method (FEM. In this study, a quadruple discrete element method (QDEM was developed for dynamic analysis of viscoelastic materials using a simpler algorithm compared to the standard FEM. QDEM easily incorporates the contact algorithm used in DEM. As the first step toward multi-body simulation, the fundamental performance of QDEM was investigated for viscoelastic analysis. The amplitude and frequency of cantilever elastic vibration were nearly equal to those obtained by the standard FEM. A comparison of creep recovery tests with an analytical solution showed good agreement between them. In addition, good correlation between the attenuation degree and the real physical viscosity was confirmed for viscoelastic vibration analysis. Therefore, the high accuracy of QDEM in the fundamental analysis of infinitesimal viscoelastic deformations was verified. Finally, the impact response of a ballast and sleeper under cyclic loading on a railway track was analyzed using QDEM as an application of deformable multi-body dynamics. The results showed that the vibration of the ballasted track was qualitatively in good agreement with the actual measurements. Moreover, the ballast layer with high friction reduced the ballasted track deterioration. This study suggests that QDEM, as an alternative to DEM and FEM, can provide deeper insights into the contact dynamics of a large number of deformable bodies.
Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.
2017-03-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.
International Nuclear Information System (INIS)
Dellerue, Serge
2000-01-01
Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr
The systematics of the deexcitation of hot nuclei and the onset of multibody decay
International Nuclear Information System (INIS)
Bowman, D.R.; Peaslee, G.F.; Colonna, N.
1989-03-01
Results from the asymmetric reactions 80 and 100 MeV/uLa + C are presented and compared to earlier work with the same system at 18 and 50 MeV/u. Fragment-fragment correlations, cross sections, and distributions in velocity space indicate the continued dominance of a quasi-binary decay mechanism with increased emission of light charged particles. The distributions in velocity also indicate a progression toward a ''fireball'' type of reaction mechanism. However, the angular distributions of the emitted fragments are incompatible with statistical production mechanisms that have successfully explained the lower energy results, and indicate the dynamical nature of the emission process. Dalitz plots of triple complex fragment coincidences are presented in order to investigate the nature of the multibody decays. 18 refs., 9 figs
Null Space Integration Method for Constrained Multibody Systems with No Constraint Violation
International Nuclear Information System (INIS)
Terze, Zdravko; Lefeber, Dirk; Muftic, Osman
2001-01-01
A method for integrating equations of motion of constrained multibody systems with no constraint violation is presented. A mathematical model, shaped as a differential-algebraic system of index 1, is transformed into a system of ordinary differential equations using the null-space projection method. Equations of motion are set in a non-minimal form. During integration, violations of constraints are corrected by solving constraint equations at the position and velocity level, utilizing the metric of the system's configuration space, and projective criterion to the coordinate partitioning method. The method is applied to dynamic simulation of 3D constrained biomechanical system. The simulation results are evaluated by comparing them to the values of characteristic parameters obtained by kinematics analysis of analyzed motion based unmeasured kinematics data
Parallel computing and molecular dynamics of biological membranes
International Nuclear Information System (INIS)
La Penna, G.; Letardi, S.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Salina, G.
1998-01-01
In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)
Rheology of liquid n-triacontane: Molecular dynamics simulation
International Nuclear Information System (INIS)
Kondratyuk, N D; Norman, G E; Stegailov, V V
2016-01-01
Molecular dynamics is applied to calculate diffusion coefficients of n-triacontane C 30 H 62 using Einstein-Smoluchowski and Green-Kubo relations. The displacement 〈Δr 2 〉( t ) has a subdiffusive part 〈Δr 2 〉 ∼ t α , caused by molecular crowding at low temperatures. Longtime asymptotes of 〈v(0)v(t)〉 are collated with the hydrodynamic tail t -3/2 demonstrated for atomic liquids. The influence of these asymptotes on the compliance of Einstein-Smoluchowski and Green-Kubo methods is analyzed. The effects of the force field parameters on the diffusion process are treated. The results are compared with experimental data. (paper)
Sugar transport across lactose permease probed by steered molecular dynamics
DEFF Research Database (Denmark)
Jensen, Morten Østergaard; Yin, Ying; Tajkhorshid, Emad
2007-01-01
Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic...... details of lactose interaction with the lumen of LacY during its permeation. Lactose induces a widening of the narrowest parts of the channel during permeation, the widening being largest within the periplasmic half-channel. During permeation, the water-filled lumen of LacY only partially hydrates lactose......, forcing it to interact with channel lining residues. Lactose forms a multitude of direct sugar-channel hydrogen bonds, predominantly with residues of the flexible N-domain, which is known to contribute a major part of LacY's affinity for lactose. In the periplasmic half-channel lactose predominantly...
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane.
Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping
2012-12-01
We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.
Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar
This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...... of enzyme kinetics in non-aqueous media, it has been a fruitful approach to fix the enzyme hydration level by controlling the water activity of the medium. In this work, a protocol is therefore developed for determining the water activity in non-aqueous protein simulations. The method relies on determining...... integration, while for small systems, it seems to be even better. The method is applied to compute the excess Gibbs energy of the mixtures of water and organic solvents used in the simulations of CALB. This allows to determine the water activity of the simulated systems and thus to compare protein properties...
Molecular dynamics study of lubricant depletion by pulsed laser heating
Seo, Young Woo; Rosenkranz, Andreas; Talke, Frank E.
2018-05-01
In this study, molecular dynamics simulations were performed to numerically investigate the effect of pulsed laser heating on lubricant depletion. The maximum temperature, the lubricant depletion width, the number of evaporated lubricant beads and the number of fragmented lubricant chains were studied as a function of laser peak power, pulse duration and repetition rate. A continuous-wave laser and a square pulse laser were simulated and compared to a Gaussian pulse laser. With increasing repetition rate, pulsed laser heating was found to approach continuous-wave laser heating.
Thermal conductivity of water: Molecular dynamics and generalized hydrodynamics results
Bertolini, Davide; Tani, Alessandro
1997-10-01
Equilibrium molecular dynamics simulations have been carried out in the microcanonical ensemble at 300 and 255 K on the extended simple point charge (SPC/E) model of water [Berendsen et al., J. Phys. Chem. 91, 6269 (1987)]. In addition to a number of static and dynamic properties, thermal conductivity λ has been calculated via Green-Kubo integration of the heat current time correlation functions (CF's) in the atomic and molecular formalism, at wave number k=0. The calculated values (0.67+/-0.04 W/mK at 300 K and 0.52+/-0.03 W/mK at 255 K) are in good agreement with the experimental data (0.61 W/mK at 300 K and 0.49 W/mK at 255 K). A negative long-time tail of the heat current CF, more apparent at 255 K, is responsible for the anomalous decrease of λ with temperature. An analysis of the dynamical modes contributing to λ has shown that its value is due to two low-frequency exponential-like modes, a faster collisional mode, with positive contribution, and a slower one, which determines the negative long-time tail. A comparison of the molecular and atomic spectra of the heat current CF has suggested that higher-frequency modes should not contribute to λ in this temperature range. Generalized thermal diffusivity DT(k) decreases as a function of k, after an initial minor increase at k=kmin. The k dependence of the generalized thermodynamic properties has been calculated in the atomic and molecular formalisms. The observed differences have been traced back to intramolecular or intermolecular rotational effects and related to the partial structure functions. Finally, from the results we calculated it appears that the SPC/E model gives results in better agreement with experimental data than the transferable intermolecular potential with four points TIP4P water model [Jorgensen et al., J. Chem. Phys. 79, 926 (1983)], with a larger improvement for, e.g., diffusion, viscosities, and dielectric properties and a smaller one for thermal conductivity. The SPC/E model shares
Molecular hydrodynamic approach to dynamical correlations in quantum liquids
International Nuclear Information System (INIS)
Rabani, Eran; Reichman, David R.
2002-01-01
A quantum molecular hydrodynamic formalism is developed for the study of dynamics in quantum liquids. The method combines exact static input, generated by path-integral Monte Carlo, and an approximate form of the quantum memory function for the solution of the exact quantum generalized Langevin equation under consideration. This methodology is applied to the study of the spectrum of density fluctuations in liquid para-H 2 . Using a physically motivated approximation for the memory function, semiquantitative agreement is obtained for S(k,ω) in comparison to the recent experiments of Bermejo et al. [Phys. Rev. Lett. 84, 5359 (2000)]. Improvement of the methodology and future applications are discussed
Molecular Dynamics Simulations on Evaporation of Droplets with Dissolved Salts
Jin-Liang Xu; Min Chen; Xiao-Dong Wang; Bing-Bing Wang
2013-01-01
Molecular dynamics simulations are used to study the evaporation of water droplets containing either dissolved LiCl, NaCl or KCl salt in a gaseous surrounding (nitrogen) with a constant high temperature of 600 K. The initial droplet has 298 K temperature and contains 1,120 water molecules, 0, 40, 80 or 120 salt molecules. The effects of the salt type and concentration on the evaporation rate are examined. Three stages with different evaporation rates are observed for all cases. In the initial...
Molecular nonlinear dynamics and protein thermal uncertainty quantification
Xia, Kelin; Wei, Guo-Wei
2014-01-01
This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. PMID:24697365
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
International Nuclear Information System (INIS)
Mugnai, Mauro L.; Elber, Ron
2015-01-01
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide
Full quantum treatment of charge dynamics in amorphous molecular semiconductors
de Vries, Xander; Friederich, Pascal; Wenzel, Wolfgang; Coehoorn, Reinder; Bobbert, Peter A.
2018-02-01
We present a treatment of charge dynamics in amorphous molecular semiconductors that accounts for the coupling of charges to all intramolecular phonon modes in a fully quantum mechanical way. Based on ab initio calculations, we derive charge transfer rates that improve on the widely used semiclassical Marcus rate and obtain benchmark results for the mobility and energetic relaxation of electrons and holes in three semiconductors commonly applied in organic light-emitting diodes. Surprisingly, we find very similar results when using the simple Miller-Abrahams rate. We conclude that extracting the disorder strength from temperature-dependent charge transport studies is very possible but extracting the reorganization energy is not.
The density functional theory and the charged fluid molecular dynamics
International Nuclear Information System (INIS)
Hansen, J.P.; Zerah, G.
1993-01-01
Car and Parrinello had the idea of combining the density functional theory (Hohenberg, Kohn and Sham) to the 'molecular dynamics' numerical modelling method, in order to simulate metallic or co-valent solids and liquids from the first principles. The objective of this paper is to present a simplified version of this method ab initio, applicable to classical and quantal charged systems. The method is illustrated with recent results on charged colloidal suspensions and highly correlated electron-proton plasmas. 1 fig., 21 refs
Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.
2009-01-01
and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...... computations of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems.3,16,17,18 For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence...
Molecular dynamics simulations of oscillatory flows in microfluidic channels
DEFF Research Database (Denmark)
Hansen, J.S.; Ottesen, Johnny T.
2006-01-01
In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system...
Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations
Directory of Open Access Journals (Sweden)
Wolfgang Schreiner
2012-01-01
Full Text Available Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt has reached a stationary shape, the simulation has not yet converged.
Molecular dynamics computer simulations based on NMR data
International Nuclear Information System (INIS)
Vlieg, J. de.
1989-01-01
In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs
Quantum-Accurate Molecular Dynamics Potential for Tungsten
Energy Technology Data Exchange (ETDEWEB)
Wood, Mitchell; Thompson, Aidan P.
2017-03-01
The purpose of this short contribution is to report on the development of a Spectral Neighbor Analysis Potential (SNAP) for tungsten. We have focused on the characterization of elastic and defect properties of the pure material in order to support molecular dynamics simulations of plasma-facing materials in fusion reactors. A parallel genetic algorithm approach was used to efficiently search for fitting parameters optimized against a large number of objective functions. In addition, we have shown that this many-body tungsten potential can be used in conjunction with a simple helium pair potential1 to produce accurate defect formation energies for the W-He binary system.
Thermodynamics of small clusters of atoms: A molecular dynamics simulation
DEFF Research Database (Denmark)
Damgaard Kristensen, W.; Jensen, E. J.; Cotterill, Rodney M J
1974-01-01
The thermodynamic properties of clusters containing 55, 135, and 429 atoms have been calculated using the molecular dynamics method. Structural and vibrational properties of the clusters were examined at different temperatures in both the solid and the liquid phase. The nature of the melting...... transition was investigated, and a number of properties, such as melting temperature, latent heat of melting, and premelting phenomena, were found to vary with cluster size. These properties were also found to depend on the structure of the solid phase. In this phase the configuration of lowest free energy...
Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution
Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.
2011-01-01
Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molec...
Ti and Zr surfaces studied by molecular dynamics
International Nuclear Information System (INIS)
Pascuet, Maria I.; Passianot, Roberto C.; Monti, Ana M.
2003-01-01
The interaction between point defects technique and the (0001), (1-210), (10-10) surfaces in Ti and Zr is studied by the molecular dynamics technique. Both of metals are in the hexagonal structure and within a temperature range of 100 to 900 K. The atomic interactions are modeled by EAM-type many-body potentials, that were used previously in static simulations. New migration mechanisms are unraveled and others are verified with respect to those already proposed in the static studies. Also included is an analysis of the vacancy stability in the sub-surface layers of the prismatic surfaces. (author)
Nonlinear rotor dynamics of 2D molecular array: topology reconstruction
International Nuclear Information System (INIS)
Lykah, V.A.; Syrkin, E.S.
2011-01-01
Molecular layers with rotational degrees of freedom and quadrupolar interaction between linear molecules are investigated theoretically. We found earlier that alternative orientation of the molecules along and perpendicular to an axis of the rectangular lattice is preferable. Here we find the integral of motion and give the topology analysis of the possible dynamical phases and special points in the long-wave limit. We find the strong anisotropy in the angle space: directions of easy excitation ('valleys') exist. We show the potential relief reconstruction in dependence on the adsorbed lattice anisotropy.
Dynamical image-charge effect in molecular tunnel junctions
DEFF Research Database (Denmark)
Jin, Chengjun; Thygesen, Kristian Sommer
2014-01-01
the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z(2), where Z is the quasiparticle renormalization factor, compared to the static IC approximation...... that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels....
Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics
Mathiazhagan, S.; Anup, S.
2016-08-01
Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.
Stability mechanisms of a thermophilic laccase probed by molecular dynamics
DEFF Research Database (Denmark)
Christensen, Niels Johan; Kepp, Kasper Planeta
2013-01-01
Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response...... integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F(-) intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes....
Frank, Martin
2015-01-01
Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).
Porting of serial molecular dynamics code on MIMD platforms
International Nuclear Information System (INIS)
Celino, M.
1995-05-01
A molecular Dynamics (MD) code, utilized for the study of atomistic models of metallic systems has been parallelized for MIMD (Multiple Instructions Multiple Data) parallel platforms by means of the Parallel Virtual Machine (PVM) message passing library. Since the parallelization implies modifications of the sequential algorithms, these are described from the point of view of the Statistical Mechanics theory. Furthermore, techniques and parallelization strategies utilized and the MD parallel code are described in detail. Benchmarks on several MIMD platforms (IBM SP1 and SP2, Cray T3D, Cluster of workstations) allow performances evaluation of the code versus the different characteristics of the parallel platforms
Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals
International Nuclear Information System (INIS)
Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon
2000-01-01
We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the direction form intersecting stacking faults by slippage along {111} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society
DEFF Research Database (Denmark)
Sun, Jialiang; Tian, Qiang; Hu, Haiyan
2018-01-01
Recent years have witnessed the application of topology optimization to flexible multibody systems (FMBS) so as to enhance their dynamic performances. In this study, an explicit topology optimization approach is proposed for an FMBS with variable-length bodies via the moving morphable components...... (MMC). Using the arbitrary Lagrangian–Eulerian (ALE) formulation, the thin plate elements of the absolute nodal coordinate formulation (ANCF) are used to describe the platelike bodies with variable length. For the thin plate element of ALE–ANCF, the elastic force and additional inertial force, as well...
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
Energy Technology Data Exchange (ETDEWEB)
Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)
1994-12-31
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.
Molecular dynamics simulation of radiation damage cascades in diamond
Energy Technology Data Exchange (ETDEWEB)
Buchan, J. T. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Robinson, M. [Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia); Christie, H. J.; Roach, D. L.; Ross, D. K. [Physics and Materials Research Centre, School of Computing, Science and Engineering, University of Salford, Salford, Greater Manchester M5 4WT (United Kingdom); Marks, N. A. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia)
2015-06-28
Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
International Nuclear Information System (INIS)
Vashishta, Priya; Kalia, Rajiv
2005-01-01
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report
Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.
2009-01-01
and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...... dynamics (MD) simulations of a hydrophilic air-water-silica system using the MD package FASTTUBE. We employ quantum chemistry calculation to obtain air-silica interaction parameters for the simulations. Our simulations are based in the following force fields: i) The silica-silica interaction is based...... of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems. For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence of air. Hence...
Molecular dynamics simulations of cluster fission and fusion processes
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia
2004-01-01
Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
International Nuclear Information System (INIS)
Wei Gu; Garcia, A.E.; Schoenborn, B.P.
1994-01-01
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies
Haptization of molecular dynamics simulation with thermal display
International Nuclear Information System (INIS)
Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki
2010-01-01
Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)
Deformation mechanisms in nanotwinned copper by molecular dynamics simulation
Energy Technology Data Exchange (ETDEWEB)
Zhao, Xing [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China); Lu, Cheng, E-mail: chenglu@uow.edu.au [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Tieu, Anh Kiet; Pei, Linqing; Zhang, Liang; Su, Lihong [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Zhan, Lihua [State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China)
2017-02-27
Nanotwinned materials exhibit simultaneous ultrahigh strength and high ductility which is attributed to the interactions between dislocations and twin boundaries but the specific deformation mechanisms are rarely seen in experiments at the atomic level. Here we use large scale molecular dynamics simulations to explore this intricate interplay during the plastic deformation of nanotwinned Cu. We demonstrate that the dominant deformation mechanism transits dynamically from slip transfer to twin boundary migration to slip-twin interactions as the twin boundary orientation changes from horizontal to slant, and then to a vertical direction. Building on the fundamental physics of dislocation processes from computer simulations and combining the available experimental investigations, we unravel the underlying deformation mechanisms for nanotwinned Cu, incorporating all three distinct dislocation processes. Our results give insights into systematically engineering the nanoscale twins to fabricate nanotwinned metals or alloys that have high strength and considerable ductility.
Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts
Directory of Open Access Journals (Sweden)
Kazuaki Z. Takahashi
2017-01-01
Full Text Available Long-timescale molecular dynamics simulations were performed to estimate the actual physical nature of a united-atom model of polyethylene (PE. Several scaling laws for representative polymer properties are compared to theoretical predictions. Internal structure results indicate a clear departure from theoretical predictions that assume ideal chain statics. Chain motion deviates from predictions that assume ideal motion of short chains. With regard to linear viscoelasticity, the presence or absence of entanglements strongly affects the duration of the theoretical behavior. Overall, the results indicate that Gaussian statics and dynamics are not necessarily established for real atomistic models of PE. Moreover, the actual physical nature should be carefully considered when using atomistic models for applications that expect typical polymer behaviors.
First Principles Modelling of Shape Memory Alloys Molecular Dynamics Simulations
Kastner, Oliver
2012-01-01
Materials sciences relate the macroscopic properties of materials to their microscopic structure and postulate the need for holistic multiscale research. The investigation of shape memory alloys is a prime example in this regard. This particular class of materials exhibits strong coupling of temperature, strain and stress, determined by solid state phase transformations of their metallic lattices. The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and covers thermodynamical, micro-mechanical and crystallographical aspects. It addresses scientists in these research fields and thei...
Molecular dynamics simulations of glycerol glass-forming liquid
International Nuclear Information System (INIS)
Blieck, J.; Affouard, F.; Bordat, P.; Lerbret, A.; Descamps, M.
2005-01-01
Structural and dynamical properties of liquid glycerol have been investigated by Molecular Dynamics simulations. An improved model based on a slight reparametrisation of the all-atoms AMBER force field used in [R. Chelli, P. Procacci, G. Cardini, R.G.D. Valle, S. Califano, Phys. Chem. Chem. Phys. 1 (1999) 871] is presented. The structure remains satisfactory, qualitatively similar to that obtained from the original model. This new model is also found to reproduce significantly better the diffusion coefficient and the correlations times as they can be deduced from neutron spin echo (NSE) experiments. Structural heterogeneities revealed as a pre-peak of the static structure factor S(Q) close to Q ∼ 0.6 A -1 are observed. Our results are also found compatible with predictions of the Mode Coupling Theory
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.
2013-03-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.
Molecular dynamics simulations of a lithium/sodium carbonate mixture.
Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo
2016-03-01
The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates.
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.; Allen, J.W.; Green, W.H.
2013-01-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
2016-05-01
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.
Charge Carrier Dynamics at Silver Nanocluster-Molecular Acceptor Interfaces
Almansaf, Abdulkhaleq
2017-07-01
A fundamental understanding of interfacial charge transfer at donor-acceptor interfaces is very crucial as it is considered among the most important dynamical processes for optimizing performance in many light harvesting systems, including photovoltaics and photo-catalysis. In general, the photo-generated singlet excitons in photoactive materials exhibit very short lifetimes because of their dipole-allowed spin radiative decay and short diffusion lengths. In contrast, the radiative decay of triplet excitons is dipole forbidden; therefore, their lifetimes are considerably longer. The discussion in this thesis primarily focuses on the relevant parameters that are involved in charge separation (CS), charge transfer (CT), intersystem crossing (ISC) rate, triplet state lifetime, and carrier recombination (CR) at silver nanocluster (NCs) molecular-acceptors interfaces. A combination of steady-state and femto- and nanosecond broadband transient absorption spectroscopies were used to investigate the charge carrier dynamics in various donor-acceptor systems. Additionally, this thesis was prolonged to investigate some important factors that influence the charge carrier dynamics in Ag29 silver NCs donor-acceptor systems, such as the metal doping and chemical structure of the nanocluster and molecular acceptors. Interestingly, clear correlations between the steady-state measurements and timeresolved spectroscopy results are found. In the first study, we have investigated the interfacial charge transfer dynamics in positively charged meso units of 5, 10, 15, 20-tetra (1- methyl-4-pyridino)-porphyrin tetra (p-toluene sulfonate) (TMPyP) and neutral charged 5, 10, 15, 20-tetra (4-pyridyl)-porphyrin (TPyP), with negatively charged undoped and gold (Au)- doped silver Ag29 NCs. Moreover, this study showed the impact of Au doping on the charge carrier dynamics of the system. In the second study, we have investigated the interfacial charge transfer dynamics in [Pt2 Ag23 Cl7 (PPh3
Energy Technology Data Exchange (ETDEWEB)
Saiz, Fernan [Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, London, SW7 2A7 (United Kingdom); Gamero-Castaño, Manuel, E-mail: mgameroc@uci.edu [Department of Mechanical and Aerospace Engineering, University of California, Irvine, California, 92697 (United States)
2016-06-15
The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.
International Nuclear Information System (INIS)
Saiz, Fernan; Gamero-Castaño, Manuel
2016-01-01
The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.
Shekhar, Adarsh
Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in
Rotationally resolved flurorescence as a probe of molecular photoionization dynamics
International Nuclear Information System (INIS)
Poliakoff, E.D.; Kakar, S.; Choi, H.C.
1993-01-01
We present rotationally resolved data for N 2 (2σ u -1 ) photoionization in the excitation energy range 19 ≤ hν ≤ 35 eV. These are the first rotationally resolved measurements on the photoion over an extended spectral range above the ionization threshold. The requisite resolution is obtained by measuring rotationally resolved fluorescence from electronically excited photoions created by synchrotron radiation. This technique is useful for studying dynamical features embedded deep in the ionization continua and should supplement laser-based methods that are limited to probing near-threshold phenomena. The present study shows that the outgoing photoelectron can alter the rotational motion of the more massive photoion by exchanging angular momentum and this partitioning of angular momentum depends on the ionization dynamics. Thus, our data directly probe electron-molecule interactions and are sensitive probes of scattering dynamics. We are currently investigating dynamical features such as shape resonances and Cooper minima with rotational resolution for deciphering microscopic aspects of molecular scattering and these efforts will be discussed
Dynamic coherence in excitonic molecular complexes under various excitation conditions
Energy Technology Data Exchange (ETDEWEB)
Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz
2014-08-17
Highlights: • Dynamic coherence does not improve energy transfer efficiency in natural conditions. • Photo-induced quantum jumps are discussed in classical context. • Natural time scale of a light excitation event is identified. • Coherence in FMO complex averages out under excitation by neighboring antenna. • This result is valid even in absence of dissipation. - Abstract: We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity – an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna–Matthews–Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.
International Nuclear Information System (INIS)
Ito, A.; Kenmotsu, T.; Kikuhara, Y.; Inai, K.; Ohya, K.; Wang, Y.; Irle, S.; Morokuma, K.; Nakamura, H.
2009-01-01
Full text: To understand the plasma-wall interaction on divertor plates, we investigate the interaction of hydrogen atoms and carbon materials used in the high heat flux components by the use of the following simulations. Monte-Carlo (MC) method based on binary collision approximation can calculate the sputtering process of hydrogen atoms on the carbon material quickly. Classical molecular dynamics (MD) method employs multi-body potential models and can treat realistic structures of crystal and molecule. The ab-initio method can calculate electron energy in quantum mechanics, which is regarded as realistic potential for atoms. In the present paper, the interaction of the hydrogen and the carbon material is investigated using the multi-scale (MC, MD and ab-initio) methods. The bombardment of hydrogen atoms onto the carbon material is simulated by the ACAT-code of the MC method, which cannot represent the structure of crystal, and the MD method using modified reactive empirical bond order (REBO) potential, which treats single crystal graphite and amorphous carbon. Consequently, we clarify that the sputtering yield and the reflection rate calculated by the ACAT-code agree with those on the amorphous carbon calculated by the MD. Moreover, there are many kinds of REBO potential for the MD. Adsorption, reflection and penetration rates between a hydrogen atom and a graphene surface are calculated by the MD simulations using the two kinds of potential model. For the incident energy of less than 1 eV, the MD simulation using the modified REBO potential, which is based on Brenner's REBO potential in 2002, shows that reflection is dominant, while the most popular Brenner's REBO potential in 1990 shows that adsorption is dominant. This reflection of the low energy injection is caused by a small potential barrier for the hydrogen atom in the modified REBO potential. The small potential barrier is confirmed by the ab-initio calculations, which are hybrid DFT (B3LYP/cc-pVDZ), ab
Sex speeds adaptation by altering the dynamics of molecular evolution.
McDonald, Michael J; Rice, Daniel P; Desai, Michael M
2016-03-10
Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.
Molecular Dynamics Approach in Designing Thermostable Aspergillus niger Xylanase
Malau, N. D.; Sianturi, M.
2017-03-01
Molecular dynamics methods we have applied as a tool in designing thermostable Aspergillus niger Xylanase, by examining Root Mean Square Deviation (RMSD) and The Stability of the Secondary Structure of enzymes structure at its optimum temperature and compare with its high temperature behavior. As RMSD represents structural fluctuation at a particular temperature, a better understanding of this factor will suggest approaches to bioengineer these enzymes to enhance their thermostability. In this work molecular dynamic simulations of Aspergillus niger xylanase (ANX) have been carried at 400K (optimum catalytic temperature) for 2.5 ns and 500K (ANX reported inactive temperature) for 2.5 ns. Analysis have shown that the Root Mean Square Deviation (RMSD) significant increase at higher temperatures compared at optimum temperature and some of the secondary structures of ANX that have been damaged at high temperature. Structural analysis revealed that the fluctuations of the α-helix and β-sheet regions are larger at higher temperatures compared to the fluctuations at optimum temperature.
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing
2012-01-01
The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
Directory of Open Access Journals (Sweden)
Ji-Long Zhang
Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.
Stability of nanofluids: Molecular dynamic approach and experimental study
International Nuclear Information System (INIS)
Farzaneh, H.; Behzadmehr, A.; Yaghoubi, M.; Samimi, A.; Sarvari, S.M.H.
2016-01-01
Highlights: • Nanofluid stability is investigated and discussed. • A molecular dynamic approach, considering different forces on the nanoparticles, is adopted. • Stability diagrams are presented for different thermo-fluid conditions. • An experimental investigation is carried out to confirm the theoretical approach. - Abstract: Nanofluids as volumetric absorbent in solar energy conversion devices or as working fluid in different heat exchangers have been proposed by various researchers. However, dispersion stability of nanofluids is an important issue that must be well addressed before any industrial applications. Conditions such as severe temperature gradient, high temperature of heat transfer fluid, nanoparticle mean diameters and types of nanoparticles and base fluid are among the most effective parameters on the stability of nanofluid. A molecular dynamic approach, considering kinetic energy of nanoparticles and DLVO potential energy between nanoparticles, is adopted to study the nanofluid stability for different nanofluids at different working conditions. Different forces such as Brownian, thermophoresis, drag and DLVO are considered to introduce the stability diagrams. The latter presents the conditions for which a nanofluid can be stable. In addition an experimental investigation is carried out to find a stable nanofluid and to show the validity of the theoretical approach. There is a good agreement between the experimental and theoretical results that confirms the validity of our theoretical approach.
Adaptive sampling strategies with high-throughput molecular dynamics
Clementi, Cecilia
Despite recent significant hardware and software developments, the complete thermodynamic and kinetic characterization of large macromolecular complexes by molecular simulations still presents significant challenges. The high dimensionality of these systems and the complexity of the associated potential energy surfaces (creating multiple metastable regions connected by high free energy barriers) does not usually allow to adequately sample the relevant regions of their configurational space by means of a single, long Molecular Dynamics (MD) trajectory. Several different approaches have been proposed to tackle this sampling problem. We focus on the development of ensemble simulation strategies, where data from a large number of weakly coupled simulations are integrated to explore the configurational landscape of a complex system more efficiently. Ensemble methods are of increasing interest as the hardware roadmap is now mostly based on increasing core counts, rather than clock speeds. The main challenge in the development of an ensemble approach for efficient sampling is in the design of strategies to adaptively distribute the trajectories over the relevant regions of the systems' configurational space, without using any a priori information on the system global properties. We will discuss the definition of smart adaptive sampling approaches that can redirect computational resources towards unexplored yet relevant regions. Our approaches are based on new developments in dimensionality reduction for high dimensional dynamical systems, and optimal redistribution of resources. NSF CHE-1152344, NSF CHE-1265929, Welch Foundation C-1570.
Step by step parallel programming method for molecular dynamics code
International Nuclear Information System (INIS)
Orii, Shigeo; Ohta, Toshio
1996-07-01
Parallel programming for a numerical simulation program of molecular dynamics is carried out with a step-by-step programming technique using the two phase method. As a result, within the range of a certain computing parameters, it is found to obtain parallel performance by using the level of parallel programming which decomposes the calculation according to indices of do-loops into each processor on the vector parallel computer VPP500 and the scalar parallel computer Paragon. It is also found that VPP500 shows parallel performance in wider range computing parameters. The reason is that the time cost of the program parts, which can not be reduced by the do-loop level of the parallel programming, can be reduced to the negligible level by the vectorization. After that, the time consuming parts of the program are concentrated on less parts that can be accelerated by the do-loop level of the parallel programming. This report shows the step-by-step parallel programming method and the parallel performance of the molecular dynamics code on VPP500 and Paragon. (author)
The molecular dynamics simulation of ion-induced ripple growth
International Nuclear Information System (INIS)
Suele, P.; Heinig, K.-H.
2009-01-01
The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength (λ) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths (λ 35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in λ long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for λ>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.
A new parallel molecular dynamics algorithm for organic systems
International Nuclear Information System (INIS)
Plimpton, S.; Hendrickson, B.; Heffelfinger, G.
1993-01-01
A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed
Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
Okumura, Hisashi
2008-09-28
Partial multicanonical algorithm is proposed for molecular dynamics and Monte Carlo simulations. The partial multicanonical simulation samples a wide range of a part of the potential-energy terms, which is necessary to sample the conformational space widely, whereas a wide range of total potential energy is sampled in the multicanonical algorithm. Thus, one can concentrate the effort to determine the weight factor only on the important energy terms in the partial multicanonical simulation. The partial multicanonical, multicanonical, and canonical molecular dynamics algorithms were applied to an alanine dipeptide in explicit water solvent. The canonical simulation sampled the states of P(II), C(5), alpha(R), and alpha(P). The multicanonical simulation covered the alpha(L) state as well as these states. The partial multicanonical simulation also sampled the C(7) (ax) state in addition to the states that were sampled by the multicanonical simulation. In the partial multicanonical simulation, furthermore, backbone dihedral angles phi and psi rotated more frequently than those in the multicanonical and canonical simulations. These results mean that the partial multicanonical algorithm has a higher sampling efficiency than the multicanonical and canonical algorithms.
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel
International Nuclear Information System (INIS)
Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.
2011-01-01
This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12σ, 14σ and 16σ and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.
Huge-scale molecular dynamics simulation of multibubble nuclei
Watanabe, Hiroshi
2013-12-01
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.
Zhao, Lei; Cheng, Jiangtao
2017-09-07
In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.
International Nuclear Information System (INIS)
Bhowmik, Rahul; Katti, Kalpana S.; Verma, Devendra; Katti, Dinesh R.
2007-01-01
Polymer-hydroxyapatite (HAP) composites are widely investigated for their potential use as bone replacement materials. The molecular interactions at mineral polymer interface are known to have significant role of mechanical response of the composite system. Modeling interactions between such dissimilar molecules using molecular dynamics (MD) is an area of current interest. Molecular dynamics studies require potential function or force field parameters. Some force fields are described in literature that represents the structure of hydroxyapatite reasonably well. Yet, the applicability of these force fields for studying the interaction between dissimilar materials (such as mineral and polymer) is limited, as there is no accurate representation of polymer in these force fields. We have obtained the parameters of consistent valence force field (CVFF) for monoclinic hydroxyapatite. Validation of parameters was done by comparing the computationally obtained unit cell parameters, vibrational spectra and atomic distances with XRD and FTIR experiments. Using the obtained parameters of HAP, and available parameters of polymer (polyacrylic acid), interaction study was performed with MD simulations. The MD simulations showed that several hydrogen bonds may form between HAP and polyacrylic acid depending upon the exposed surface of HAP. Also there are some favourable planes of HAP where polyacrylic acid is most likely to attach. We have also simulated the mineralization of HAP using a 'synthetic biomineralization'. These modeling studies are supported by photoacoustic spectroscopy experiments on both porous and non porous composite samples for potential joint replacement and bone tissue engineering applications
Vision-Augmented Molecular Dynamics Simulation of Nanoindentation
Directory of Open Access Journals (Sweden)
Rajab Al-Sayegh
2015-01-01
Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.
Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.
Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei
2018-06-05
The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.
Lattice dynamics of a crystal with a molecular impurity
International Nuclear Information System (INIS)
Sahoo, D.; Venkataraman, G.
1975-01-01
The dynamics of a crystal containing a molecular impurity is discussed with allowance for the effects of internal vibrations of the molecule. Cartesian coordinates are used to describe internal vibrations, angular oscillations and centre of mass translations of the impurity, and the displacement of atoms of the host lattice. Next the Hamiltonian is set up and the equations of motion derived. In this process, use is made of Dirac brackets when dealing with vibrational coordinates (of the molecule) which have redundancy and constraints. A method of solution of the normal modes of the system is indicated by using the defect space matrixpartitioning technique. The special case of a rigid molecular impurity is then discussed along with the relevance of the present formalism in the interpretation of a recent neutron scattering experiment. It is also shown how the results of crystal-field approximation model and those of the molecular model approximation are obtained as further special cases of the present formalism. A comparison of the present work with those of others has been made. (author)
Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.
Directory of Open Access Journals (Sweden)
Federica Chiappori
Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.
The Art of Molecular Dynamics Simulation (by D. C. Rapaport)
Molner, Stephen P.
1999-02-01
Cambridge University Press: New York, 1996. 400 pp. ISBN 0 521 44561 2. $74.95. This book describes the extremely powerful techniques of molecular dynamics simulation. The techniques involve solving the classical many-body problems in contexts relevant to the study of matter at the atomic level. The method allows the prediction of static and dynamics properties of substances directly from the underlying interactions between molecules. This is, of course, a very broad subject and the author has adopted a dual approach in that the text is partly tutorial and also contains a large number of computer programs for practical use. Rapaport has adopted the attitude of trying the simplest method first. Atoms are modeled as point particles interacting through point potentials. Molecules are represented by atoms with orientation dependent forces, or as extended structures each containing several interaction sites. The molecules may be rigid, flexible, or somewhere in between, and if there are internal degrees of freedom there will be internal forces as well. The intent of the book is not to discuss the design of molecular models, but rather to make use of existing models, and from a pedagogical viewpoint the simpler the model the better. The aim of the book is to demonstrate the general methodology of molecular dynamics simulation by example, not to review the large body of literature covering the many different kinds of models developed for specific applications. The text is partly tutorial, but also contains a large number of computer programs for practical use. This volume will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner. The material covers a wide range of practical methods and real applications and is organized as a series of case studies. The typical case study includes a summary of the theoretical background used for the formulation of the computational approach. That is described by either a
Bolhuis, Peter
Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.
Classical molecular dynamics simulation of electronically non-adiabatic processes.
Miller, William H; Cotton, Stephen J
2016-12-22
Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).
Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben
2017-08-22
A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.
Energy Technology Data Exchange (ETDEWEB)
Car, R.; Parrinello, M.
1988-01-18
An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.
Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids
International Nuclear Information System (INIS)
De Leeuw, S.W.; Brakkee, M.J.D.
1990-01-01
Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs
Molecular dynamics simulation of electron trapping in the sapphire lattice
International Nuclear Information System (INIS)
Rambaut, C.; Oh, K.H.; Fayeulle, S.; Kohanoff, J.
1995-10-01
Energy storage and release in dielectric materials can be described on the basis of the charge trapping mechanism. Most phenomenological aspects have been recently rationalized in terms of the space charge mode. Dynamical aspects are studied here by performing Molecular Dynamics simulations. We show that an excess electron introduced into the sapphire lattice (α -Al 2 O 3 ) can be trapped only at a limited number of sites. The energy gained by allowing the electron to localize in these sites is of the order of 4-5 eV, in good agreement with the results of the space charge model. Displacements of the neighboring ions due to the implanted charge are shown to be localized in a small region of about 5 A. Detrapping is observed at 250 K. The ionic displacements turn out to play an important role in modifying the potential landscape by lowering, in a dynamical way, the barriers that cause localization at low temperature. (author). 18 refs, 7 figs, 2 tabs
Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies
Simon, A.; Rapacioli, M.; Rouaut, G.; Trinquier, G.; Gadéa, F. X.
2017-03-01
We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica
2012-10-09
NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.
Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions
Energy Technology Data Exchange (ETDEWEB)
Fattebert, J.-L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Richards, D.F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Glosli, J.N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2012-12-01
We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·10^{6} particles on 65,536 MPI tasks.
The MOLDY short-range molecular dynamics package
Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.
2011-12-01
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as
Satoh, Akira
2010-01-01
This book presents the most important and main concepts of the molecular and microsimulation techniques. It enables readers to improve their skills in developing simulation programs by providing physical problems and sample simulation programs for them to use. Provides tools to develop skills in developing simulations programs Includes sample simulation programs for the reader to use Appendix explains Fortran and C languages in simple terms to allow the non-expert to use them.
Directory of Open Access Journals (Sweden)
Rong Shen
2015-10-01
Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good
Molecular dynamics simulation of dislocations in uranium dioxide
Energy Technology Data Exchange (ETDEWEB)
Fossati, Paul [CEA, DEN, DPC, SCCME, F-91191 Gif-sur-Yvette Cedex (France); Van Brutzel, Laurent, E-mail: laurent.vanbrutzel@cea.fr [CEA, DEN, DPC, SCCME, F-91191 Gif-sur-Yvette Cedex (France); Devincre, Benoît [LEM, CNRS-ONERA, 29 avenue de la Division Leclerc, F-92322 Châtillon Cedex (France)
2013-11-15
The plasticity of the fluorite structure in UO{sub 2} is investigated with molecular dynamics simulation and empirical potential. The stacking fault energies and the dislocation core structures with Burgers vector a/2 〈110〉 are systematically calculated. All dislocation core structures show a significant increase of the oxygen sub-lattice disorder at temperatures higher than 1500 K. The threshold stress for dislocation glide is found to decrease with increasing temperature but its values is always very high, several GPa at 0 K and several hundred of MPa at 2000 K. A relation between the dislocation mobility dependence with temperature and the increase of the oxygen sub-lattice disorder in the dislocation cores is established.
A hybrid algorithm for parallel molecular dynamics simulations
Mangiardi, Chris M.; Meyer, R.
2017-10-01
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.
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 calculation of shear viscosity for molten salt
International Nuclear Information System (INIS)
Okamoto, Yoshihiro; Yokokawa, Mitsuo; Ogawa, Toru
1993-12-01
A computer program of molecular dynamics simulation has been made to calculate shear viscosity of molten salt. Correlation function for an off-diagonal component of stress tensor can be obtained as the results of calculation. Shear viscosity is calculated by integration of the correlation function based on the Kubo-type formula. Shear viscosities for a molten KCl ranging in temperature from 1047K to 1273K were calculated using the program. Calculation of 10 5 steps (1 step corresponds to 5 x 10 -15 s) was performed for each temperature in the 216 ions system. The obtained results were in good agreement with the reported experimental values. The program has been vectorized to achieve a faster computation in supercomputer. It makes possible to calculate the viscosity using a large number of statistics amounting to several million MD steps. (author)
Molecular dynamics simulation of carbon nanostructures: The C60 buckminsterfullerene
International Nuclear Information System (INIS)
Laszlo, Istvan; Zsoldos, Ibolya
2012-01-01
Molecular dynamics calculations can reveal the physical and chemical properties of various carbon nanostructures or can help to devise the possible formation pathways. In our days the most well-known carbon nanostructures are the fullerenes, the nanotubes, and the graphene. The fullerenes and nanotubes can be thought of as being formed from graphene sheets, i.e., single layers of carbon atoms arranged in a honeycomb lattice. Usually the nature does not follow the mathematical constructions. Although the first time the C 60 and the C 70 were produced by laser irradiated graphite, the fullerene formation theories are based on various fragments of carbon chains and networks of pentagonal and hexagonal rings. In the present article various formation pathways for the buckminsterfullerene C 60 molecule will be presented. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Coding considerations for standalone molecular dynamics simulations of atomistic structures
Ocaya, R. O.; Terblans, J. J.
2017-10-01
The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.
Molecular dynamic simulations of the sputtering of multilayer organic systems
Postawa, Z; Piaskowy, J; Krantzman, K; Winograd, N; Garrison, B J
2003-01-01
Sputtering of organic overlayers has been modeled using molecular dynamics computer simulations. The investigated systems are composed of benzene molecules condensed into one, two and three layers on an Ag left brace 1 1 1 right brace surface. The formed organic overlayers were bombarded with 4 keV Ar projectiles at normal incidence. The development of the collision cascade in the organic overlayer was investigated. The sputtering yield, mass, internal and kinetic energy distributions of ejected particles have been analyzed as a function of the thickness of the organic layer. The results show that all emission characteristics are sensitive to the variation of layer thickness. Although most of the ejected intact benzene molecules originate from the topmost layer, the emission of particles located initially in second and third layers is significant. The analysis indicates that the metallic substrate plays a dominant role in the ejection of intact organic molecules.
A molecular dynamics study of helium bombardments on tungsten nanoparticles
Li, Min; Hou, Qing; Cui, Jiechao; Wang, Jun
2018-06-01
Molecular dynamics simulations were conducted to study the bombardment process of a single helium atom on a tungsten nanoparticle. Helium atoms ranging from 50 eV to 50 keV were injected into tungsten nanoparticles with a diameter in the range of 2-12 nm. The retention and reflection of projectiles and sputtering of nanoparticles were calculated at various times. The results were found to be relative to the nanoparticle size and projectile energy. The projectile energy of 100 eV contributes to the largest retention of helium atoms in tungsten nanoparticles. The most obvious difference in reflection exists in the range of 3-10 keV. Around 66% of sputtering atoms is in forward direction for projectiles with incident energy higher than 10 keV. Moreover, the axial direction of the nanoparticles was demonstrated to influence the bombardment to some degree.
Molecular dynamics simulation of deformation twin in rocksalt vanadium nitride
International Nuclear Information System (INIS)
Fu, Tao; Peng, Xianghe; Zhao, Yinbo; Li, Tengfei; Li, Qibin; Wang, Zhongchang
2016-01-01
We perform molecular dynamics simulation of nano-indentation with a cylindrical indenter to investigate the formation mechanism of deformation twin in vanadium nitride (VN) with a rocksalt structure. We find that the deformation twins occur during the loading stage, and subsequently conduct a systematic analysis of nucleation, propagation and thickening of a deformation twin. We find that the nucleation of a partial dislocation and its propagation to form a stacking fault are premise of deformation twin formation. The sequential nucleation and propagation of partial dislocation on adjacent parallel {111} planes are found to cause the thickening of the deformation twin. Moreover, the deformation twins can exist in VN at room temperature. - Highlights: • MD simulations of indentation are performed to study the deformation twin in VN. • The deformation twins can occur in VN during the loading stage. • The nucleation, propagation and thickening of a deformation twin are analyzed. • The deformation twins can exist in VN at room temperature.
Statistical properties of anti-symmetrized molecular dynamics
International Nuclear Information System (INIS)
Ohnishi, A.; Randrup, J.
1993-01-01
We study the statistical equilibrium properties of the recently developed anti-symmetrized molecular dynamics model for heavy-ion reactions. We consider A non-interacting fermions in one dimension, either bound in a common harmonic potential or moving freely within an interval, and perform a Metropolis sampling of the corresponding parameter space. Generally the average excitation and the specific heat, considered as functions of the imposed temperature, behave in a classical manner when the canonical weight is calculated in the mean-field approximation. However, it is possible to obtain results that are much closer to the quantal behavior by modifying the weight to take approximate account of the energy fluctuations within the individual wave packets. (orig.)
Molecular dynamics simulation of annealed ZnO surfaces
Energy Technology Data Exchange (ETDEWEB)
Min, Tjun Kit; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)
2015-04-24
The effect of thermally annealing a slab of wurtzite ZnO, terminated by two surfaces, (0001) (which is oxygen-terminated) and (0001{sup ¯}) (which is Zn-terminated), is investigated via molecular dynamics simulation by using reactive force field (ReaxFF). We found that upon heating beyond a threshold temperature of ∼700 K, surface oxygen atoms begin to sublimate from the (0001) surface. The ratio of oxygen leaving the surface at a given temperature increases as the heating temperature increases. A range of phenomena occurring at the atomic level on the (0001) surface has also been explored, such as formation of oxygen dimers on the surface and evolution of partial charge distribution in the slab during the annealing process. It was found that the partial charge distribution as a function of the depth from the surface undergoes a qualitative change when the annealing temperature is above the threshold temperature.
Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.
Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao
2018-02-01
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.
Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Mathiazhagan, S., E-mail: smathi.research@gmail.com; Anup, S., E-mail: anupiist@gmail.com
2016-08-19
Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.
Molecular Dynamics Studies of Thermal Induced Chemistry in Tatb
Quenneville, J.; Germann, T. C.; Thompson, A. P.; Kober, E. M.
2007-12-01
A reactive force field (ReaxFF) is used with molecular dynamics to probe the chemistry induced by intense heating (`accelerated cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 32-molecule simulations, we calculate the reaction rate as a function of temperature and compare the Arrhenius-predicted activation energy with experiment. Decomposition product evolution (mainly N2, H2O, CO2 and graphitic carbon clusters) is followed using a 576-molecule larger simulation, which also illustrates the effect of system size on both carbon clustering and reaction rate.
Kernel optimization for short-range molecular dynamics
Hu, Changjun; Wang, Xianmeng; Li, Jianjiang; He, Xinfu; Li, Shigang; Feng, Yangde; Yang, Shaofeng; Bai, He
2017-02-01
To optimize short-range force computations in Molecular Dynamics (MD) simulations, multi-threading and SIMD optimizations are presented in this paper. With respect to multi-threading optimization, a Partition-and-Separate-Calculation (PSC) method is designed to avoid write conflicts caused by using Newton's third law. Serial bottlenecks are eliminated with no additional memory usage. The method is implemented by using the OpenMP model. Furthermore, the PSC method is employed on Intel Xeon Phi coprocessors in both native and offload models. We also evaluate the performance of the PSC method under different thread affinities on the MIC architecture. In the SIMD execution, we explain the performance influence in the PSC method, considering the "if-clause" of the cutoff radius check. The experiment results show that our PSC method is relatively more efficient compared to some traditional methods. In double precision, our 256-bit SIMD implementation is about 3 times faster than the scalar version.
Melting of Cu nanoclusters by molecular dynamics simulation
Energy Technology Data Exchange (ETDEWEB)
Wang, Li; Zhang, Yanning; Bian, Xiufang; Chen, Ying
2003-04-14
We present a detailed molecular dynamics study of the melting of copper nanoclusters with up to 8628 atoms within the framework of the embedded-atom method. The finding indicates that there exists an intermediate nanocrystal regime above 456 atoms. The linear relation between the cluster size and its thermodynamics properties is obeyed in this regime. Melting first occurs at the surface of the clusters, leading to T{sub m,N}=T{sub m,Bulk}-{alpha}N{sup -1/3}, dropping from T{sub m,Bulk}=1360 K to T{sub m,456}=990 K. In addition, the size, surface energy as well as the root mean square displacement (RMSD) of the clusters in the intermediate regime have been investigated.
Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E
2017-01-01
Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...... to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration....... The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure...
Molecular dynamics simulations of field emission from a planar nanodiode
Energy Technology Data Exchange (ETDEWEB)
Torfason, Kristinn; Valfells, Agust; Manolescu, Andrei [School of Science and Engineering, Reykjavik University, Menntavegur 1, IS-101 Reykjavik (Iceland)
2015-03-15
High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space-charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current [Y. Y. Lau, Y. Liu, and R. K. Parker, Phys. Plasmas 1, 2082 (1994) and Y. Feng and J. P. Verboncoeur, Phys. Plasmas 13, 073105 (2006)]. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.
Lightweight computational steering of very large scale molecular dynamics simulations
International Nuclear Information System (INIS)
Beazley, D.M.
1996-01-01
We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages
Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics
International Nuclear Information System (INIS)
Mathiazhagan, S.; Anup, S.
2016-01-01
Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.
Crossed molecular beam studies of unimolecular reaction dynamics
International Nuclear Information System (INIS)
Buss, R.J.
1979-04-01
The study of seven radical-molecule reactions using the crossed molecular beam technique with supersonic nozzle beams is reported. Product angular and velocity distributions were obtained and compared with statistical calculations in order to identify dynamical features of the reactions. In the reaction of chlorine and fluorine atoms with vinyl bromide, the product energy distributions are found to deviate from predictions of the statistical model. A similar effect is observed in the reaction of chlorine atoms with 1, 2 and 3-bromopropene. The reaction of oxygen atoms with ICl and CF 3 I has been used to obtain an improved value of the IO bond energy, 55.0 +- 2.0 kcal mol -1 . In all reactions studied, the product energy and angular distributions are found to be coupled, and this is attributed to a kinematic effect of the conservation of angular momentum
Estimating Arrhenius parameters using temperature programmed molecular dynamics
International Nuclear Information System (INIS)
Imandi, Venkataramana; Chatterjee, Abhijit
2016-01-01
Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.
Molecular dynamics simulation of thermal conductivities of superlattice nanowires
Institute of Scientific and Technical Information of China (English)
YANG; Juekuan(杨决宽); CHEN; Yunfei(陈云飞); YAN; Jingping(颜景平)
2003-01-01
Nonequilibrium molecular dynamics simulations were carried out to investigate heat transfer in superlattice nanowires. Results show that for fixed period length superlattice nanowires, the ratio of the total interfacial thermal resistance to the total thermal resistance and the effective thermal conductivities are invariant with the changes in interface numbers. Increasing the period length leads to an increase in the average interfacial thermal resistance, which indicates that the interfacial thermal resistance depends not only on the materials that constitute the alternating segments of superlattice nanowires, but also on the lattice strain throughout the segments. The modification of the lattice structure due to the lattice mismatch should be taken into account in the acoustic mismatch model. Simulation results also demonstrated the size confinement effect on the thermal conductivities for low dimensional structures, i.e. the thermal conductivities and the interfacial thermal resistance increase as the nanowire cross-sectional area increases.
Isolating strong-field dynamics in molecular systems
Orenstein, Gal; Pedatzur, Oren; Uzan, Ayelet J.; Bruner, Barry D.; Mairesse, Yann; Dudovich, Nirit
2017-05-01
Strong-field ionization followed by recollision provides a unique pump-probe measurement which reveals a range of electronic processes, combining sub-Angstrom spatial and attosecond temporal resolution. A major limitation of this approach is imposed by the coupling between the spatial and temporal degrees of freedom. In this paper we focus on the study of high harmonic generation and demonstrate the ability to isolate the internal dynamics—decoupling the temporal information from the spatial one. By applying an in situ approach we reveal the universality of the intrinsic pump-probe measurement and establish its validity in molecular systems. When several orbitals are involved we identify the fingerprint of the transition from the single-channel case into the multiple-channel dynamics, where complex multielectron phenomena are expected to be observed.
Estimating Arrhenius parameters using temperature programmed molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Imandi, Venkataramana; Chatterjee, Abhijit, E-mail: abhijit@che.iitb.ac.in [Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076 (India)
2016-07-21
Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.
Molecular dynamics characterization of as-implanted damage in silicon
International Nuclear Information System (INIS)
Santos, Ivan; Marques, Luis A.; Pelaz, Lourdes; Lopez, Pedro; Aboy, Maria; Barbolla, Juan
2005-01-01
We have analyzed the as-implanted damage produced in silicon by B, Si and Ge ions using molecular dynamics (MD) simulations. Implantations were carried out at 50 K to avoid damage migration and annealing. In order to make a statistical study of the damage features, we have simulated hundreds of independent cascades for each ion for the same nuclear deposited energy. We have obtained that the average number of displaced atoms (DA) from perfect lattice positions and the size of defect clusters formed increases with ion mass. This dependence has not been obtained from equivalent binary collisions simulations. This indicates that multiple interactions play an important role in the generation of damage. Amorphous regions are directly formed during the collisional phase of the cascade of Ge and Si ions