Osmosis : a molecular dynamics computer simulation study
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.
2010-01-01
As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…
Bergstra, J.A.; Bethke, I.
2002-01-01
Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is
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 de......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...... rate, different dehydrated structures were observed. Removing all water molecules immediately and removing water relatively fast (10 water molecules/10 ps) resulted in an amorphous system, whereas relatively slow computational dehydration (3 water molecules/10 ps) resulted in a crystalline anhydrate...
Workflow Management Systems for Molecular Dynamics on Leadership Computers
Wells, Jack; Panitkin, Sergey; Oleynik, Danila; Jha, Shantenu
Molecular Dynamics (MD) simulations play an important role in a range of disciplines from Material Science to Biophysical systems and account for a large fraction of cycles consumed on computing resources. Increasingly science problems require the successful execution of ''many'' MD simulations as opposed to a single MD simulation. There is a need to provide scalable and flexible approaches to the execution of the workload. We present preliminary results on the Titan computer at the Oak Ridge Leadership Computing Facility that demonstrate a general capability to manage workload execution agnostic of a specific MD simulation kernel or execution pattern, and in a manner that integrates disparate grid-based and supercomputing resources. Our results build upon our extensive experience of distributed workload management in the high-energy physics ATLAS project using PanDA (Production and Distributed Analysis System), coupled with recent conceptual advances in our understanding of workload management on heterogeneous resources. We will discuss how we will generalize these initial capabilities towards a more production level service on DOE leadership resources. This research is sponsored by US DOE/ASCR and used resources of the OLCF computing facility.
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
High performance computer code for molecular dynamics simulations
International Nuclear Information System (INIS)
Levay, I.; Toekesi, K.
2007-01-01
Complete text of publication follows. Molecular Dynamics (MD) simulation is a widely used technique for modeling complicated physical phenomena. Since 2005 we are developing a MD simulations code for PC computers. The computer code is written in C++ object oriented programming language. The aim of our work is twofold: a) to develop a fast computer code for the study of random walk of guest atoms in Be crystal, b) 3 dimensional (3D) visualization of the particles motion. In this case we mimic the motion of the guest atoms in the crystal (diffusion-type motion), and the motion of atoms in the crystallattice (crystal deformation). Nowadays, it is common to use Graphics Devices in intensive computational problems. There are several ways to use this extreme processing performance, but never before was so easy to programming these devices as now. The CUDA (Compute Unified Device) Architecture introduced by nVidia Corporation in 2007 is a very useful for every processor hungry application. A Unified-architecture GPU include 96-128, or more stream processors, so the raw calculation performance is 576(!) GFLOPS. It is ten times faster, than the fastest dual Core CPU [Fig.1]. Our improved MD simulation software uses this new technology, which speed up our software and the code run 10 times faster in the critical calculation code segment. Although the GPU is a very powerful tool, it has a strongly paralleled structure. It means, that we have to create an algorithm, which works on several processors without deadlock. Our code currently uses 256 threads, shared and constant on-chip memory, instead of global memory, which is 100 times slower than others. It is possible to implement the total algorithm on GPU, therefore we do not need to download and upload the data in every iteration. On behalf of maximal throughput, every thread run with the same instructions
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
Nonequilibrium molecular dynamics
Wm.G.Hoover; C.G.Hoover
2005-01-01
Nonequilibrium Molecular Dynamics is a powerful simulation tool. Like its equilibrium cousin, nonequilibrium molecular dynamics is based on time-reversible equations of motion. But unlike conventional mechanics, nonequilibrium molecular dynamics provides a consistent microscopic basis for the irreversible macroscopic Second Law of Thermodynamics. We recall here how fast computers led to the development of nonequilibrium molecular dynamics from the statistical mechanics of the 1950s. Computer-...
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
Petascale molecular dynamics simulation using the fast multipole method on K computer
Ohno, Yousuke
2014-10-01
In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Osei-Kuffuor, Daniel [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Fattebert, Jean-Luc [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10^{-4} Ha/Bohr.
Spijker, Peter; Markvoort, Albert J; Nedea, Silvia V; Hilbers, Peter A J
2010-01-01
For understanding the behavior of a gas close to a channel wall it is important to model the gas-wall interactions as detailed as possible. When using molecular dynamics simulations these interactions can be modeled explicitly, but the computations are time consuming. Replacing the explicit wall with a wall model reduces the computational time but the same characteristics should still remain. Elaborate wall models, such as the Maxwell-Yamamoto model or the Cercignani-Lampis model need a phenomenological parameter (the accommodation coefficient) for the description of the gas-wall interaction as an input. Therefore, computing these accommodation coefficients in a reliable way is very important. In this paper, two systems (platinum walls with either argon or xenon gas confined between them) are investigated and are used for comparison of the accommodation coefficients for the wall models and the explicit molecular dynamics simulations. Velocity correlations between incoming and outgoing particles colliding with the wall have been used to compare explicit simulations and wall models even further. Furthermore, based on these velocity correlations, a method to compute the accommodation coefficients is presented, and these newly computed accommodation coefficients are used to show improved correlation behavior for the wall models.
Cyclo-lib: a database of computational molecular dynamics simulations of cyclodextrins.
Mixcoha, Edgar; Rosende, Roberto; Garcia-Fandino, Rebeca; Piñeiro, Ángel
2016-11-01
Cyclodextrins (CDs) are amongst the most versatile/multi-functional molecules used in molecular research and chemical applications. They are natural cyclic oligosaccharides typically employed to encapsulate hydrophobic groups in their central cavity. This allows solubilizing, protecting or reducing the toxicity of a large variety of different molecules including drugs, dyes and surfactant agents. In spite of their great potential, atomic level information of these molecules, which is key for their function, is really scarce. Computational Molecular Dynamics (MD) simulations have the potential to efficiently fill this gap, providing structural-dynamic information at atomic level in time scales ranging from ps to μs. Cyclo-lib is a database with a publicly accessible web-interface containing structural and dynamic analysis obtained from computational MD simulation trajectories (250 ns long) of native and modified CDs in explicit water molecules. Cyclo-lib currently includes 70 CDs typically employed for fundamental and industrial research. Tools for comparative analysis between different CDs, as well as to restrict the analysis to specific time-segments within the trajectories are also available. Cyclo-lib provides atomic resolution information aimed to complement experimental results performed with the same molecules. The database is freely available under http://cyclo-lib.mduse.com/ CONTACT: Angel.Pineiro@usc.es. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Parallel computations of molecular dynamics trajectories using the stochastic path approach
Zaloj, Veaceslav; Elber, Ron
2000-06-01
A novel protocol to parallelize molecular dynamics trajectories is discussed and tested on a cluster of PCs running the NT operating system. The new technique does not propagate the solution in small time steps, but uses instead a global optimization of a functional of the whole trajectory. The new approach is especially attractive for parallel and distributed computing and its advantages (and disadvantages) are presented. Two numerical examples are discussed: (a) A conformational transition in a solvated dipeptide, and (b) The R→T conformational transition in solvated hemoglobin.
The Early Years of Molecular Dynamics and Computers at UCRL, LRL, LLL, and LLNL
Mansigh Karlsen, Mary Ann
I'm the young woman in the picture shown in Fig. 12.1 that appeared with the invitation to the Symposium to celebrate Berni Alder's ninetieth birthday. I worked with Berni for over 25 years on the computer programs that provided the data he needed to write the fifteen papers published in scientific journals on Studies in Molecular Dynamics. My name appears at the end of each one thanking me for computer support. It has been interesting to look on the Internet to find my name in the middle of many foreign languages, including Japanese characters and Russian Cyrillic script. It shows how Berni's work has been of interest to many scientists all over the world from the earliest years. Figure 12.1 was also included with articles written when he received the National Medal of Science from President Obama in 2009…
Nonequilibrium molecular dynamics
Directory of Open Access Journals (Sweden)
Wm.G.Hoover
2005-01-01
Full Text Available Nonequilibrium Molecular Dynamics is a powerful simulation tool. Like its equilibrium cousin, nonequilibrium molecular dynamics is based on time-reversible equations of motion. But unlike conventional mechanics, nonequilibrium molecular dynamics provides a consistent microscopic basis for the irreversible macroscopic Second Law of Thermodynamics. We recall here how fast computers led to the development of nonequilibrium molecular dynamics from the statistical mechanics of the 1950s. Computer-based theories facilitated revolutionary breakthroughs in understanding during the 1970s and 1980s. The new idea key to the nonequilibrium development was the replacement of the external thermodynamic environment by internal control variables. The new variables can control temperature, or pressure, or energy, or stress, or heat flux. These thermostat, barostat, ergostat, ... variables can control and maintain nonequilibrium states. We illustrate the methods with a simple example well-suited to student exploration, a thermostatted harmonic oscillator exposed to a temperature gradient.
Gupta, Akanksha; Ganesh, Rajaraman; Joy, Ashwin
2018-01-01
In this paper, we perform comparative studies of compressible Kolmogorov flow in the two-dimensional strongly coupled dusty plasma by means of atomistic or molecular dynamics (MD) and continuum or computational fluid dynamics (CFD) methods. Recently, using MD simulation, generation of molecular shear heat at the atomistic level is shown to reduce the average coupling strength of the system and destruct the vortical structures. To suppress the molecular heat, a novel method of a thermostat, namely, the configurational thermostat is introduced by which the microscale heat generated by the shear flow has shown to be thermostatted out efficiently without compromising the large scale vortex dynamics. While using a configurational thermostat, it has been found that the growth rate obtained from both the studies is the same with the marginal difference. To make the comparison with the continuum fluid model, we perform the same study using the generalised hydrodynamic model, wherein molecular shear heating phenomena is completely absent, however, viscous dissipation is there at the macroscale level. For this purpose, an Advanced Generalised SPECTral Code has been developed to study the linear and nonlinear aspects of the Kolmogorov flow in the incompressible and compressible limit for viscoelastic fluids. All the phenomenological parameters used in CFD simulations have been calculated from MD simulations. Code is benchmarked against the eigen value solver in the linear regime. Linear growth-rates calculated from the phenomenological fluid model is found to be close to that obtained from MD simulation for the same set of input parameters. The transition from laminar to turbulent flow has been found at a critical value of Reynolds number Rc in both the macroscopic (CFD) and microscopic (MD) simulation. Rc in MD is smaller than the one obtained by CFD simulation. In the nonlinear regime of CFD, the mode becomes unstable and vortex formation happens earlier than in MD. The
MOLOCH computer code for molecular-dynamics simulation of processes in condensed matter
Directory of Open Access Journals (Sweden)
Derbenev I.V.
2011-01-01
Full Text Available Theoretical and experimental investigation into properties of condensed matter is one of the mainstreams in RFNC-VNIITF scientific activity. The method of molecular dynamics (MD is an innovative method of theoretical materials science. Modern supercomputers allow the direct simulation of collective effects in multibillion atom sample, making it possible to model physical processes on the atomistic level, including material response to dynamic load, radiation damage, influence of defects and alloying additions upon material mechanical properties, or aging of actinides. During past ten years, the computer code MOLOCH has been developed at RFNC-VNIITF. It is a parallel code suitable for massive parallel computing. Modern programming techniques were used to make the code almost 100% efficient. Practically all instruments required for modelling were implemented in the code: a potential builder for different materials, simulation of physical processes in arbitrary 3D geometry, and calculated data processing. A set of tests was developed to analyse algorithms efficiency. It can be used to compare codes with different MD implementation between each other.
Molecular dynamics computer simulation study of Pdn (n=13, 19, 38 and 55) clusters
International Nuclear Information System (INIS)
Karabacak, M.; Oezcelik, S.; Guevenc, Z.B.
2002-01-01
Using constant-energy molecular dynamics and thermal quenching simulations, we have studied minimum-energy structures and energetics, Pd n (n=13, 19, 38, and 55) clusters employing the Voter and Chen's version of parameterisation of the embedded-atom potential surface. Isomer statistics for Pdn ( n = 13 and 19 ) is obtained from 10000 initial independent configurations, which have been generated along high-energy trajectories (chosen energy values are high enough to melt the clusters). The thermal quenching technique is employed to remove the internal kinetic energy of the clusters. The locally stable isomers are separated from metastable ones. Probabilities belonging to sampling the basins of attractions of each isomers are computed, and then, isomers' energy spectra are analyzed
Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.
Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R
2015-07-08
We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.
MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations.
Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto
2014-08-06
We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(-1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.
HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis.
Durrant, Jacob D; McCammon, J Andrew
2011-11-01
In the current work, we present a hydrogen-bond analysis of 2673 ligand-receptor complexes that suggests the total number of hydrogen bonds formed between a ligand and its receptor is a poor predictor of ligand potency; furthermore, even that poor prediction does not suggest a statistically significant correlation between hydrogen-bond formation and potency. While we are not the first to suggest that hydrogen bonds on average do not generally contribute to ligand binding affinities, this additional evidence is nevertheless interesting. The primary role of hydrogen bonds may instead be to ensure specificity, to correctly position the ligand within the active site, and to hold the protein active site in a ligand-friendly conformation. We also present a new computer program called HBonanza (hydrogen-bond analyzer) that aids the analysis and visualization of hydrogen-bond networks. HBonanza, which can be used to analyze single structures or the many structures of a molecular dynamics trajectory, is open source and python implemented, making it easily editable, customizable, and platform independent. Unlike many other freely available hydrogen-bond analysis tools, HBonanza provides not only a text-based table describing the hydrogen-bond network, but also a Tcl script to facilitate visualization in VMD, a popular molecular visualization program. Visualization in other programs is also possible. A copy of HBonanza can be obtained free of charge from http://www.nbcr.net/hbonanza. Copyright © 2011 Elsevier Inc. All rights reserved.
Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E
International Nuclear Information System (INIS)
Kumar, Ambuj; Purohit, Rituraj
2012-01-01
Aneuploidy and chromosomal instability (CIN) are hallmarks of most solid tumors. Mutations in centroemere proteins have been observed in promoting aneuploidy and tumorigenesis. Recent studies reported that Centromere-associated protein-E (CENP-E) is involved in inducing cancers. In this study we investigated the pathogenic effect of 132 nsSNPs reported in CENP-E using computational platform. Y63H point mutation found to be associated with cancer using SIFT, Polyphen, PhD-SNP, MutPred, CanPredict and Dr. Cancer tools. Further we investigated the binding affinity of ATP molecule to the CENP-E motor domain. Complementarity scores obtained from docking studies showed significant loss in ATP binding affinity of mutant structure. Molecular dynamics simulation was carried to examine the structural consequences of Y63H mutation. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R g ), solvent accessibility surface area (SASA), energy value, hydrogen bond (NH Bond), eigenvector projection, trace of covariance matrix and atom density analysis results showed notable loss in stability for mutant structure. Y63H mutation was also shown to disrupt the native conformation of ATP binding region in CENP-E motor domain. Docking studies for remaining 18 mutations at 63rd residue position as well as other two computationally predicted disease associated mutations S22L and P69S were also carried to investigate their affect on ATP binding affinity of CENP-E motor domain. Our study provided a promising computational methodology to study the tumorigenic consequences of nsSNPs that have not been characterized and clear clue to the wet lab scientist.
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.
Puzyrkov, Dmitry; Polyakov, Sergey; Podryga, Viktoriia; Markizov, Sergey
2018-02-01
At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computations. A complex computational task can be performed over different HPC systems. It requires output data synchronization between the storage chosen by a scientist and the HPC system used for computations. The design of the computational domain is also quite a problem. It requires complex software tools and algorithms for proper atomistic data generation on HPC systems. The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this calculations, and presents the part of its concept aimed at initial data generation on the HPC systems.
Directory of Open Access Journals (Sweden)
Puzyrkov Dmitry
2018-01-01
Full Text Available At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computations. A complex computational task can be performed over different HPC systems. It requires output data synchronization between the storage chosen by a scientist and the HPC system used for computations. The design of the computational domain is also quite a problem. It requires complex software tools and algorithms for proper atomistic data generation on HPC systems. The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this calculations, and presents the part of its concept aimed at initial data generation on the HPC systems.
International Nuclear Information System (INIS)
Diaz de la Rubia, T.
1989-01-01
The primary state of damage present in a solid as a result of particle irradiation has been a topic of interest to the physics and materials research community over the last forty years. Energetic displacement cascades resulting from the heavy ion irradiation of a solid play a prominent role in radiation damage and non-equilibrium processing of materials; however, their study has been hampered by the small size (∼10 -20 cm 3 ) and short lifetime (∼10 -11 s) as well as by their highly non-homogeneous nature. In this work, the molecular dynamics computer simulation technique is employed to study the structure and dynamics of energetic displacement cascades in Cu and Ni. The atomic interactions in Cu were described with the use of the Gibson II form of the Born-Mayer pair potential while for Ni the Johnson-Erginsoy pair potential was employed. Calculations were also carried out with the use of the embedded atom method many-body potentials. The results provide the first detailed microscopic description of the evolution of the cascade. The author shows for the first time, that a process akin to melting takes place in the core of the cascade. Atomic mixing, point defect production and point defect agglomeration, all processes directly related to the evolution of the cascade, are then explained in terms of a simple model in which the liquid-like nature of the cascade plays a dominant role in determining the primary state of damage
Energy Technology Data Exchange (ETDEWEB)
Bowers, Geoffrey [Alfred Univ., NY (United States)
2017-04-05
United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).
2014-01-01
Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...
Farantos, Stavros C
2014-01-01
This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.
Computational exploration of single-protein mechanics by steered molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Sotomayor, Marcos [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio (United States)
2015-12-31
Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictions must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.
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 computing origins and promises
Rambidi, Nicholas G
2014-01-01
Molecular Computing explores whether molecular primitives can prove to be real alternatives to contemporary semiconductor means. The text discusses molecular primitives and circuitry for information processing devices.
DEFF Research Database (Denmark)
Solov'yov, Ilia; Yakubovich, Alexander V.; Nikolaev, Pavel V.
2012-01-01
We present a multipurpose computer code MesoBioNano Explorer (MBN Explorer). The package allows to model molecular systems of varied level of complexity. In particular, MBN Explorer is suited to compute system's energy, to optimize molecular structure as well as to consider the molecular and random...... higher) than the computational efficiency of other software packages, making MBN Explorer a possible alternative to the available codes....
International Nuclear Information System (INIS)
Kirkpatrick, R. James; Kalinichev, Andrey G.
2008-01-01
Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches to important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for
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
Gu, Yongfeng; VanCourt, Tom; Herbordt, Martin C.
2008-01-01
FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code. PMID:19412319
Gu, Yongfeng; Vancourt, Tom; Herbordt, Martin C
2008-05-01
FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code.
Nonequilibrium molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
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....
Kasahara, Kota; Kinoshita, Kengo
2016-01-01
Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML), which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.
Lindner, Benjamin; Smith, Jeremy C.
2012-07-01
Massively parallel computers now permit the molecular dynamics (MD) simulation of multi-million atom systems on time scales up to the microsecond. However, the subsequent analysis of the resulting simulation trajectories has now become a high performance computing problem in itself. Here, we present software for calculating X-ray and neutron scattering intensities from MD simulation data that scales well on massively parallel supercomputers. The calculation and data staging schemes used maximize the degree of parallelism and minimize the IO bandwidth requirements. The strong scaling tested on the Jaguar Petaflop Cray XT5 at Oak Ridge National Laboratory exhibits virtually linear scaling up to 7000 cores for most benchmark systems. Since both MPI and thread parallelism is supported, the software is flexible enough to cover scaling demands for different types of scattering calculations. The result is a high performance tool capable of unifying large-scale supercomputing and a wide variety of neutron/synchrotron technology. Catalogue identifier: AELW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 1 003 742 No. of bytes in distributed program, including test data, etc.: 798 Distribution format: tar.gz Programming language: C++, OpenMPI Computer: Distributed Memory, Cluster of Computers with high performance network, Supercomputer Operating system: UNIX, LINUX, OSX Has the code been vectorized or parallelized?: Yes, the code has been parallelized using MPI directives. Tested with up to 7000 processors RAM: Up to 1 Gbytes/core Classification: 6.5, 8 External routines: Boost Library, FFTW3, CMAKE, GNU C++ Compiler, OpenMPI, LibXML, LAPACK Nature of problem: Recent developments in supercomputing allow molecular dynamics simulations to
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.
Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji
2017-09-30
GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Computational Workbench for Multibody Dynamics
Edmonds, Karina
2007-01-01
PyCraft is a computer program that provides an interactive, workbenchlike computing environment for developing and testing algorithms for multibody dynamics. Examples of multibody dynamic systems amenable to analysis with the help of PyCraft include land vehicles, spacecraft, robots, and molecular models. PyCraft is based on the Spatial-Operator- Algebra (SOA) formulation for multibody dynamics. The SOA operators enable construction of simple and compact representations of complex multibody dynamical equations. Within the Py-Craft computational workbench, users can, essentially, use the high-level SOA operator notation to represent the variety of dynamical quantities and algorithms and to perform computations interactively. PyCraft provides a Python-language interface to underlying C++ code. Working with SOA concepts, a user can create and manipulate Python-level operator classes in order to implement and evaluate new dynamical quantities and algorithms. During use of PyCraft, virtually all SOA-based algorithms are available for computational experiments.
A sampling of molecular dynamics
Sindhikara, Daniel Jon
The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: increasing efficiency, measuring convergence, avoiding pitfalls, and an application and analysis of a biological system. Chapters 3 and 4 deal with an enhanced sampling algorithm called "replica exchange molecular dynamics" which is designed to speed-up molecular dynamics simulations. The optimization of a key parameter of these simulations is analyzed. In these successive projects, it was found conclusively that maximizing "exchange attempt frequency" is the most efficient way to run a replica exchange molecular dynamics simulation. Chapter 5 describes an enhanced metric for convergence in parallel simulations called the normalized ergodic measure. The metric is applied to several properties for several replica exchange simulations. Advantages of this metric over other methods are described. Chapter 6 describes the implementation and optimization of an enhanced sampling algorithm similar to replica exchange molecular dynamics called multicanonical algorithm replica exchange molecular dynamics. The algorithm was implemented into a biomolecular simulation suite called AMBER. Additionally several parameters were analyzed and optimized. In Chapter 7, a pitfall in molecular dynamics is observed in biological systems that is caused by negligent use of a simulation's "thermostat". It was found that if the same pseudorandom number seed were used for multiple systems, they eventually synchronize. In this project, synchronization was observed in biological molecules. Various negative effects including corruption of data are pointed out. Chapter 8 describes molecular dynamics simulation of NikR, a homotetrameric nickel
International Nuclear Information System (INIS)
Myeong, Hyeon Guk
1999-06-01
This book deals with computational fluid dynamics with basic and history of numerical fluid dynamics, introduction of finite volume method using one-dimensional heat conduction equation, solution of two-dimensional heat conduction equation, solution of Navier-Stokes equation, fluid with heat transport, turbulent flow and turbulent model, Navier-Stokes solution by generalized coordinate system such as coordinate conversion, conversion of basic equation, program and example of calculation, application of abnormal problem and high speed solution of numerical fluid dynamics.
Molecular dynamics simulations.
Lindahl, Erik
2015-01-01
Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.
Interactive molecular dynamics
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
Directory of Open Access Journals (Sweden)
Kumaraswamy Naidu Chitrala
Full Text Available Breast cancer is one of the most common cancers among the women around the world. Several genes are known to be responsible for conferring the susceptibility to breast cancer. Among them, TP53 is one of the major genetic risk factor which is known to be mutated in many of the breast tumor types. TP53 mutations in breast cancer are known to be related to a poor prognosis and chemo resistance. This renders them as a promising molecular target for the treatment of breast cancer. In this study, we present a computational based screening and molecular dynamic simulation of breast cancer associated deleterious non-synonymous single nucleotide polymorphisms in TP53. We have predicted three deleterious coding non-synonymous single nucleotide polymorphisms rs11540654 (R110P, rs17849781 (P278A and rs28934874 (P151T in TP53 with a phenotype in breast tumors using computational tools SIFT, Polyphen-2 and MutDB. We have performed molecular dynamics simulations to study the structural and dynamic effects of these TP53 mutations in comparison to the wild-type protein. Results from our simulations revealed a detailed consequence of the mutations on the p53 DNA-binding core domain that may provide insight for therapeutic approaches in breast cancer.
Computational methods for molecular imaging
Shi, Kuangyu; Li, Shuo
2015-01-01
This volume contains original submissions on the development and application of molecular imaging computing. The editors invited authors to submit high-quality contributions on a wide range of topics including, but not limited to: • Image Synthesis & Reconstruction of Emission Tomography (PET, SPECT) and other Molecular Imaging Modalities • Molecular Imaging Enhancement • Data Analysis of Clinical & Pre-clinical Molecular Imaging • Multi-Modal Image Processing (PET/CT, PET/MR, SPECT/CT, etc.) • Machine Learning and Data Mining in Molecular Imaging. Molecular imaging is an evolving clinical and research discipline enabling the visualization, characterization and quantification of biological processes taking place at the cellular and subcellular levels within intact living subjects. Computational methods play an important role in the development of molecular imaging, from image synthesis to data analysis and from clinical diagnosis to therapy individualization. This work will bring readers fro...
Programming an interpreter using molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the
Computer representation of molecular surfaces
International Nuclear Information System (INIS)
Max, N.L.
1981-01-01
This review article surveys recent work on computer representation of molecular surfaces. Several different algorithms are discussed for producing vector or raster drawings of space-filling models formed as the union of spheres. Other smoother surfaces are also considered
Shukla, Rohit; Shukla, Harish; Kalita, Parismita; Sonkar, Amit; Pandey, Tripti; Singh, Dev Bukhsh; Kumar, Awanish; Tripathi, Timir
2017-07-04
Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. F. gigantica thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 30 compounds were found to fit well for re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC15970091, ZINC9312362, and ZINC9312661) were identified. These three ligands were further subjected to molecular dynamics simulation (MDS) to compare the dynamics and stability of the protein structure after binding of the ligands. The binding free energy analyses were calculated to determine the intermolecular interactions. The results suggested that the two compounds had a binding free energy of -82.237, and -109.52 kJ.mol -1 for compounds with IDs ZINC9312362 and ZINC9312661, respectively. These predicted compounds displayed considerable pharmacological and structural properties to be drug candidates. We concluded that these two compounds could be potential drug candidates to fight against F. gigantica parasites.
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
Directory of Open Access Journals (Sweden)
J. Gujt
2017-12-01
Full Text Available Isothermal-isobaric molecular dynamics simulations have been performed to examine a broad set of properties of the model water-1,2-dimethoxyethane (DME mixture as a function of composition. The SPC-E and TIP4P-Ew water models and the modified TraPPE model for DME were applied. Our principal focus was to explore the trends of behaviour of the structural properties in terms of the radial distribution functions, coordination numbers and number of hydrogen bonds between molecules of different species, and of conformations of DME molecules. Thermodynamic properties, such as density, molar volume, enthalpy of mixing and heat capacity at constant pressure have been examined. Finally, the self-diffusion coefficients of species and the dielectric constant of the system were calculated and analyzed.
Improved Computation of Dynamic Stresses
Ghosh, Tarun K.
1991-01-01
Method combining modified computational procedure with preprocessing and postprocessing program yields additional data and reduces time and cost of using DYNRE1 module of STARDYNE computer program to compute distributions of stresses in machinery under dynamic loads.
Magoules, Frederic
2011-01-01
Exploring new variations of classical methods as well as recent approaches appearing in the field, Computational Fluid Dynamics demonstrates the extensive use of numerical techniques and mathematical models in fluid mechanics. It presents various numerical methods, including finite volume, finite difference, finite element, spectral, smoothed particle hydrodynamics (SPH), mixed-element-volume, and free surface flow.Taking a unified point of view, the book first introduces the basis of finite volume, weighted residual, and spectral approaches. The contributors present the SPH method, a novel ap
Essential Computational Fluid Dynamics
Zikanov, Oleg
2011-01-01
This book serves as a complete and self-contained introduction to the principles of Computational Fluid Dynamic (CFD) analysis. It is deliberately short (at approximately 300 pages) and can be used as a text for the first part of the course of applied CFD followed by a software tutorial. The main objectives of this non-traditional format are: 1) To introduce and explain, using simple examples where possible, the principles and methods of CFD analysis and to demystify the `black box’ of a CFD software tool, and 2) To provide a basic understanding of how CFD problems are set and
Molecular dynamics for irradiation driven chemistry
DEFF Research Database (Denmark)
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-01-01
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......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...... capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern...
Kim, Meekyum Olivia; Feng, Xinxin; Feixas, Ferran; Zhu, Wei; Lindert, Steffen; Bogue, Shannon; Sinko, William; de Oliveira, César; Rao, Guodong; Oldfield, Eric; McCammon, James Andrew
2015-06-01
With the rise in antibiotic resistance, there is interest in discovering new drugs active against new targets. Here, we investigate the dynamic structures of three isoprenoid synthases from Mycobacterium tuberculosis using molecular dynamics (MD) methods with a view to discovering new drug leads. Two of the enzymes, cis-farnesyl diphosphate synthase (cis-FPPS) and cis-decaprenyl diphosphate synthase (cis-DPPS), are involved in bacterial cell wall biosynthesis, while the third, tuberculosinyl adenosine synthase (Rv3378c), is involved in virulence factor formation. The MD results for these three enzymes were then compared with previous results on undecaprenyl diphosphate synthase (UPPS) by means of active site volume fluctuation and principal component analyses. In addition, an analysis of the binding of prenyl diphosphates to cis-FPPS, cis-DPPS, and UPPS utilizing the new MD results is reported. We also screened libraries of inhibitors against cis-DPPS, finding ~1 μm inhibitors, and used the receiver operating characteristic-area under the curve (ROC-AUC) method to test the predictive power of X-ray and MD-derived cis-DPPS receptors. We found that one compound with potent M. tuberculosis cell growth inhibition activity was an IC(50) ~0.5- to 20-μm inhibitor (depending on substrate) of cis-DPPS, a ~660-nm inhibitor of Rv3378c as well as a 4.8-μm inhibitor of cis-FPPS, opening up the possibility of multitarget inhibition involving both cell wall biosynthesis and virulence factor formation. © 2014 John Wiley & Sons A/S.
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
Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip
2017-10-01
In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.
Liu, Fengjiao; Zhang, John Z. H.; Mei, Ye
2016-06-01
Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.
Computational fluid dynamic applications
Energy Technology Data Exchange (ETDEWEB)
Chang, S.-L.; Lottes, S. A.; Zhou, C. Q.
2000-04-03
The rapid advancement of computational capability including speed and memory size has prompted the wide use of computational fluid dynamics (CFD) codes to simulate complex flow systems. CFD simulations are used to study the operating problems encountered in system, to evaluate the impacts of operation/design parameters on the performance of a system, and to investigate novel design concepts. CFD codes are generally developed based on the conservation laws of mass, momentum, and energy that govern the characteristics of a flow. The governing equations are simplified and discretized for a selected computational grid system. Numerical methods are selected to simplify and calculate approximate flow properties. For turbulent, reacting, and multiphase flow systems the complex processes relating to these aspects of the flow, i.e., turbulent diffusion, combustion kinetics, interfacial drag and heat and mass transfer, etc., are described in mathematical models, based on a combination of fundamental physics and empirical data, that are incorporated into the code. CFD simulation has been applied to a large variety of practical and industrial scale flow systems.
Molecular Magnets for Quantum Computation
Kuroda, Takayoshi
2009-06-01
We review recent progress in molecular magnets especially in the viewpoint of the application for quantum computing. After a brief introduction to single-molecule magnets (SMMs), a method for qubit manipulation by using non-equidistant spin sublevels of a SMM will be introduced. A weakly-coupled dimer of two SMMs is also a candidate for quantum computing, which shows no quantum tunneling of magnetization (QTM) at zero field. In the AF ring Cr7Ni system, the large tunnel splitting is a great advantage to reduce decoherence during manipulation, which can be a possible candidate to realize quantum computer devices in future.
Directory of Open Access Journals (Sweden)
Qifeng Bai
Full Text Available We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD simulations and free energy calculations. To test the effectiveness of MolGridCal, we screened potential ligands for β2 adrenergic receptor (β2AR from a database containing 50,000 small molecules. MolGridCal can not only send tasks to the grid server automatically, but also can distribute tasks using the screensaver function. As for the results of virtual screening, the known agonist BI-167107 of β2AR is ranked among the top 2% of the screened candidates, indicating MolGridCal program can give reasonable results. To further study the binding mode and refine the results of MolGridCal, more accurate docking and scoring methods are used to estimate the binding affinity for the top three molecules (agonist BI-167107, neutral antagonist alprenolol and inverse agonist ICI 118,551. The results indicate agonist BI-167107 has the best binding affinity. MD simulation and free energy calculation are employed to investigate the dynamic interaction mechanism between the ligands and β2AR. The results show that the agonist BI-167107 also has the lowest binding free energy. This study can provide a new way to perform virtual screening effectively through integrating molecular docking based on grid computing, MD simulations and free energy calculations. The source codes of MolGridCal are freely available at http://molgridcal.codeplex.com.
Analysis of the Time Reversible Born-Oppenheimer Molecular Dynamics
Lin, Lin; Lu, Jianfeng; Shao, Sihong
2013-01-01
We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD) scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition as well as the accuracy of TRBOMD for computing physical properties such as the phonon frequency obtained from the molecular dynamic simulation. We connect and compare TRBOMD with the Car-Parrinello molecular...
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)
Miyamoto, Akira; Sato, Etsuko; Sato, Ryo; Inaba, Kenji; Hatakeyama, Nozomu
2014-01-01
In collaboration with experimental experts we have reported in the present conference (Hatakeyama, N. et al., “Experiment-integrated multi-scale, multi-physics computational chemistry simulation applied to corrosion behaviour of BWR structural materials”) the results of multi-scale multi-physics computational chemistry simulations applied to the corrosion behaviour of BWR structural materials. In macro-scale, a macroscopic simulator of anode polarization curve was developed to solve the spatially one-dimensional electrochemical equations on the material surface in continuum level in order to understand the corrosion behaviour of typical BWR structural material, SUS304. The experimental anode polarization behaviours of each pure metal were reproduced by fitting all the rates of electrochemical reactions and then the anode polarization curve of SUS304 was calculated by using the same parameters and found to reproduce the experimental behaviour successfully. In meso-scale, a kinetic Monte Carlo (KMC) simulator was applied to an actual-time simulation of the morphological corrosion behaviour under the influence of an applied voltage. In micro-scale, an ultra-accelerated quantum chemical molecular dynamics (UA-QCMD) code was applied to various metallic oxide surfaces of Fe 2 O 3 , Fe 3 O 4 , Cr 2 O 3 modelled as same as water molecules and dissolved metallic ions on the surfaces, then the dissolution and segregation behaviours were successfully simulated dynamically by using UA-QCMD. In this paper we describe details of the multi-scale, multi-physics computational chemistry method especially the UA-QCMD method. This method is approximately 10,000,000 times faster than conventional first-principles molecular dynamics methods based on density-functional theory (DFT), and the accuracy was also validated for various metals and metal oxides compared with DFT results. To assure multi-scale multi-physics computational chemistry simulation based on the UA-QCMD method for
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
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
Molecular Science Computing: 2010 Greenbook
Energy Technology Data Exchange (ETDEWEB)
De Jong, Wibe A.; Cowley, David E.; Dunning, Thom H.; Vorpagel, Erich R.
2010-04-02
This 2010 Greenbook outlines the science drivers for performing integrated computational environmental molecular research at EMSL and defines the next-generation HPC capabilities that must be developed at the MSC to address this critical research. The EMSL MSC Science Panel used EMSL’s vision and science focus and white papers from current and potential future EMSL scientific user communities to define the scientific direction and resulting HPC resource requirements presented in this 2010 Greenbook.
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.
Energy Technology Data Exchange (ETDEWEB)
Pask, J E; Sukumar, N; Guney, M; Hu, W
2011-02-28
completely general, applicable to any crystal symmetry and to both metals and insulators alike. We have developed and implemented a full self-consistent Kohn-Sham method, including both total energies and forces for molecular dynamics, and developed a full MPI parallel implementation for large-scale calculations. We have applied the method to the gamut of physical systems, from simple insulating systems with light atoms to complex d- and f-electron systems, requiring large numbers of atomic-orbital enrichments. In every case, the new PU FE method attained the required accuracies with substantially fewer degrees of freedom, typically by an order of magnitude or more, than the current state-of-the-art PW method. Finally, our initial MPI implementation has shown excellent parallel scaling of the most time-critical parts of the code up to 1728 processors, with clear indications of what will be required to achieve comparable scaling for the rest. Having shown that the key remaining disadvantage of real-space methods can in fact be overcome, the work has attracted significant attention: with sixteen invited talks, both domestic and international, so far; two papers published and another in preparation; and three new university and/or national laboratory collaborations, securing external funding to pursue a number of related research directions. Having demonstrated the proof of principle, work now centers on the necessary extensions and optimizations required to bring the prototype method and code delivered here to production applications.
Synthetic biology: engineering molecular computers
CERN. Geneva
2018-01-01
Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...
Multiscale Reactive Molecular Dynamics
2012-08-15
as a linear combination of several possible bond- ing topologies ( diabatic states) that are coupled to one an- other through the off-diagonal elements...adapts and dynamically identifies bonding topolo- gies to include as the simulation progresses. These bonding topologies form a basis of diabatic ...the original geometric factor. The diabatic correction term, VCORR , used here was labeled in previous MS-EVB models as a repulsive interaction, VREP
State-Dependent Molecular Dynamics
Directory of Open Access Journals (Sweden)
Ciann-Dong Yang
2014-10-01
Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
State-dependent molecular dynamics.
Yang, Ciann-Dong; Weng, Hung-Jen
2014-10-09
This paper proposes a new mixed quantum mechanics (QM)-molecular mechanics (MM) approach, where MM is replaced by quantum Hamilton mechanics (QHM), which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
Murthy, P. Krishna; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Suneetha, V.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Suchetan, P. A.
2017-04-01
4-benzyl-5-oxomorpholine-3-carbamide has been synthesized; single crystals were grown by slow evaporation solution growth technique at room temperature and characterized by single crystal X-ray diffraction, FT-IR, FT-Raman and 1H-NMR. The compound crystallizes in the monoclinic space group P21/n. The molecular geometry of the compound was optimized by using Density Functional Theory (DFT/B3LYP) method with 6-311++G(d,p) basis set in the ground state and geometric parameters are in agreement with the X-ray analysis results of the structure. The experimental vibrational spectra were compared with the calculated spectra and each vibrational wave number was assigned on the basis of potential energy distribution (PED). The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbital's (HOMOs) and lowest unoccupied molecular orbital's (LUMOs). Besides molecular electrostatic potential (MEP), frontier molecular orbital's (FMOs), some global reactivity descriptors, thermodynamic properties, non-linear optical (NLO) behavior and Mullikan charge analysis of the title compound were computed with the same method in gas phase, theoretically. Potential reactive sites of the title compound have been identified by average local ionization energy and Fukui functions, both mapped to the electron density surface. Bond dissociation energies for all single acyclic bonds have been calculated in order to investigate autoxidation and degradation properties of the title compound. Atoms with pronounced interactions with water molecules have been detected by calculations of radial distribution functions after molecular dynamics simulations. The experimental results are compared with the theoretical calculations using DFT methods for the fortification of the paper. Further the docking studies revealed that the title compound as a docked ligand forms a stable complex with pyrrole inhibitor with a binding affinity value of -7.5 kcal/mol. This
Toward molecular catalysts by computer.
Raugei, Simone; DuBois, Daniel L; Rousseau, Roger; Chen, Shentan; Ho, Ming-Hsun; Bullock, R Morris; Dupuis, Michel
2015-02-17
CONSPECTUS: Rational design of molecular catalysts requires a systematic approach to designing ligands with specific functionality and precisely tailored electronic and steric properties. It then becomes possible to devise computer protocols to design catalysts by computer. In this Account, we first review how thermodynamic properties such as redox potentials (E°), acidity constants (pKa), and hydride donor abilities (ΔGH(-)) form the basis for a framework for the systematic design of molecular catalysts for reactions that are critical for a secure energy future. We illustrate this for hydrogen evolution and oxidation, oxygen reduction, and CO conversion, and we give references to other instances where it has been successfully applied. The framework is amenable to quantum-chemical calculations and conducive to predictions by computer. We review how density functional theory allows the determination and prediction of these thermodynamic properties within an accuracy relevant to experimentalists (∼0.06 eV for redox potentials, ∼1 pKa unit for pKa values, and 1-2 kcal/mol for hydricities). Computation yielded correlations among thermodynamic properties as they reflect the electron population in the d shell of the metal center, thus substantiating empirical correlations used by experimentalists. These correlations point to the key role of redox potentials and other properties (pKa of the parent aminium for the proton-relay-based catalysts designed in our laboratory) that are easily accessible experimentally or computationally in reducing the parameter space for design. These properties suffice to fully determine free energies maps and profiles associated with catalytic cycles, i.e., the relative energies of intermediates. Their prediction puts us in a position to distinguish a priori between desirable and undesirable pathways and mechanisms. Efficient catalysts have flat free energy profiles that avoid high activation barriers due to low- and high
Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J
2016-03-21
We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution.
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.
Computational methods in stochastic dynamics
Papadrakakis, Manolis; Papadopoulos, Vissarion
2011-01-01
Covering what is an emerging frontier in research, this book focuses on advanced computational methods and software tools. These can be of huge assistance in tackling complex problems in stochastic dynamic and seismic analysis as well as structure design.
Directory of Open Access Journals (Sweden)
Suri Moonsamy
2014-04-01
Full Text Available Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we proposed ten novel compounds as potential CCR5-dependent HIV-1 entry inhibitors. Via validated docking calculations, binding free energies revealed that novel leads demonstrated better binding affinities with CCR5 compared to maraviroc, an FDA-approved HIV-1 entry inhibitor and in clinical use. Per-residue interaction energy decomposition analysis on the averaged MD structure showed that hydrophobic active residues Trp86, Tyr89 and Tyr108 contributed the most to inhibitor binding. The validated 3D-QSAR model showed a high cross-validated rcv2 value of 0.84 using three principal components and non-cross-validated r2 value of 0.941. It was also revealed that almost all compounds in the test set and training set yielded a good predicted value. Information gained from this study could shed light on the activity of a new series of lead compounds as potential HIV entry inhibitors and serve as a powerful tool in the drug design and development machinery.
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
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...
Computational Fluid Dynamics in Ventilation
DEFF Research Database (Denmark)
Nielsen, Peter V.; Allard, Francis; Awbi, Hazim B.
2008-01-01
Computational Fluid Dynamics in Ventilation Design is a new title in the is a new title in the REHVA guidebook series. The guidebook is written for people who need to use and discuss results based on CFD predictions, and it gives insight into the subject for those who are not used to work with CFD...
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
Molecular quantum dynamics. From theory to applications
International Nuclear Information System (INIS)
Gatti, Fabien
2014-01-01
calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.
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
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.
Computer Simulations of Molecular Propellers
National Research Council Canada - National Science Library
Vacek, Jaroslav
1999-01-01
...). The new program will be used to explore computationally a variety of possible structures for the synthesis of new materials capable acquiring significant internal mechanical angular momentum along...
Principles of computational fluid dynamics
Wesseling, Pieter
2001-01-01
The book is aimed at graduate students, researchers, engineers and physicists involved in flow computations. An up-to-date account is given of the present state-of-the-art of numerical methods employed in computational fluid dynamics. The underlying numerical principles are treated with a fair amount of detail, using elementary mathematical analysis. Attention is given to difficulties arising from geometric complexity of the flow domain and of nonuniform structured boundary-fitted grids. Uniform accuracy and efficiency for singular perturbation problems is studied, pointing the way to accurate computation of flows at high Reynolds number. Much attention is given to stability analysis, and useful stability conditions are provided, some of them new, for many numerical schemes used in practice. Unified methods for compressible and incompressible flows are discussed. Numerical analysis of the shallow-water equations is included. The theory of hyperbolic conservation laws is treated. Godunov's order barrier and ho...
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...
Dynamic computing random access memory
International Nuclear Information System (INIS)
Traversa, F L; Bonani, F; Pershin, Y V; Di Ventra, M
2014-01-01
The present von Neumann computing paradigm involves a significant amount of information transfer between a central processing unit and memory, with concomitant limitations in the actual execution speed. However, it has been recently argued that a different form of computation, dubbed memcomputing (Di Ventra and Pershin 2013 Nat. Phys. 9 200–2) and inspired by the operation of our brain, can resolve the intrinsic limitations of present day architectures by allowing for computing and storing of information on the same physical platform. Here we show a simple and practical realization of memcomputing that utilizes easy-to-build memcapacitive systems. We name this architecture dynamic computing random access memory (DCRAM). We show that DCRAM provides massively-parallel and polymorphic digital logic, namely it allows for different logic operations with the same architecture, by varying only the control signals. In addition, by taking into account realistic parameters, its energy expenditures can be as low as a few fJ per operation. DCRAM is fully compatible with CMOS technology, can be realized with current fabrication facilities, and therefore can really serve as an alternative to the present computing technology. (paper)
Computation in Dynamically Bounded Asymmetric Systems
Rutishauser, Ueli; Slotine, Jean-Jacques; Douglas, Rodney
2015-01-01
Previous explanations of computations performed by recurrent networks have focused on symmetrically connected saturating neurons and their convergence toward attractors. Here we analyze the behavior of asymmetrical connected networks of linear threshold neurons, whose positive response is unbounded. We show that, for a wide range of parameters, this asymmetry brings interesting and computationally useful dynamical properties. When driven by input, the network explores potential solutions through highly unstable ‘expansion’ dynamics. This expansion is steered and constrained by negative divergence of the dynamics, which ensures that the dimensionality of the solution space continues to reduce until an acceptable solution manifold is reached. Then the system contracts stably on this manifold towards its final solution trajectory. The unstable positive feedback and cross inhibition that underlie expansion and divergence are common motifs in molecular and neuronal networks. Therefore we propose that very simple organizational constraints that combine these motifs can lead to spontaneous computation and so to the spontaneous modification of entropy that is characteristic of living systems. PMID:25617645
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.
ICFD - Interdisciplinary Computational Fluid Dynamics
International Nuclear Information System (INIS)
Hankey, W.L.
1985-01-01
Interdisciplinary Computational Fluid Dynamics is that field in which the Navier-Stokes equations are coupled to another set of equations for the solution of interaction problems. Although it is currently possible to apply numerical algorithms and grid generation methods to such problems, together with the conservation form for governing equations and arrangements of field data which exploit vector processor hardwares, novel technology is called for in the modeling of complex interface boundary conditions and the incorporation of constitutive relationships for state variables and transport processes. It is also necessary to model such subgrid scale phenomena as turbulence, evaporation, atomization, devolatization, nucleation, chemical reactions, surface tension, and surface roughness. 33 references
Computational Fluid Dynamics in Ventilation
DEFF Research Database (Denmark)
Nielsen, Peter V.; Allard, Francis; Awbi, Hazim B.
2008-01-01
Computational Fluid Dynamics in Ventilation Design is a new title in the is a new title in the REHVA guidebook series. The guidebook is written for people who need to use and discuss results based on CFD predictions, and it gives insight into the subject for those who are not used to work with CFD....... The guidebook is also written for people working with CFD which have to be more aware of how this numerical method is applied in the area of ventilation. The guidebook has, for example, chapters that are very important for CFD quality control in general and for the quality control of ventilation related...
Molecular Realizations of Quantum Computing 2007
Nakahara, Mikio; Ota, Yukihiro; Rahimi, Robabeh; Kondo, Yasushi; Tada-Umezaki, Masahito
2009-06-01
Liquid-state NMR quantum computer: working principle and some examples / Y. Kondo -- Flux qubits, tunable coupling and beyond / A. O. Niskanen -- Josephson phase qubits, and quantum communication via a resonant cavity / M. A. Sillanpää -- Quantum computing using pulse-based electron-nuclear double resonance (ENDOR): molecular spin-qubits / K. Sato ... [et al.] -- Fullerene C[symbol]: a possible molecular quantum computer / T. Wakabayashi -- Molecular magnets for quantum computation / T. Kuroda -- Errors in a plausible scheme of quantum gates in Kane's model / Y. Ota -- Yet another formulation for quantum simultaneous noncooperative bimatrix games / A. SaiToh, R. Rahimi, M. Nakahara -- Continuous-variable teleportation of single-photon states and an accidental cloning of a photonic qubit in two-channel teleportation / T. Ide.
Molecular computing: paths to chemical Turing machines.
Varghese, Shaji; Elemans, Johannes A A W; Rowan, Alan E; Nolte, Roeland J M
2015-11-13
To comply with the rapidly increasing demand of information storage and processing, new strategies for computing are needed. The idea of molecular computing, where basic computations occur through molecular, supramolecular, or biomolecular approaches, rather than electronically, has long captivated researchers. The prospects of using molecules and (bio)macromolecules for computing is not without precedent. Nature is replete with examples where the handling and storing of data occurs with high efficiencies, low energy costs, and high-density information encoding. The design and assembly of computers that function according to the universal approaches of computing, such as those in a Turing machine, might be realized in a chemical way in the future; this is both fascinating and extremely challenging. In this perspective, we highlight molecular and (bio)macromolecular systems that have been designed and synthesized so far with the objective of using them for computing purposes. We also present a blueprint of a molecular Turing machine, which is based on a catalytic device that glides along a polymer tape and, while moving, prints binary information on this tape in the form of oxygen atoms.
Evolutionary computation for dynamic optimization problems
Yao, Xin
2013-01-01
This book provides a compilation on the state-of-the-art and recent advances of evolutionary computation for dynamic optimization problems. The motivation for this book arises from the fact that many real-world optimization problems and engineering systems are subject to dynamic environments, where changes occur over time. Key issues for addressing dynamic optimization problems in evolutionary computation, including fundamentals, algorithm design, theoretical analysis, and real-world applications, are presented. "Evolutionary Computation for Dynamic Optimization Problems" is a valuable reference to scientists, researchers, professionals and students in the field of engineering and science, particularly in the areas of computational intelligence, nature- and bio-inspired computing, and evolutionary computation.
Computational methods for molecular docking
Energy Technology Data Exchange (ETDEWEB)
Klebe, G. [BASF AG, Ludwigshafen (Germany); Lengauer, T.
1995-12-31
This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Recently, it has been demonstrated that the knowledge of the three-dimensional structure of the protein can be used to derive new protein ligands with improved binding properties. This tutorial focuses on the following questions: What is its binding affinity toward a particular receptor? What are putative conformations of a ligand at the binding site? What are the similarities of different ligands in terms of their recognition capabilities? Where and in which orientation will a ligand bind to the active site? How is a new putative protein ligand selected? An overview is presented of the algorithms which are presently used to handle and predict protein-ligand interactions and to dock small molecule ligands into proteins.
Molecular Dynamics Simulations for Predicting Surface Wetting
Directory of Open Access Journals (Sweden)
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
Nonequilibrium molecular dynamics: The first 25 years
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
On the parallelization of molecular dynamics codes
Trabado, G. P.; Plata, O.; Zapata, E. L.
2002-08-01
Molecular dynamics (MD) codes present a high degree of spatial data locality and a significant amount of independent computations. However, most of the parallelization strategies are usually based on the manual transformation of sequential programs either by completely rewriting the code with message passing routines or using specific libraries intended for writing new MD programs. In this paper we propose a new library-based approach (DDLY) which supports parallelization of existing short-range MD sequential codes. The novelty of this approach is that it can directly handle the distribution of common data structures used in MD codes to represent data (arrays, Verlet lists, link cells), using domain decomposition. Thus, the insertion of run-time support for distribution and communication in a MD program does not imply significant changes to its structure. The method is simple, efficient and portable. It may be also used to extend existing parallel programming languages, such as HPF.
Principles of computational fluid dynamics
International Nuclear Information System (INIS)
Wesseling, P.
2001-01-01
The book is aimed at graduate students, researchers, engineers and physicists involved in flow computations. An up-to-date account is given of the present state- of-the-art of numerical methods employed in computational fluid dynamics. The underlying numerical principles are treated with a fair amount of detail, using elementary mathematical analysis. Attention is given to difficulties arising from geometric complexity of the flow domain and of nonuniform structured boundary-fitted grids. Uniform accuracy and efficiency for singular perturbation problems is studied, pointing the way to accurate computation of flows at high Reynolds number. Much attention is given to stability analysis, and useful stability conditions are provided, some of them new, for many numerical schemes used in practice. Unified methods for compressible and incompressible flows are discussed. Numerical analysis of the shallow-water equations is included. The theory of hyperbolic conservation laws is treated. Godunov's order barrier and how to overcome it by means of slope-limited schemes is discussed. An introduction is given to efficient iterative solution methods, using Krylov subspace and multigrid acceleration. Many pointers are given to recent literature, to help the reader to quickly reach the current research frontier. (orig.)
Computational methods for fluid dynamics
Ferziger, Joel H
2002-01-01
In its 3rd revised and extended edition the book offers an overview of the techniques used to solve problems in fluid mechanics on computers and describes in detail those most often used in practice. Included are advanced methods in computational fluid dynamics, like direct and large-eddy simulation of turbulence, multigrid methods, parallel computing, moving grids, structured, block-structured and unstructured boundary-fitted grids, free surface flows. The 3rd edition contains a new section dealing with grid quality and an extended description of discretization methods. The book shows common roots and basic principles for many different methods. The book also contains a great deal of practical advice for code developers and users, it is designed to be equally useful to beginners and experts. The issues of numerical accuracy, estimation and reduction of numerical errors are dealt with in detail, with many examples. A full-feature user-friendly demo-version of a commercial CFD software has been added, which ca...
Efficient SDH Computation In Molecular Simulations Data.
Tu, Yi-Cheng; Chen, Shaoping; Pandit, Sagar; Kumar, Anand; Grupcev, Vladimir
2012-10-01
Analysis of large particle or molecular simulation data is integral part of the basic-science research community. It often involves computing functions such as point-to-point interactions of particles. Spatial distance histogram (SDH) is one such vital computation in scientific discovery. SDH is frequently used to compute Radial Distribution Function (RDF), and it takes quadratic time to compute using naive approach. Naive SDH computation is even more expensive as it is computed continuously over certain period of time to analyze simulation systems. Tree-based SDH computation is a popular approach. In this paper we look at different tree-based SDH computation techniques and briefly discuss about their performance. We present different strategies to improve the performance of these techniques. Specifically, we study the density map (DM) based SDH computation techniques. A DM is essentially a grid dividing simulated space into cells (3D cubes) of equal size (volume), which can be easily implemented by augmenting a Quad-tree (or Oct-tree) index. DMs are used in various configurations to compute SDH continuously over snapshots of the simulation system. The performance improvements using some of these configurations is presented in this paper. We also present the effect of utilizing computation power of Graphics Processing Units (GPUs) in computing SDH.
Directory of Open Access Journals (Sweden)
Yuxin Zhang
2012-02-01
Full Text Available Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π–π, CH–π and CH–CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.
Artificial surface-mounted molecular rotors: Molecular dynamics simulations
Czech Academy of Sciences Publication Activity Database
Vacek, Jaroslav; Michl, Josef
2007-01-01
Roč. 17, č. 5 (2007), s. 730-739 ISSN 1616-301X R&D Projects: GA AV ČR IAA400550616; GA MŠk ME 857 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular dynamics * molecular machines * nanomaterials Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.496, year: 2007
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...
Visualization of Computational Fluid Dynamics
Gerald-Yamasaki, Michael; Hultquist, Jeff; Bryson, Steve; Kenwright, David; Lane, David; Walatka, Pamela; Clucas, Jean; Watson, Velvin; Lasinski, T. A. (Technical Monitor)
1995-01-01
Scientific visualization serves the dual purpose of exploration and exposition of the results of numerical simulations of fluid flow. Along with the basic visualization process which transforms source data into images, there are four additional components to a complete visualization system: Source Data Processing, User Interface and Control, Presentation, and Information Management. The requirements imposed by the desired mode of operation (i.e. real-time, interactive, or batch) and the source data have their effect on each of these visualization system components. The special requirements imposed by the wide variety and size of the source data provided by the numerical simulation of fluid flow presents an enormous challenge to the visualization system designer. We describe the visualization system components including specific visualization techniques and how the mode of operation and source data requirements effect the construction of computational fluid dynamics visualization systems.
Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations
De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut
2011-01-01
With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices
Molecular Dynamics and Bioactivity of a Novel Mutated Human ...
African Journals Online (AJOL)
version 3.5,. Accelrys Inc., San Diego, CA) was used for protein design and molecular dynamics simulation. The analysis of the MD data was made using Origin Pro (version 9.0). Mean ± standard error of mean (SEM) of the data were computed.
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 ...
Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.
Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal
2018-01-01
Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.
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...
A molecular computer to classify cells
CERN. Geneva
2018-01-01
If only we had a small molecular computer to leverage this disparity, programmable to optimally recognize different classes of cells and, once inside a target cell, to execute an action. Like what a student team researched for this year's synthetic biology iGEM competition.
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.
Manas, Nor Hasmaliana Abdul; Bakar, Farah Diba Abu; Illias, Rosli Md
2016-06-01
Maltogenic amylase (MAG1) from Bacillus lehensis G1 displayed the highest hydrolysis activity on β-cyclodextrin (β-CD) to produce maltose as a main product and exhibited high transglycosylation activity on malto-oligosaccharides with polymerization degree of three and above. These substrate and product specificities of MAG1 were elucidated from structural point of view in this study. A three-dimensional structure of MAG1 was constructed using homology modeling. Docking of β-CD and malto-oligosaccharides was then performed in the MAG1 active site. An aromatic platform in the active site was identified which is responsible in substrate recognition especially in determining the enzyme's preference toward β-CD. Molecular dynamics (MD) simulation showed MAG1 structure is most stable when docked with β-CD and least stable when docked with maltose. The docking analysis and MD simulation showed that the main subsites for substrate stabilization in the active site are -2, -1, +1 and +2. A bulky residue, Trp359 at the +2 subsite was identified to cause steric interference to the bound linear malto-oligosaccharides thus prevented it to occupy subsite +3, which can only be reached by a highly bent glucose molecule such as β-CD. The resulted modes of binding from docking simulation show a good correlation with the experimentally determined hydrolysis pattern. The subsite structure generated from this study led to a possible mode of action that revealed how maltose was mainly produced during hydrolysis. Furthermore, maltose only occupies subsite +1 and +2, therefore could not be hydrolyzed or transglycosylated by the enzyme. This important knowledge has paved the way for a novel structure-based molecular design for modulation of its catalytic activities. Copyright © 2016 Elsevier Inc. All rights reserved.
Molecular dynamics simulations and novel drug discovery.
Liu, Xuewei; Shi, Danfeng; Zhou, Shuangyan; Liu, Hongli; Liu, Huanxiang; Yao, Xiaojun
2018-01-01
Molecular dynamics (MD) simulations can provide not only plentiful dynamical structural information on biomacromolecules but also a wealth of energetic information about protein and ligand interactions. Such information is very important to understanding the structure-function relationship of the target and the essence of protein-ligand interactions and to guiding the drug discovery and design process. Thus, MD simulations have been applied widely and successfully in each step of modern drug discovery. Areas covered: In this review, the authors review the applications of MD simulations in novel drug discovery, including the pathogenic mechanisms of amyloidosis diseases, virtual screening and the interaction mechanisms between drugs and targets. Expert opinion: MD simulations have been used widely in investigating the pathogenic mechanisms of diseases caused by protein misfolding, in virtual screening, and in investigating drug resistance mechanisms caused by mutations of the target. These issues are very difficult to solve by experimental methods alone. Thus, in the future, MD simulations will have wider application with the further improvement of computational capacity and the development of better sampling methods and more accurate force fields together with more efficient analysis methods.
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 dynamics of a proguanil derivative
African Journals Online (AJOL)
pc
ABSTRACT. Proguanil is a prophylactic antimalarial drug t stopping the malaria parasites from reprod molecular dynamics of a derivative of Progua benzene ring of the molecule of Proguanil derivative. The molecular geometries of chemical calculations at the Restricted Hatre. 31G(d,p) and 6-31++G. Also, Density Func.
Molecular ions, Rydberg spectroscopy and dynamics
International Nuclear Information System (INIS)
Jungen, Ch.
2015-01-01
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering
Molecular ions, Rydberg spectroscopy and dynamics
Energy Technology Data Exchange (ETDEWEB)
Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)
2015-01-22
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.
Negri, Ana; Marco, Esther; Damborsky, Jiri; Gago, Federico
2007-10-01
The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.
A computational fluid dynamics algorithm on a massively parallel computer
International Nuclear Information System (INIS)
Jespersen, D.C.; Levit, C.
1989-01-01
The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. The authors investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicitly time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. The authors find that the Connection Machine can achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as conventional supercomputers
Multiple grid methods for classical molecular dynamics.
Skeel, Robert D; Tezcan, Ismail; Hardy, David J
2002-04-30
Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, which are based on the hierarchical interpolation of interaction potentials on multiple grids. The concepts and details underlying multigrid interpolation are described. For integration of molecular dynamics the use of different time steps for different interactions allows longer time steps for many of the interactions, and this can be combined with multiple grids in space. Comparison is made to the fast multipole method, and evidence is presented suggesting that for molecular simulations multigrid methods may be superior to the fast multipole method and other tree methods.
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
Modeling Computer Virus and Its Dynamics
Peng, Mei; He, Xing; Huang, Junjian; Dong, Tao
2013-01-01
Based on that the computer will be infected by infected computer and exposed computer, and some of the computers which are in suscepitible status and exposed status can get immunity by antivirus ability, a novel coumputer virus model is established. The dynamic behaviors of this model are investigated. First, the basic reproduction number R0, which is a threshold of the computer virus spreading in internet, is determined. Second, this model has a virus-free equilibrium P0, which means that th...
Fiber lubrication: A molecular dynamics simulation study
Liu, Hongyi
Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence
Directory of Open Access Journals (Sweden)
Jitendra Maharana
Full Text Available Nucleotide-binding oligomerization domain-containing protein 1 (NOD1 and NOD2 are cytosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively and undergoes conformational alternation and ATP-dependent self-oligomerization of NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT domain confines our understanding about the NOD-mediated signaling mechanism. Here, we predicted the structure of NACHT domain of both NOD1 and NOD2 from model organism zebrafish (Danio rerio using computational methods. Our study highlighted the differential ATP binding modes in NOD1 and NOD2. In NOD1, γ-phosphate of ATP faced toward the central nucleotide binding cavity like NLRC4, whereas in NOD2 the cavity was occupied by adenine moiety. The conserved 'Lysine' at Walker A formed hydrogen bonds (H-bonds and Aspartic acid (Walker B formed electrostatic interaction with ATP. At Sensor 1, Arg328 of NOD1 exhibited an H-bond with ATP, whereas corresponding Arg404 of NOD2 did not. 'Proline' of GxP motif (Pro386 of NOD1 and Pro464 of NOD2 interacted with adenine moiety and His511 at Sensor 2 of NOD1 interacted with γ-phosphate group of ATP. In contrast, His579 of NOD2 interacted with the adenine moiety having a relatively inverted orientation. Our findings are well supplemented with the molecular interaction of ATP with NLRC4, and consistent with mutagenesis data reported for human, which indicates evolutionary shared NOD signaling mechanism. Together, this study provides novel insights into ATP binding mechanism, and highlights the differential ATP binding modes in zebrafish NOD1 and NOD2.
Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms
Directory of Open Access Journals (Sweden)
Christian R. Trott
2012-09-01
Full Text Available Classical equilibrium molecular dynamics (MD simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC and TIP4P water models applied to simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. The FPGA-based accelerator MD-GRAPE 3 was used to accelerate substantially the computation of non-bonded forces, while GPU-based platforms were also used in conjunction with CUDA-enabled versions of the LAMMPS MD software packages to reduce computational time dramatically. The dependence of molecular system size and scaling with number of processors was also investigated. Considering performance relative to power consumption, it is seen that GPU-based computing is quite attractive.
Dynamics and Thermodynamics of Molecular Machines
DEFF Research Database (Denmark)
Golubeva, Natalia
2014-01-01
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......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...... 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...
Fluid dynamics theory, computation, and numerical simulation
Pozrikidis, C
2001-01-01
Fluid Dynamics Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes Two distinguishing features of the discourse are solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty Matlab codes are presented and discussed for a broad...
Bresme, F; Armstrong, J
2014-01-07
We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the "local" thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation.
Advanced Computational Fluid Dynamics (CFD)
National Aeronautics and Space Administration — It is time for the next generation of aerothermodynamic CFD software, including unstructured gridding, low dissipation fluxes, dynamic simulations, and modern...
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 simulations through GPU video games technologies.
Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations.
Computational Fluid Dynamics and Room Air Movement
DEFF Research Database (Denmark)
Nielsen, Peter Vilhelm
2004-01-01
Nielsen, P.V. Computational Fluid Dynamics and Room Air Movement. Indoor Air, International Journal of Indoor Environment and Health, Vol. 14, Supplement 7, pp. 134-143, 2004. ABSTRACT Computational Fluid Dynamics (CFD) and new developments of CFD in the indoor environment as well as quality...... considerations are important elements in the study of energy consumption, thermal comfort and indoor air quality in buildings. The paper discusses the quality level of Computational Fluid Dynamics and the involved schemes (first, second and third order schemes) by the use of the Smith and Hutton problem...
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.
Control of Mechanotransduction by Molecular Clutch Dynamics.
Elosegui-Artola, Alberto; Trepat, Xavier; Roca-Cusachs, Pere
2018-02-26
The linkage of cells to their microenvironment is mediated by a series of bonds that dynamically engage and disengage, in what has been conceptualized as the molecular clutch model. Whereas this model has long been employed to describe actin cytoskeleton and cell migration dynamics, it has recently been proposed to also explain mechanotransduction (i.e., the process by which cells convert mechanical signals from their environment into biochemical signals). Here we review the current understanding on how cell dynamics and mechanotransduction are driven by molecular clutch dynamics and its master regulator, the force loading rate. Throughout this Review, we place a specific emphasis on the quantitative prediction of cell response enabled by combined experimental and theoretical approaches. Copyright © 2018 Elsevier Ltd. All rights reserved.
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.
Quantum spin dynamics in molecular magnets
International Nuclear Information System (INIS)
Leuenberger, M.N.; Meier, F.; Loss, D.
2003-01-01
The detailed theoretical understanding of quantum spin dynamics in various molecular magnets is an important step on the roadway to technological applications of these systems. Quantum effects in both ferromagnetic and antiferromagnetic molecular clusters are, by now, theoretically well understood. Ferromagnetic molecular clusters allow one to study the interplay of incoherent quantum tunneling and thermally activated transitions between states with different spin orientation. The Berry phase oscillations found in Fe 8 are signatures of the quantum mechanical interference of different tunneling paths. Antiferromagnetic molecular clusters are promising candidates for the observation of coherent quantum tunneling on the mesoscopic scale. Although challenging, application of molecular magnetic clusters for data storage and quantum data processing are within experimental reach already with present day technology. Refs. 77 (author)
Dynamics and Thermodynamics of Molecular Machines
DEFF Research Database (Denmark)
Golubeva, Natalia
2014-01-01
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...... 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...... transport, move on crowded tracks where they can encounter other motors, a phenomenon referred to as molecular motor traffic. In the second part, traffic models of kinesin motors under an external mechanical load are considered, and the efficiency at maximum power (EMP) is calculated as a convenient measure...
Thermal Conductivity of Supercooled Water: An Equilibrium Molecular Dynamics Exploration.
English, Niall J; Tse, John S
2014-11-06
The thermal conductivity of both supercooled and ambient-temperature water at atmospheric pressure has been computed over the 140-270 K temperature range for three popular water models via equilibrium molecular dynamics in the Green-Kubo setting. No strong temperature dependence of thermal conductivity was observed. The underlying phonon modes contributing to thermal conduction processes have been examined in the present work, and it has been established that (translational) acoustic modes dominate in supercooled water.
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.
Fluid dynamics computer programs for NERVA turbopump
Brunner, J. J.
1972-01-01
During the design of the NERVA turbopump, numerous computer programs were developed for the analyses of fluid dynamic problems within the machine. Program descriptions, example cases, users instructions, and listings for the majority of these programs are presented.
Computational study of a dynamic contact problem
Directory of Open Access Journals (Sweden)
Jigarkumar Patel
2013-10-01
Full Text Available In this article, we describe a computational framework to study the influence of a normal crack on the dynamics of a cantilever beam; i.e., changes in its natural frequency, amplitude and period of vibration, etc.
Emission of water clusters: molecular dynamic simulation
International Nuclear Information System (INIS)
Kutliev, U.O.; Kalandarov, K.S.
2006-01-01
Full text: Secondary ion mass spectrometry (SIMS) is a wonderful technique for providing mass spectrometric information of molecules on surfaces. Theoretical studies of the keV bombardment of organic films on metallic surfaces have contributed to our understanding of the mechanisms governing these processes. Many experiments of keV bombardment, however, are performed both thick and thin organic targets [1]. Molecular systems investigated experimentally by SIMS include adsorbed films on a metal substrate, molecular solids, polymers, or even biological cells. In this account, we focus on thin organic layers on metal substrates as they are used for analytical purposes, are intriguing from a fundamental viewpoint, and are computationally tractable [2]. There are we present molecular dynamics (MD) simulations aimed at obtaining such a microscopic picture and mass spectrum of sputtering particles. Because of the importance of H 2 O in many of the experiments, we have chosen it as our system. Water is also attractive as a system because of the extensive literature available on its physical properties. The interaction potentials available for MD simulations of H 2 O are sufficiently reliable such that a quantitative analysis of the simulation results can be directly related to the parameters of water. From the variety of substrate materials used in different experiments, we have chosen to perform our simulations using Au. This substance is chosen to match preliminary experiments with the selective killing of cells by inserted Au nanoparticles and because of the availability of good interaction potentials for gold. In the simulations, we bombarded by ions Ar the surface Au(III) covered by ice film. The interaction potential employed to describe the H 2 O-H 2 O interaction is the simple-point-charge (SPC) water potential developed by Berendsen et al. [3]. This potential has been used extensively to study the properties of H 2 O as a solid [4, 5]. It has been shown that the
Computational Studies in Molecular Geochemistry and Biogeochemistry
Energy Technology Data Exchange (ETDEWEB)
Felmy, Andrew R.; Bylaska, Eric J.; Dixon, David A.; Dupuis, Michel; Halley, James W.; Kawai, R.; Rosso, Kevin M.; Rustad, James R.; Smith, Paul E.; Straatsma, TP; Voth, Gregory A.; Weare, John H.; Yuen, David A.
2006-04-18
The ability to predict the transport and transformations of contaminants within the subsurface is critical for decisions on virtually every waste disposal option facing the Department of Energy (DOE), from remediation technologies such as in situ bioremediation to evaluations of the safety of nuclear waste repositories. With this fact in mind, the DOE has recently sponsored a series of workshops on the development of a Strategic Simulation Plan on applications of high perform-ance computing to national problems of significance to the DOE. One of the areas selected for application was in the area of subsurface transport and environmental chemistry. Within the SSP on subsurface transport and environmental chemistry several areas were identified where applications of high performance computing could potentially significantly advance our knowledge of contaminant fate and transport. Within each of these areas molecular level simulations were specifically identified as a key capability necessary for the development of a fundamental mechanistic understanding of complex biogeochemical processes. This effort consists of a series of specific molecular level simulations and program development in four key areas of geochemistry/biogeochemistry (i.e., aqueous hydrolysis, redox chemistry, mineral surface interactions, and microbial surface properties). By addressing these four differ-ent, but computationally related, areas it becomes possible to assemble a team of investigators with the necessary expertise in high performance computing, molecular simulation, and geochemistry/biogeochemistry to make significant progress in each area. The specific targeted geochemical/biogeochemical issues include: Microbial surface mediated processes: the effects of lipopolysacchardies present on gram-negative bacteria. Environmental redox chemistry: Dechlorination pathways of carbon tetrachloride and other polychlorinated compounds in the subsurface. Mineral surface interactions: Describing
Fluid dynamics theory, computation, and numerical simulation
Pozrikidis, C
2017-01-01
This book provides an accessible introduction to the basic theory of fluid mechanics and computational fluid dynamics (CFD) from a modern perspective that unifies theory and numerical computation. Methods of scientific computing are introduced alongside with theoretical analysis and MATLAB® codes are presented and discussed for a broad range of topics: from interfacial shapes in hydrostatics, to vortex dynamics, to viscous flow, to turbulent flow, to panel methods for flow past airfoils. The third edition includes new topics, additional examples, solved and unsolved problems, and revised images. It adds more computational algorithms and MATLAB programs. It also incorporates discussion of the latest version of the fluid dynamics software library FDLIB, which is freely available online. FDLIB offers an extensive range of computer codes that demonstrate the implementation of elementary and advanced algorithms and provide an invaluable resource for research, teaching, classroom instruction, and self-study. This ...
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.
Molecular dynamics simulations and quantum chemical calculations ...
African Journals Online (AJOL)
Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...
Molecular dynamics 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
An ab initio molecular dynamics study
Indian Academy of Sciences (India)
Abstract. The hydration structure and translocation of an excess proton in hydrogen bonded water clusters of two different sizes are investigated by means of finite tempera- ture quantum simulations. The simulations are performed by employing the method of. Car–Parrinello molecular dynamics where the forces on the ...
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 on the interaction mechanism ...
Indian Academy of Sciences (India)
Investigation on the microscopic interaction between polymer inhibitors and calcium phosphate contributes to the understanding of their scale inhibition mechanism. The results obtained may provide a theoretical guidance to developing new scale inhibitors. In this study, molecular dynamics simulations have been ...
Molecular dynamics modeling of structural battery components
Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.
2015-01-01
A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion
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:
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 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.)
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.
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...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...
A Computational Fluid Dynamics Algorithm on a Massively Parallel Computer
Jespersen, Dennis C.; Levit, Creon
1989-01-01
The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. We investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicit time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. We find that the Connection Machine ran achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as today's most powerful conventional supercomputers.
Molecular dynamics simulations of weak detonations.
Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie
2011-12-01
Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal.
Hardware for dynamic quantum computing.
Ryan, Colm A; Johnson, Blake R; Ristè, Diego; Donovan, Brian; Ohki, Thomas A
2017-10-01
We describe the hardware, gateware, and software developed at Raytheon BBN Technologies for dynamic quantum information processing experiments on superconducting qubits. In dynamic experiments, real-time qubit state information is fed back or fed forward within a fraction of the qubits' coherence time to dynamically change the implemented sequence. The hardware presented here covers both control and readout of superconducting qubits. For readout, we created a custom signal processing gateware and software stack on commercial hardware to convert pulses in a heterodyne receiver into qubit state assignments with minimal latency, alongside data taking capability. For control, we developed custom hardware with gateware and software for pulse sequencing and steering information distribution that is capable of arbitrary control flow in a fraction of superconducting qubit coherence times. Both readout and control platforms make extensive use of field programmable gate arrays to enable tailored qubit control systems in a reconfigurable fabric suitable for iterative development.
The Dynamic Geometrisation of Computer Programming
Sinclair, Nathalie; Patterson, Margaret
2018-01-01
The goal of this paper is to explore dynamic geometry environments (DGE) as a type of computer programming language. Using projects created by secondary students in one particular DGE, we analyse the extent to which the various aspects of computational thinking--including both ways of doing things and particular concepts--were evident in their…
COMPUTER PROGRAMME FOR THE DYNAMIC ANALYSIS
African Journals Online (AJOL)
ES OBE
ABSTRACT. The traditional method of dynamic analysis of tall rigid frames assumes the shear frame model. Models that allow joint rotations with/without the inclusion of the column axial loads give improved results but pose much more computational difficulty. In this work a computer program Natfrequency that determines ...
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
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.
Computational plasticity algorithm for particle dynamics simulations
Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.
2018-01-01
The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.
Dynamics and computation in functional shifts
Namikawa, Jun; Hashimoto, Takashi
2004-07-01
We introduce a new type of shift dynamics as an extended model of symbolic dynamics, and investigate the characteristics of shift spaces from the viewpoints of both dynamics and computation. This shift dynamics is called a functional shift, which is defined by a set of bi-infinite sequences of some functions on a set of symbols. To analyse the complexity of functional shifts, we measure them in terms of topological entropy, and locate their languages in the Chomsky hierarchy. Through this study, we argue that considering functional shifts from the viewpoints of both dynamics and computation gives us opposite results about the complexity of systems. We also describe a new class of shift spaces whose languages are not recursively enumerable.
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
Modeling Computer Virus and Its Dynamics
Directory of Open Access Journals (Sweden)
Mei Peng
2013-01-01
Full Text Available Based on that the computer will be infected by infected computer and exposed computer, and some of the computers which are in suscepitible status and exposed status can get immunity by antivirus ability, a novel coumputer virus model is established. The dynamic behaviors of this model are investigated. First, the basic reproduction number R0, which is a threshold of the computer virus spreading in internet, is determined. Second, this model has a virus-free equilibrium P0, which means that the infected part of the computer disappears, and the virus dies out, and P0 is a globally asymptotically stable equilibrium if R01 then this model has only one viral equilibrium P*, which means that the computer persists at a constant endemic level, and P* is also globally asymptotically stable. Finally, some numerical examples are given to demonstrate the analytical results.
Córdova-Sintjago, Tania C.; Liu, Yue; Booth, Raymond G.
2015-02-01
To understand molecular determinants for ligand activation of the serotonin 5-HT2C G protein-coupled receptor (GPCR), a drug target for obesity and neuropsychiatric disorders, a 5-HT2C homology model was built according to an adrenergic β2 GPCR (β2AR) structure and validated using a 5-HT2B GPCR crystal structure. The models were equilibrated in a simulated phosphatidyl choline membrane for ligand docking and molecular dynamics studies. Ligands included (2S, 4R)-(-)-trans-4-(3'-bromo- and trifluoro-phenyl)-N,N-dimethyl-1,2,3,4-tetrahydronaphthalene-2-amine (3'-Br-PAT and 3'-CF3-PAT), a 5-HT2C agonist and inverse agonist, respectively. Distinct interactions of 3'-Br-PAT and 3'-CF3-PAT at the wild-type (WT) 5-HT2C receptor model were observed and experimental 5-HT2C receptor mutagenesis studies were undertaken to validate the modelling results. For example, the inverse agonist 3'-CF3-PAT docked deeper in the WT 5-HT2C binding pocket and altered the orientation of transmembrane helices (TM) 6 in comparison to the agonist 3'-Br-PAT, suggesting that changes in TM orientation that result from ligand binding impact function. For both PATs, mutation of 5-HT2C residues S3.36, T3.37, and F5.47 to alanine resulted in significantly decreased affinity, as predicted from modelling results. It was concluded that upon PAT binding, 5-HT2C residues T3.37 and F5.47 in TMs 3 and 5, respectively, engage in inter-helical interactions with TMs 4 and 6, respectively. The movement of TMs 5 and 6 upon agonist and inverse agonist ligand binding observed in the 5-HT2C receptor modelling studies was similar to movements reported for the activation and deactivation of the β2AR, suggesting common mechanisms among aminergic neurotransmitter GPCRs.
Three-Dimensional Computational Fluid Dynamics
Energy Technology Data Exchange (ETDEWEB)
Haworth, D.C.; O' Rourke, P.J.; Ranganathan, R.
1998-09-01
Computational fluid dynamics (CFD) is one discipline falling under the broad heading of computer-aided engineering (CAE). CAE, together with computer-aided design (CAD) and computer-aided manufacturing (CAM), comprise a mathematical-based approach to engineering product and process design, analysis and fabrication. In this overview of CFD for the design engineer, our purposes are three-fold: (1) to define the scope of CFD and motivate its utility for engineering, (2) to provide a basic technical foundation for CFD, and (3) to convey how CFD is incorporated into engineering product and process design.
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)
Transforming bases to bytes: Molecular computing with DNA
Indian Academy of Sciences (India)
Despite the popular image of silicon-based computers for computation, an embryonic field of mole- cular computation is emerging, where molecules in solution perform computational operations. DNA, which is known to store biological information, is being used as a substrate for molecular computation. In this review, we ...
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.
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
A stochastic phase-field model determined from molecular dynamics
von Schwerin, Erik
2010-03-17
The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.
Molecular dynamics simulations of nanobubbles and nanodrops
Maheshwari, Shantanu
2018-01-01
Understanding of bubbles and drops at the nanoscale is of primary importance to many technological applications. Although lot of theoretical understanding has been developed in the last few decades for larger size bubbles and drops, fundamental understanding of nanobubbles and nanodrops in some aspects is still inadequate. In this thesis we revealed and explained a few phenomena related to the stability and growth/dissolution of nanobubbles and nanodrops with the help from molecular dynamics ...
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
Visualizing Energy on Target: Molecular Dynamics Simulations
2017-12-01
from the increased number of intermolecular interactions at the higher mass densities . This may also be why the size of the hot spot increases with...of energy deposition by a shocked diatomic gas into a stationary target is studied as a function of multiple variables including gas density , impact...into the vibrational channels of the gas is a function of the density . 15. SUBJECT TERMS molecular dynamics, energy deposition, rovibrational
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
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.
Software agents in molecular computational biology.
Keele, John W; Wray, James E
2005-12-01
Progress made in applying agent systems to molecular computational biology is reviewed and strategies by which to exploit agent technology to greater advantage are investigated. Communities of software agents could play an important role in helping genome scientists design reagents for future research. The advent of genome sequencing in cattle and swine increases the complexity of data analysis required to conduct research in livestock genomics. Databases are always expanding and semantic differences among data are common. Agent platforms have been developed to deal with generic issues such as agent communication, life cycle management and advertisement of services (white and yellow pages). This frees computational biologists from the drudgery of having to re-invent the wheel on these common chores, giving them more time to focus on biology and bioinformatics. Agent platforms that comply with the Foundation for Intelligent Physical Agents (FIPA) standards are able to interoperate. In other words, agents developed on different platforms can communicate and cooperate with one another if domain-specific higher-level communication protocol details are agreed upon between different agent developers. Many software agent platforms are peer-to-peer, which means that even if some of the agents and data repositories are temporarily unavailable, a subset of the goals of the system can still be met. Past use of software agents in bioinformatics indicates that an agent approach should prove fruitful. Examination of current problems in bioinformatics indicates that existing agent platforms should be adaptable to novel situations.
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
A Parallel Iterative Method for Computing Molecular Absorption Spectra.
Koval, Peter; Foerster, Dietrich; Coulaud, Olivier
2010-09-14
We describe a fast parallel iterative method for computing molecular absorption spectra within TDDFT linear response and using the LCAO method. We use a local basis of "dominant products" to parametrize the space of orbital products that occur in the LCAO approach. In this basis, the dynamic polarizability is computed iteratively within an appropriate Krylov subspace. The iterative procedure uses a matrix-free GMRES method to determine the (interacting) density response. The resulting code is about 1 order of magnitude faster than our previous full-matrix method. This acceleration makes the speed of our TDDFT code comparable with codes based on Casida's equation. The implementation of our method uses hybrid MPI and OpenMP parallelization in which load balancing and memory access are optimized. To validate our approach and to establish benchmarks, we compute spectra of large molecules on various types of parallel machines. The methods developed here are fairly general, and we believe they will find useful applications in molecular physics/chemistry, even for problems that are beyond TDDFT, such as organic semiconductors, particularly in photovoltaics.
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)
An introduction to Computational Fluid Dynamics
DEFF Research Database (Denmark)
Sørensen, Lars Schiøtt
1999-01-01
CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building.......CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building....
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
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.
Traffic Dynamics of Computer Networks
Fekete, Attila
2008-10-01
Two important aspects of the Internet, namely the properties of its topology and the characteristics of its data traffic, have attracted growing attention of the physics community. My thesis has considered problems of both aspects. First I studied the stochastic behavior of TCP, the primary algorithm governing traffic in the current Internet, in an elementary network scenario consisting of a standalone infinite-sized buffer and an access link. The effect of the fast recovery and fast retransmission (FR/FR) algorithms is also considered. I showed that my model can be extended further to involve the effect of link propagation delay, characteristic of WAN. I continued my thesis with the investigation of finite-sized semi-bottleneck buffers, where packets can be dropped not only at the link, but also at the buffer. I demonstrated that the behavior of the system depends only on a certain combination of the parameters. Moreover, an analytic formula was derived that gives the ratio of packet loss rate at the buffer to the total packet loss rate. This formula makes it possible to treat buffer-losses as if they were link-losses. Finally, I studied computer networks from a structural perspective. I demonstrated through fluid simulations that the distribution of resources, specifically the link bandwidth, has a serious impact on the global performance of the network. Then I analyzed the distribution of edge betweenness in a growing scale-free tree under the condition that a local property, the in-degree of the "younger" node of an arbitrary edge, is known in order to find an optimum distribution of link capacity. The derived formula is exact even for finite-sized networks. I also calculated the conditional expectation of edge betweenness, rescaled for infinite networks.
Lombardo, Giuseppe M.; Portalone, Gustavo; Colapietro, Marcello; Rescifina, Antonio; Punzo, Francesco
2011-05-01
The ability of caffeic acid to act as antioxidant against hyperoxo-radicals as well as its recently found therapeutic properties in the treatment of hepatocarcinoma, still make this compound, more than 20 years later the refinement of its crystal structure, object of study. It belongs to the vast family of humic substances, which play a key role in the biodegradation processes and easily form complexes with ions widely diffused in the environment. This class of compounds is therefore interesting for potential environmental chemistry applications concerning the possible complexation of heavy metals. Our study focused on the characterization of caffeic acid as a starting necessary step, which will be followed in the future by the application of our findings on the study of the properties of caffeate anion interaction with heavy metal ions. To reach this goal, we applied a low cost approach - in terms of computational time and resources - aimed at the achievement of a high resolution, robust and trustable structure using the X-ray single crystal data, recollected with a higher resolution, as touchstone for a detailed check. A comparison between the calculations carried out with density functional theory (DFT), Hartree-Fock (HF) method and post SCF second order Møller-Plesset perturbation method (MP2), at the 6-31G ** level of the theory, molecular mechanics (MM) and molecular dynamics (MD) was performed. As a consequence we explained on one hand the possible reasons for the pitfalls of the DFT approach and on the other the benefits of using a good and robust force field developed for condensed phases, as AMBER, with MM and MD. The reliability of the latter, highlighted by the overall agreement extended up to the anisotropic displacement parameters calculated by means of MD and the ones gathered by X-ray measurements, makes it very promising for the above-mentioned goals.
Computational fluid dynamics a practical approach
Tu, Jiyuan; Liu, Chaoqun
2018-01-01
Computational Fluid Dynamics: A Practical Approach, Third Edition, is an introduction to CFD fundamentals and commercial CFD software to solve engineering problems. The book is designed for a wide variety of engineering students new to CFD, and for practicing engineers learning CFD for the first time. Combining an appropriate level of mathematical background, worked examples, computer screen shots, and step-by-step processes, this book walks the reader through modeling and computing, as well as interpreting CFD results. This new edition has been updated throughout, with new content and improved figures, examples and problems.
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 algorithms for quantum Monte Carlo methods
Miura, Shinichi
2009-11-01
In the present Letter, novel molecular dynamics methods compatible with corresponding quantum Monte Carlo methods are developed. One is a variational molecular dynamics method that is a molecular dynamics analog of quantum variational Monte Carlo method. The other is a variational path integral molecular dynamics method, which is based on the path integral molecular dynamics method for finite temperature systems by Tuckerman et al. [M. Tuckerman, B.J. Berne, G.J. Martyna, M.L. Klein, J. Chem. Phys. 99 (1993) 2796]. These methods are applied to model systems including the liquid helium-4, demonstrated to work satisfactorily for the tested ground state calculations.
Computational Fluid Dynamics in Ventilation Design
DEFF Research Database (Denmark)
Nielsen, Peter V.
2008-01-01
This paper is based on the new REHVA Guidebook Computational Fluid Dynamics in Ventilation Design (Nielsen et al. 2007) written by Peter V. Nielsen, Francis(Nielsen 2007) written by Peter V. Nielsen, Francis Allard, Hazim B. Awbi, Lars Davidson and Alois Schälin. The guidebook is made for people...
A Stochastic Dynamic Model of Computer Viruses
Directory of Open Access Journals (Sweden)
Chunming Zhang
2012-01-01
Full Text Available A stochastic computer virus spread model is proposed and its dynamic behavior is fully investigated. Specifically, we prove the existence and uniqueness of positive solutions, and the stability of the virus-free equilibrium and viral equilibrium by constructing Lyapunov functions and applying Ito's formula. Some numerical simulations are finally given to illustrate our main results.
Computational fluid dynamics in greenhouses: A review
African Journals Online (AJOL)
use
2011-12-05
Dec 5, 2011 ... Computational fluid dynamics is a tool that has been used in recent years to develop numerical models that improve our understanding of the interaction of variables that make up the climate inside greenhouses. In the past five years, more realistic studies have appeared due mainly to the development of ...
Engineering applications of computational fluid dynamics
Awang, Mokhtar
2015-01-01
This volume presents the results of Computational Fluid Dynamics (CFD) analysis that can be used for conceptual studies of product design, detail product development, process troubleshooting. It demonstrates the benefit of CFD modeling as a cost saving, timely, safe and easy to scale-up methodology.
Molecular Sieve Bench Testing and Computer Modeling
Mohamadinejad, Habib; DaLee, Robert C.; Blackmon, James B.
1995-01-01
The design of an efficient four-bed molecular sieve (4BMS) CO2 removal system for the International Space Station depends on many mission parameters, such as duration, crew size, cost of power, volume, fluid interface properties, etc. A need for space vehicle CO2 removal system models capable of accurately performing extrapolated hardware predictions is inevitable due to the change of the parameters which influences the CO2 removal system capacity. The purpose is to investigate the mathematical techniques required for a model capable of accurate extrapolated performance predictions and to obtain test data required to estimate mass transfer coefficients and verify the computer model. Models have been developed to demonstrate that the finite difference technique can be successfully applied to sorbents and conditions used in spacecraft CO2 removal systems. The nonisothermal, axially dispersed, plug flow model with linear driving force for 5X sorbent and pore diffusion for silica gel are then applied to test data. A more complex model, a non-darcian model (two dimensional), has also been developed for simulation of the test data. This model takes into account the channeling effect on column breakthrough. Four FORTRAN computer programs are presented: a two-dimensional model of flow adsorption/desorption in a packed bed; a one-dimensional model of flow adsorption/desorption in a packed bed; a model of thermal vacuum desorption; and a model of a tri-sectional packed bed with two different sorbent materials. The programs are capable of simulating up to four gas constituents for each process, which can be increased with a few minor changes.
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)
Molecular Dynamics: from basic techniques to applications (A Molecular Dynamics Primer)
Hernández, E. R.
2008-11-01
It is now 50 years since the first papers describing the use of Molecular Dynamics (MD) were published by Alder and Wainright, and since then, together with Monte Carlo (MC) techniques, MD has become an essential tool in the theoretical study of materials properties at finite temperatures. In its early days, MD was used in combination with simple yet general models, such as hard spheres or Lennard-Jones models of liquids, systems which, though simple, were nevertheless not amenable to an analytical statistical mechanical treatment. Nowadays, however, MD is most frequently used in combination with rather sophisticated models, ranging all the way between empirical force fields to first-principles methods, with the aim of describing as accurately as possible any given material. From a computational aid in statistical mechanics and many-body physics, MD has evolved to become a widely used tool in physical chemistry, condensed matter physics, biology, geology and materials science. The aim of this course is to describe the basic algorithms of MD, and to provide attendees with the necessary theoretical background in order to enable them to use MD simulations in their research work. Also, examples of the use of MD in different scientific disciplines will be provided, with the aim of illustrating the the many possibilities and the wide spread use of MD simulation techniques in scientific research today.
Molecular dynamic results on transport properties
Energy Technology Data Exchange (ETDEWEB)
Alder, B.J.; Alley, W.E.
1978-06-01
Following a broad discussion of generalized hydrodynamics, three examples are given to illustrate how useful this approach is in extending hydrodynamics to nearly the scale of molecular dimensions and the time between collisions, principally by including viscoelastic effects. The three examples concern the behavior of the velocity autocorrelation function, the decay of fluctuations in a resonating system, and the calculation of the dynamic structure factor obtained from neutron scattering. In the latter case the molecular dynamics results are also compared to the predictions of generalized kinetic theory. Finally it is shown how to implement generalized hydrodynamics both on a microscopic and macroscopic level. Hydrodynamics is unable to account for the long time tails in the velocity autocorrelation functions and the divergent Burnett coefficients observed for the Lorentz gas. Instead, the long time behavior of the Burnett coefficient and the distribution of displacements (the self part of the dynamic structure factor) can be accounted for by a random walk with a waiting time distribution which is chosen to give the correct velocity autocorrelation function. This random walk predicts, in agreement with the observations, that this displacement distribution is Gaussian at long times for the Lorentz gas, while for hard disks it has been found not to be so.
Computational Methods in Stochastic Dynamics Volume 2
Stefanou, George; Papadopoulos, Vissarion
2013-01-01
The considerable influence of inherent uncertainties on structural behavior has led the engineering community to recognize the importance of a stochastic approach to structural problems. Issues related to uncertainty quantification and its influence on the reliability of the computational models are continuously gaining in significance. In particular, the problems of dynamic response analysis and reliability assessment of structures with uncertain system and excitation parameters have been the subject of continuous research over the last two decades as a result of the increasing availability of powerful computing resources and technology. This book is a follow up of a previous book with the same subject (ISBN 978-90-481-9986-0) and focuses on advanced computational methods and software tools which can highly assist in tackling complex problems in stochastic dynamic/seismic analysis and design of structures. The selected chapters are authored by some of the most active scholars in their respective areas and...
MDVRY: a polarizable classical molecular dynamics package for biomolecules
Souaille, M.; Loirat, H.; Borgis, D.; Gaigeot, M. P.
2009-02-01
The MDVRY classical molecular dynamics package is presented for the study of biomolecules in the gas and liquid phase. Electrostatic polarization has been implemented in the formalism of point induced dipoles following the model of Thole. Two schemes have been implemented for the calculation of induced dipoles, i.e. resolution of the self-consistent equations and a 'Car-Parrinello' dynamical approach. In this latter, the induced dipoles are calculated at each time step of the dynamics through the dynamics of additional degrees of freedom associated with the dipoles. This method saves computer time and allows to study polarized solvated proteins at a very low CPU cost. The program is written in C-language and runs on LINUX machines. A detailed manual of the code is given. The main features of the package are illustrated taking on examples of proteins in the gas phase or immersed in liquid water. Program summaryProgram title: MDVRY Catalogue identifier: AEBY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 39 156 No. of bytes in distributed program, including test data, etc.: 277 197 Distribution format: tar.bz2 Programming language: C Computer: Linux machines with FFTW Fourier Transform package installed Operating system: Linux machines, SUSE & RedHat distributions Classification: 3, 16.13, 23 External routines: FFTW ( http://www.fftw.org/) Nature of problem: Molecular Dynamics Software package. Solution method: Velocity Verlet algorithm. The implemented force field is composed of intra-molecular interactions and inter-molecular interactions (electrostatics, polarization, van der Waals). Polarization is accounted through induced point dipoles at each atomic site. Supplementary degrees of freedom are
Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein
Asafi, M. S.; Yildirim, A.; Tekpinar, M.
2016-04-01
Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.
Perspective: Computer simulations of long time dynamics
Energy Technology Data Exchange (ETDEWEB)
Elber, Ron [Department of Chemistry, The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712 (United States)
2016-02-14
Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.
Manouchehri, Firouzeh; Izadmanesh, Yahya; Aghaee, Elham; Ghasemi, Jahan B
2016-10-01
The interaction of pyridoxine (Vitamin B6) with bovine serum albumin (BSA) is investigated under pseudo-physiological conditions by UV-Vis, fluorescence and FTIR spectroscopy. The intrinsic fluorescence of BSA was quenched by VB6, which was rationalized in terms of the static quenching mechanism. According to fluorescence quenching calculations, the bimolecular quenching constant (kq), dynamic quenching (KSV) and static quenching (KLB) at 310K were obtained. The efficiency of energy transfer and the distance between the donor (BSA) and the acceptor (VB6) were calculated by Foster's non-radiative energy transfer theory and were equal to 41.1% and 2.11nm. The collected UV-Vis and fluorescence spectra were combined into a row-and column-wise augmented matrix and resolved by multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS helped to estimate the stoichiometry of interactions, concentration profiles and pure spectra for three species (BSA, VB6 and VB6-BSA complex) existed in the interaction procedure. Based on the MCR-ALS results, using mass balance equations, a model was developed and binding constant of complex was calculated using non-linear least squares curve fitting. FT-IR spectra showed that the conformation of proteins was altered in presence of VB6. Finally, the combined docking and molecular dynamics (MD) simulations were used to estimate the binding affinity of VB6 to BSA. Five-nanosecond MD simulations were performed on bovine serum albumin (BSA) to study the conformational features of its ligand binding site. From MD results, eleven BSA snapshots were extracted, at every 0.5ns, to explore the binding affinity (GOLD score) of VB6 using a docking procedure. MD simulations indicated that there is a considerable flexibility in the structure of protein that affected ligand recognition. Structural analyses and docking simulations indicated that VB6 binds to site I and GOLD score values depend on the conformations of both BSA and ligand
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 simulation of ion mobility in gases
Lai, Rui; Dodds, Eric D.; Li, Hui
2018-02-01
A force field molecular dynamics method is developed to directly simulate ion drift in buffer gases driven by an electric field. The ion mobility and collision cross sections (CCSs) with relevance to ion mobility spectrometry can be obtained from the simulated drift velocity in high-density buffer gases (pressure ˜50 bars) and high electric fields (˜107 V/m). Compared to trajectory methods, the advantage of the molecular dynamics method is that it can simultaneously sample the internal dynamic motions of the ion and the ion-gas collisions. For ions with less than 100 atoms, the simulated collision cross section values can be converged to within ±1%-2% by running a 100 ns simulation for 5-19 h using one computer core. By using a set of element-based Lennard-Jones parameters that are not tuned for different atomic types in different molecules, the simulated collision cross sections for 15 small molecular ions (number of atoms ranging from 17 to 85, mass ranging from 74.1 to 609.4 g/mol) are consistent with experimental values: the mean unsigned error is 2.6 Å2 for He buffer gas and 4.4 Å2 for N2 buffer gas. The sensitivity of the simulated CCS values to random diffusion, drift velocity, electric field strength, temperature, and buffer gas density is examined.
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 Study of Alkanethiolate Self-Assembled Monolayer Coated Gold Nanoparticle
2007-06-01
of Organosulfur Compounds on Au( 111). Implications for Molecular Self-Assembly on Gold 21. Plimpton, S.J., "Fast Parallel Algorithms for Short-Range... Organosulfur Compounds SHAKE Algorithm for Molecular Dynamics." Journal of Adsorbed on Gold Single Crystals: Electron Diffraction Computational Physics, 52
Using a Computer Animation to Teach High School Molecular Biology
Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth
2008-01-01
We present an active way to use a computer animation in secondary molecular genetics class. For this purpose we developed an activity booklet that helps students to work interactively with a computer animation which deals with abstract concepts and processes in molecular biology. The achievements of the experimental group were compared with those…
Molecular dynamics in high electric fields
Energy Technology Data Exchange (ETDEWEB)
Apostol, M., E-mail: apoma@theory.nipne.ro; Cune, L.C.
2016-06-15
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.
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.
Molecular dynamics algorithms for path integrals at constant pressure
Martyna, Glenn J.; Hughes, Adam; Tuckerman, Mark E.
1999-02-01
Extended system path integral molecular dynamics algorithms have been developed that can generate efficiently averages in the quantum mechanical canonical ensemble [M. E. Tuckerman, B. J. Berne, G. J. Martyna, and M. L. Klein, J. Chem. Phys. 99, 2796 (1993)]. Here, the corresponding extended system path integral molecular dynamics algorithms appropriate to the quantum mechanical isothermal-isobaric ensembles with isotropic-only and full system cell fluctuations are presented. The former ensemble is employed to study fluid systems which do not support shear modes while the latter is employed to study solid systems. The algorithms are constructed by deriving appropriate dynamical equations of motions and developing reversible multiple time step algorithms to integrate the equations numerically. Effective parallelization schemes for distributed memory computers are presented. The new numerical methods are tested on model (a particle in a periodic potential) and realistic (liquid and solid para-hydrogen and liquid butane) systems. In addition, the methodology is extended to treat the path integral centroid dynamics scheme, [J. Cao and G. A. Voth, J. Chem. Phys. 99, 10070 (1993)], a novel method which is capable of generating semiclassical approximations to quantum mechanical time correlation functions.
Computational fluid dynamics evaluation of excessive dynamic airway collapse.
Taherian, Shahab; Rahai, Hamid; Gomez, Bernardo; Waddington, Thomas; Mazdisnian, Farhad
2017-12-01
Excessive dynamic airway collapse, which is often caused by the collapse of the posterior membrane wall during exhalation, is often misdiagnosed with other diseases; stents can provide support for the collapsing airways. The standard pulmonary function tests do not necessarily show change in functional breathing condition for evaluation of these type of diseases. Flow characteristics through a patient's airways with excessive dynamic airway collapse have been numerically investigated. A stent was placed to support the collapsing airway and to improve breathing conditions. Computed tomography images of the patient's pre- and post-stenting were used for generating 3-Dimensional models of the airways, and were imported into a computational fluid dynamics software for simulation of realistic air flow behavior. Unsteady simulations of the inspiratory phase and expiratory phase were performed with patient-specific boundary conditions for pre- and post-intervention cases to investigate the effect of stent placement on flow characteristic and possible improvements. Results of post-stent condition show reduced pressure, velocity magnitude and wall shear stress during expiration. The variation in wall shear stress, velocity magnitude and pressure drop is negligible during inspiration. Although Spirometry tests do not show significant improvements, computational fluid dynamics results show significant improvements in pre- and post-treatment results, suggesting improvement in breathing condition. Copyright © 2017 Elsevier Ltd. All rights reserved.
The brain dynamics of linguistic computation.
Murphy, Elliot
2015-01-01
Neural oscillations at distinct frequencies are increasingly being related to a number of basic and higher cognitive faculties. Oscillations enable the construction of coherently organized neuronal assemblies through establishing transitory temporal correlations. By exploring the elementary operations of the language faculty-labeling, concatenation, cyclic transfer-alongside neural dynamics, a new model of linguistic computation is proposed. It is argued that the universality of language, and the true biological source of Universal Grammar, is not to be found purely in the genome as has long been suggested, but more specifically within the extraordinarily preserved nature of mammalian brain rhythms employed in the computation of linguistic structures. Computational-representational theories are used as a guide in investigating the neurobiological foundations of the human "cognome"-the set of computations performed by the nervous system-and new directions are suggested for how the dynamics of the brain (the "dynome") operate and execute linguistic operations. The extent to which brain rhythms are the suitable neuronal processes which can capture the computational properties of the human language faculty is considered against a backdrop of existing cartographic research into the localization of linguistic interpretation. Particular focus is placed on labeling, the operation elsewhere argued to be species-specific. A Basic Label model of the human cognome-dynome is proposed, leading to clear, causally-addressable empirical predictions, to be investigated by a suggested research program, Dynamic Cognomics. In addition, a distinction between minimal and maximal degrees of explanation is introduced to differentiate between the depth of analysis provided by cartographic, rhythmic, neurochemical, and other approaches to computation.
Magnetic polyoxometalates: from molecular magnetism to molecular spintronics and quantum computing.
Clemente-Juan, Juan M; Coronado, Eugenio; Gaita-Ariño, Alejandro
2012-11-21
In this review we discuss the relevance of polyoxometalate (POM) chemistry to provide model objects in molecular magnetism. We present several potential applications in nanomagnetism, in particular, in molecular spintronics and quantum computing.
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)
Accelerated molecular dynamics simulations of protein folding.
Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew
2015-07-30
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.
The use of computers for instruction in fluid dynamics
Watson, Val
1987-01-01
Applications for computers which improve instruction in fluid dynamics are examined. Computers can be used to illustrate three-dimensional flow fields and simple fluid dynamics mechanisms, to solve fluid dynamics problems, and for electronic sketching. The usefulness of computer applications is limited by computer speed, memory, and software and the clarity and field of view of the projected display. Proposed advances in personal computers which will address these limitations are discussed. Long range applications for computers in education are considered.
Molecular dynamics simulations of collision-induced absorption: Implementation in LAMMPS
Fakhardji, W.; Gustafsson, M.
2017-02-01
We pursue simulations of collision-induced absorption in a mixture of argon and xenon gas at room temperature by means of classical molecular dynamics. The established theoretical approach (Hartmann et al. 2011 J. Chem. Phys. 134 094316) is implemented with the molecular dynamics package LAMMPS. The bound state features in the absorption spectrum are well reproduced with the molecular dynamics simulation in comparison with a laboratory measurement. The magnitude of the computed absorption, however, is underestimated in a large part of the spectrum. We suggest some aspects of the simulation that could be improved.
Thermal Transport in Carbon Nanotubes using Molecular Dynamics
Moore, Andrew; Khatun, Mahfuza
2011-10-01
We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.
Optimal dynamic remapping of data parallel computations
Nicol, David M.; Reynolds, Paul F., Jr.
1990-01-01
A large class of data parallel computations is characterized by a sequence of phases, with phase changes occurring unpredictably. Dynamic remapping of the workload to processors may be required to maintain good performance. The problem considered, for which the utility of remapping and the future behavior of the workload are uncertain, arises when phases exhibit stable execution requirements during a given phase, but requirements change radically between phases. For these situations, a workload assignment generated for one phase may hinder performance during the next phase. This problem is treated formally for a probabilistic model of computation with at most two phases. The authors address the fundamental problem of balancing the expected remapping performance gain against the delay cost, and they derive the optimal remapping decision policy. The promise of the approach is shown by application to multiprocessor implementations of an adaptive gridding fluid dynamics program and to a battlefield simulation program.
International Nuclear Information System (INIS)
Bresme, F.; Armstrong, J.
2014-01-01
We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation
The emerging role of cloud computing in molecular modelling.
Ebejer, Jean-Paul; Fulle, Simone; Morris, Garrett M; Finn, Paul W
2013-07-01
There is a growing recognition of the importance of cloud computing for large-scale and data-intensive applications. The distinguishing features of cloud computing and their relationship to other distributed computing paradigms are described, as are the strengths and weaknesses of the approach. We review the use made to date of cloud computing for molecular modelling projects and the availability of front ends for molecular modelling applications. Although the use of cloud computing technologies for molecular modelling is still in its infancy, we demonstrate its potential by presenting several case studies. Rapid growth can be expected as more applications become available and costs continue to fall; cloud computing can make a major contribution not just in terms of the availability of on-demand computing power, but could also spur innovation in the development of novel approaches that utilize that capacity in more effective ways. Copyright © 2013 Elsevier Inc. All rights reserved.
The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations
Boršnik, Urban; Miller, Benjamin T.; Brooks, Bernard R.; Janežič, Dušanka
2011-01-01
Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. PMID:21793007
Deformation mechanisms in nanotwinned copper by molecular dynamics simulation
International Nuclear Information System (INIS)
Zhao, Xing; Lu, Cheng; Tieu, Anh Kiet; Pei, Linqing; Zhang, Liang; Su, Lihong; Zhan, Lihua
2017-01-01
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.
A computational model for dynamic vision
Moezzi, Saied; Weymouth, Terry E.
1990-01-01
This paper describes a novel computational model for dynamic vision which promises to be both powerful and robust. Furthermore the paradigm is ideal for an active vision system where camera vergence changes dynamically. Its basis is the retinotopically indexed object-centered encoding of the early visual information. Specifically, the relative distances of objects to a set of referents is encoded in image registered maps. To illustrate the efficacy of the method, it is applied to the problem of dynamic stereo vision. Integration of depth information over multiple frames obtained by a moving robot generally requires precise information about the relative camera position from frame to frame. Usually, this information can only be approximated. The method facilitates the integration of depth information without direct use or knowledge of camera motion.
First principles centroid molecular dynamics simulation of high pressure ices
Ikeda, Takashi
2018-03-01
The nuclear quantum effects (NQEs) on the structural, elastic, electronic, and vibrational properties of high pressure ices (HPIs) VIII, VII, and X at 270 K were investigated via first principles centroid molecular dynamics (CMD). Our simulations clearly show that even at relatively high temperature of 270 K, the NQEs play a definite role in the pressure-induced proton order (ice VIII)-disorder (ice VII) transition occurring at ˜30 GPa in our H2O ice and the subsequent transition to the symmetric phase ice X suggested to occur at ˜80 GPa. The internal pressure computed at constant NVT conditions shows that the NQEs manifest themselves in the equation of state of HPIs. Our employed approach based on first principles CMD for computing vibrational spectra is proved to be able to reproduce well the overall features of the measured infrared and Raman spectra.
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...... of air. Hence, nanobubles have been observed and proposed as the origin of long range ``hydrophobic'' forces19-30 even for hydrophilic silica-water interfaces unusual phenomena related to nanobubbles have been observed.31-33 In this work we study the role of air on the wetting of amorphous silica...
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
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......Wetting is essential and ubiquitous in a variety of natural and technological processes. Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems...... 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...
Solving graph problems with dynamic computation structures
Babb, Jonathan W.; Frank, Matthew; Agarwal, Anant
1996-10-01
We introduce dynamic computation structures (DCS), a compilation technique to produce dynamic code for reconfigurable computing. DCS specializes directed graph instances into user-level hardware for reconfigurable architectures. Several problems such as shortest path and transitive closure exhibit the general properties of closed semirings, an algebraic structure for solving directed paths. Motivating our application domain choice of closed semiring problems is the fact that logic emulation software already maps a special case of directed graphs, namely logic netlists, onto arrays of field programmable gate arrays (FPGA). A certain type of logic emulation software called virtual wires further allows an FPGA array to be viewed as a machine-independent computing fabric. Thus, a virtual wires compiler, coupled with front-end commercial behavioral logic synthesis software, enables automatic behavioral compilation into a multi-FPGA computing fabric. We have implemented a DCS front-end compiler to parallelize the entire inner loop of the classic Bellman-Ford algorithm into synthesizable behavioral verilog. Leveraging virtual wire compilation and behavioral synthesis, we have automatically generated designs of 14 to 261 FPGAs from a single graph instance. We achieve speedups proportional to the number of graph edges - - from 10X to almost 400X versus a 125 SPECint SparcStation 10.
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.
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
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
Computer studies of multiple-quantum spin dynamics
International Nuclear Information System (INIS)
Murdoch, J.B.
1982-11-01
The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment
Computer studies of multiple-quantum spin dynamics
Energy Technology Data Exchange (ETDEWEB)
Murdoch, J.B.
1982-11-01
The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.
Molecular dynamics simulations of Pd-Ni transition metal alloys
International Nuclear Information System (INIS)
Kart, S. O.; Kart, H. H.; Uludogan, M.; Tomak, M.; Cagin, T.
2002-01-01
Molecular Dynamics simulations are performed to study bulk properties of fcc metals and metal alloys by using the quantum Sutton-Chen many-body potentials within the context of the tight-binding approach. The Molecular Dynamics algorithms we used in the simulations of Pd-Ni alloys are based on an extended Hamiltonian formalism arising from the works of Andersen (1980), Parinello and Rahman (1980), Nose (1984), Hoover (1985) and Cagin (1988). In these simulations, the effect of temperature and concentration on the solid and liquid properties are studied. Elastic constants and phonon dispersion relation are the solid properties we simulated in this work. Dynamic and static properties of liquid Pd-Ni are also computed by examining the behavior of density, enthalpy, pair distribution function and structure factor. The melting temperatures of Pd-Ni alloys are investigated. The diffusion coefficients are calculated from the mean square displacement using Einstein relation and from velocity auto-correlation function using Green-Kubo relations. The simulation results are in good agreement with the experiments
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 dynamics of ultradian glucocorticoid receptor action.
Conway-Campbell, Becky L; Pooley, John R; Hager, Gordon L; Lightman, Stafford L
2012-01-30
In recent years it has become evident that glucocorticoid receptor (GR) action in the nucleus is highly dynamic, characterized by a rapid exchange at the chromatin template. This stochastic mode of GR action couples perfectly with a deterministic pulsatile availability of endogenous ligand in vivo. The endogenous glucocorticoid hormone (cortisol in man and corticosterone in rodent) is secreted from the adrenal gland with an ultradian rhythm made up of pulses at approximately hourly intervals. These two components - the rapidly fluctuating ligand and the rapidly exchanging receptor - appear to have evolved to establish and maintain a system that is exquisitely responsive to the physiological demands of the organism. In this review, we discuss recent and innovative work that questions the idea of steady state, static hormone receptor responses, and replaces them with new concepts of stochastic mechanisms and oscillatory activity essential for optimal function in molecular and cellular systems. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.
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.
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.
Dynamical Models for Computer Viruses Propagation
Directory of Open Access Journals (Sweden)
José R. C. Piqueira
2008-01-01
Full Text Available Nowadays, digital computer systems and networks are the main engineering tools, being used in planning, design, operation, and control of all sizes of building, transportation, machinery, business, and life maintaining devices. Consequently, computer viruses became one of the most important sources of uncertainty, contributing to decrease the reliability of vital activities. A lot of antivirus programs have been developed, but they are limited to detecting and removing infections, based on previous knowledge of the virus code. In spite of having good adaptation capability, these programs work just as vaccines against diseases and are not able to prevent new infections based on the network state. Here, a trial on modeling computer viruses propagation dynamics relates it to other notable events occurring in the network permitting to establish preventive policies in the network management. Data from three different viruses are collected in the Internet and two different identification techniques, autoregressive and Fourier analyses, are applied showing that it is possible to forecast the dynamics of a new virus propagation by using the data collected from other viruses that formerly infected the network.
RPMDRATE: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu. V.; Allen, J. W.; Green, W. H.
2013-03-01
We present RPMDRATE, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH4, OH+CH4 and H+C2H6 reactions. Catalogue identifier: AENW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 94512 No. of bytes in distributed program, including test data, etc.: 1395674 Distribution format: tar.gz Programming language: Fortran 90/95, Python (version 2.6.x or later, including any version of Python 3, is recommended). Computer: Not computer specific. Operating system: Any for which Python, Fortran 90/95 compiler and the required external routines are available. Has the code been vectorized or parallelized?: The program can efficiently utilize 4096+ processors, depending on problem and available computer. At low temperatures, 110 processors are reasonable for a typical umbrella integration run with an analytic potential energy function and gradients on the latest x86-64 machines.
Dynamic X-ray computed tomography
International Nuclear Information System (INIS)
Grangeat, P.
2003-01-01
Paper Dynamic computed tomography (CT) imaging aims at reconstructing image sequences where the dynamic nature of the living human body is of primary interest. Main concerned applications are image-guided interventional procedures, functional studies and cardiac imaging. The introduction of ultra-fast rotating gantries along with multi-row detectors and in near future area detectors allows a huge progress toward the imaging of moving organs with low-contrast resolution. This paper gives an overview of the different concepts used in dynamic CT. A new reconstruction algorithm based on a voxel-specific dynamic evolution compensation is also presented. It provides four-dimensional image sequences with accurate spatio-temporal information, where each frame is reconstructed using a long-scan acquisition mode on several half-turns. In the same time, this technique permits to reduce the dose delivered per rotation while keeping the same signal to noise ratio for every frame using an adaptive motion-compensated temporal averaging. Results are illustrated on simulated data. (authors)
Computational fluid dynamics in brain aneurysms
Sforza, Daniel M.; Putman, Christopher M.; Cebral, Juan R.
2013-01-01
SUMMARY Because of its ability to deal with any geometry, image-based computational fluid dynamics (CFD) has been progressively used to investigate the role of hemodynamics in the underlying mechanisms governing the natural history of cerebral aneurysms. Despite great progress in methodological developments and many studies using patient-specific data, there are still significant controversies about the precise governing processes and divergent conclusions from apparently contradictory results. Sorting out these issues requires a global vision of the state of the art and a unified approach to solving this important scientific problem. Towards this end, this paper reviews the contributions made using patient-specific CFD models to further the understanding of these mechanisms, and highlights the great potential of patient-specific computational models for clinical use in the assessment of aneurysm rupture risk and patient management. PMID:25364852
Mos, B.; Verkerk, P.; Pouget, S.; Van Zon, A.; Bel, G.J.; De Leeuw, S.W.; Eisenbach, C.D.
2000-01-01
We determined the self part of the intermediate scattering function in liquid polyethyleneoxide (PEO) and PEO–alkali iodide complexes by means of neutron spin-echo spectroscopy and molecular dynamics (MD) computer simulations. We present the first accurate quantitative results on the segmental
Observing Distributed Computation. A Dynamic-Epistemic Approach
DEFF Research Database (Denmark)
Mardare, Radu Iulian
2007-01-01
R. Mardare. Observing Distributed Computation. A Dynamic-Epistemic Approach. In Proc. of the second Conference on Algebra and Coalgebra in Computer Science (CALCO2007), Lecture Notes in Computer Science 4624:379-393, Springer, 2007......R. Mardare. Observing Distributed Computation. A Dynamic-Epistemic Approach. In Proc. of the second Conference on Algebra and Coalgebra in Computer Science (CALCO2007), Lecture Notes in Computer Science 4624:379-393, Springer, 2007...
Computational Fluid Dynamics Technology for Hypersonic Applications
Gnoffo, Peter A.
2003-01-01
Several current challenges in computational fluid dynamics and aerothermodynamics for hypersonic vehicle applications are discussed. Example simulations are presented from code validation and code benchmarking efforts to illustrate capabilities and limitations. Opportunities to advance the state-of-art in algorithms, grid generation and adaptation, and code validation are identified. Highlights of diverse efforts to address these challenges are then discussed. One such effort to re-engineer and synthesize the existing analysis capability in LAURA, VULCAN, and FUN3D will provide context for these discussions. The critical (and evolving) role of agile software engineering practice in the capability enhancement process is also noted.
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
Computational methods in molecular imaging technologies
Gunjan, Vinit Kumar; Venkatesh, C; Amarnath, M
2017-01-01
This book highlights the experimental investigations that have been carried out on magnetic resonance imaging and computed tomography (MRI & CT) images using state-of-the-art Computational Image processing techniques, and tabulates the statistical values wherever necessary. In a very simple and straightforward way, it explains how image processing methods are used to improve the quality of medical images and facilitate analysis. It offers a valuable resource for researchers, engineers, medical doctors and bioinformatics experts alike.
Zonal methods and computational fluid dynamics
International Nuclear Information System (INIS)
Atta, E.H.
1985-01-01
Recent advances in developing numerical algorithms for solving fluid flow problems, and the continuing improvement in the speed and storage of large scale computers have made it feasible to compute the flow field about complex and realistic configurations. Current solution methods involve the use of a hierarchy of mathematical models ranging from the linearized potential equation to the Navier Stokes equations. Because of the increasing complexity of both the geometries and flowfields encountered in practical fluid flow simulation, there is a growing emphasis in computational fluid dynamics on the use of zonal methods. A zonal method is one that subdivides the total flow region into interconnected smaller regions or zones. The flow solutions in these zones are then patched together to establish the global flow field solution. Zonal methods are primarily used either to limit the complexity of the governing flow equations to a localized region or to alleviate the grid generation problems about geometrically complex and multicomponent configurations. This paper surveys the application of zonal methods for solving the flow field about two and three-dimensional configurations. Various factors affecting their accuracy and ease of implementation are also discussed. From the presented review it is concluded that zonal methods promise to be very effective for computing complex flowfields and configurations. Currently there are increasing efforts to improve their efficiency, versatility, and accuracy
Dynamics of microtubules: highlights of recent computational and experimental investigations
Barsegov, Valeri; Ross, Jennifer L.; Dima, Ruxandra I.
2017-11-01
Microtubules are found in most eukaryotic cells, with homologs in eubacteria and archea, and they have functional roles in mitosis, cell motility, intracellular transport, and the maintenance of cell shape. Numerous efforts have been expended over the last two decades to characterize the interactions between microtubules and the wide variety of microtubule associated proteins that control their dynamic behavior in cells resulting in microtubules being assembled and disassembled where and when they are required by the cell. We present the main findings regarding microtubule polymerization and depolymerization and review recent work about the molecular motors that modulate microtubule dynamics by inducing either microtubule depolymerization or severing. We also discuss the main experimental and computational approaches used to quantify the thermodynamics and mechanics of microtubule filaments.
International Nuclear Information System (INIS)
Ji, Pengfei; Zhang, Yuwen; Yang, Mo
2013-01-01
The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective
Direct modeling for computational fluid dynamics
Xu, Kun
2015-06-01
All fluid dynamic equations are valid under their modeling scales, such as the particle mean free path and mean collision time scale of the Boltzmann equation and the hydrodynamic scale of the Navier-Stokes (NS) equations. The current computational fluid dynamics (CFD) focuses on the numerical solution of partial differential equations (PDEs), and its aim is to get the accurate solution of these governing equations. Under such a CFD practice, it is hard to develop a unified scheme that covers flow physics from kinetic to hydrodynamic scales continuously because there is no such governing equation which could make a smooth transition from the Boltzmann to the NS modeling. The study of fluid dynamics needs to go beyond the traditional numerical partial differential equations. The emerging engineering applications, such as air-vehicle design for near-space flight and flow and heat transfer in micro-devices, do require further expansion of the concept of gas dynamics to a larger domain of physical reality, rather than the traditional distinguishable governing equations. At the current stage, the non-equilibrium flow physics has not yet been well explored or clearly understood due to the lack of appropriate tools. Unfortunately, under the current numerical PDE approach, it is hard to develop such a meaningful tool due to the absence of valid PDEs. In order to construct multiscale and multiphysics simulation methods similar to the modeling process of constructing the Boltzmann or the NS governing equations, the development of a numerical algorithm should be based on the first principle of physical modeling. In this paper, instead of following the traditional numerical PDE path, we introduce direct modeling as a principle for CFD algorithm development. Since all computations are conducted in a discretized space with limited cell resolution, the flow physics to be modeled has to be done in the mesh size and time step scales. Here, the CFD is more or less a direct
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.
Utilizing parallel optimization in computational fluid dynamics
Kokkolaras, Michael
1998-12-01
General problems of interest in computational fluid dynamics are investigated by means of optimization. Specifically, in the first part of the dissertation, a method of optimal incremental function approximation is developed for the adaptive solution of differential equations. Various concepts and ideas utilized by numerical techniques employed in computational mechanics and artificial neural networks (e.g. function approximation and error minimization, variational principles and weighted residuals, and adaptive grid optimization) are combined to formulate the proposed method. The basis functions and associated coefficients of a series expansion, representing the solution, are optimally selected by a parallel direct search technique at each step of the algorithm according to appropriate criteria; the solution is built sequentially. In this manner, the proposed method is adaptive in nature, although a grid is neither built nor adapted in the traditional sense using a-posteriori error estimates. Variational principles are utilized for the definition of the objective function to be extremized in the associated optimization problems, ensuring that the problem is well-posed. Complicated data structures and expensive remeshing algorithms and systems solvers are avoided. Computational efficiency is increased by using low-order basis functions and concurrent computing. Numerical results and convergence rates are reported for a range of steady-state problems, including linear and nonlinear differential equations associated with general boundary conditions, and illustrate the potential of the proposed method. Fluid dynamics applications are emphasized. Conclusions are drawn by discussing the method's limitations, advantages, and possible extensions. The second part of the dissertation is concerned with the optimization of the viscous-inviscid-interaction (VII) mechanism in an airfoil flow analysis code. The VII mechanism is based on the concept of a transpiration velocity
Demystifying computer science for molecular ecologists.
Belcaid, Mahdi; Toonen, Robert J
2015-06-01
In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373-389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated. © 2015 John Wiley & Sons Ltd.
Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M
2015-02-14
The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.
The Journal of Computer- Aided Molecular Design: a bibliometric note
Willett, Peter
2012-01-01
Summarizes the articles in, and the citations to, volumes 2-24 of the Journal of Computer- Aided Molecular Design. The citations to the journal come from almost 2000 different sources that span a very wide range of academic subjects, with the most heavily cited articles being descriptions of software systems and of computational methods.
Prediction of purification of biopharmeceuticals with molecular dynamics
Ustach, Vincent; Faller, Roland
Purification of biopharmeceuticals remains the most expensive part of protein-based drug production. In ion exchange chromatography (IEX), prediction of the elution ionic strength of host cell and target proteins has the potential to reduce the parameter space for scale-up of protein production. The complex shape and charge distribution of proteins and pores complicates predictions of the interactions in these systems. All-atom molecular dynamics methods are beyond the scope of computational limits for mass transport regimes. We present a coarse-grained model for proteins for prediction of elution pH and ionic strength. By extending the raspberry model for colloid particles to surface shapes and charge distributions of proteins, we can reproduce the behavior of proteins in IEX. The average charge states of titratatable amino acid residues at relevant pH values are determined by extrapolation from all-atom molecular dynamics at pH 7. The pH specific all-atom electrostatic field is then mapped onto the coarse-grained surface beads of the raspberry particle. The hydrodynamics are reproduced with the lattice-Boltzmann scheme. This combination of methods allows very long simulation times. The model is being validated for known elution procedures by comparing the data with experiments. Defense Threat Reduction Agency (Grant Number HDTRA1-15-1-0054).
Animated molecular dynamics simulations of hydrated Cesium-smectite interlayers
International Nuclear Information System (INIS)
Sutton, Rebecca; Sposito, Garrison
2002-01-01
Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional analytical methods. Cs+ could be seen to jump from one attracting location near a layer charge site to the next, and water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. The extent of this sharing interaction in the interlayer was determined by the smectite charge distribution, but increased with increasing water content. Water molecules also could be seen to interact directly with the mineral surface, entering its ditrigonal cavities to approach attracting charge sites. The frequency and duration of cavity habitation increased with increasing water content and tetrahedral charge, and was inhibited the more perpendicular was the structural hydroxyl orientation relative to the mineral surface. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output
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.
Kinetic distance and kinetic maps from molecular dynamics simulation.
Noé, Frank; Clementi, Cecilia
2015-10-13
Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly interconverting states. Here, we build upon diffusion map theory and define a kinetic distance metric for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here, we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets.
Accelerating molecular dynamics simulations by linear prediction of time series
Brutovsky, B.; Mülders, T.; Kneller, G. R.
2003-04-01
We present a molecular dynamics simulation scheme which allows to speed up molecular dynamics simulations by linear prediction of force time series. The explicit calculation of nonbonding forces is periodically replaced by linear prediction from past values. Applying our method to liquid oxygen consisting of flexible molecules we obtained real speedups between 5.4 and 6.5, compared to conventional molecular dynamics simulations. Here only the bond-stretching forces were calculated at each time step. We demonstrate that essential dynamical quantities, such as the mean-square displacement and the velocity autocorrelation function, are preserved.
Dynamic modeling of oil boom failure using computational fluid dynamics
International Nuclear Information System (INIS)
Goodman, R. H.; Brown, H. M.; An, C. F.; Rowe, R. D.
1997-01-01
Oil retention boom failure mechanisms have been identified and studied using computational fluid dynamics (CFD), a powerful modeling tool combining fluid dynamics and mathematics with high speed computer technology. This study utilized a commercially available CFD package, 'Fluent', to simulate the oil-water flow around a barrier. 'Drainage failure', 'droplet entrainment' and 'critical accumulation' were modeled using this software. Flow characteristics were found to be different for different failure mechanisms. In the drainage failure process, the oil slick was compressed against the barrier until the slick was deep enough for the oil to leak under the barrier. During boom failure due to droplet entrainment, the oil-water interface of the oil slick was wavy and unstable. During boom failure due to critical accumulation, the oil remained a single mass and moved under the barrier readily. The most significant observation, however, was that flow patterns around barriers are modified by the presence of oil. Therefore, towing and wave-conformity tests of booms will not be meaningful unless such tests are conducted with oil present. 15 refs., 11 figs
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.
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.
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.
Acidity constants from DFT-based molecular dynamics simulations
International Nuclear Information System (INIS)
Sulpizi, Marialore; Sprik, Michiel
2010-01-01
In this contribution we review our recently developed method for the calculation of acidity constants from density functional theory based molecular dynamics simulations. The method is based on a half reaction scheme in which protons are formally transferred from solution to the gas phase. The corresponding deprotonation free energies are computed from the vertical energy gaps for insertion or removal of protons. Combined to full proton transfer reactions, the deprotonation energies can be used to estimate relative acidity constants and also the Broensted pK a when the deprotonation free energy of a hydronium ion is used as a reference. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pK a values (20 units). The thermochemical corrections for the biasing potentials assisting and directing the insertion are discussed in some detail.
Verification and validation in computational fluid dynamics
Oberkampf, William L.; Trucano, Timothy G.
2002-04-01
Verification and validation (V&V) are the primary means to assess accuracy and reliability in computational simulations. This paper presents an extensive review of the literature in V&V in computational fluid dynamics (CFD), discusses methods and procedures for assessing V&V, and develops a number of extensions to existing ideas. The review of the development of V&V terminology and methodology points out the contributions from members of the operations research, statistics, and CFD communities. Fundamental issues in V&V are addressed, such as code verification versus solution verification, model validation versus solution validation, the distinction between error and uncertainty, conceptual sources of error and uncertainty, and the relationship between validation and prediction. The fundamental strategy of verification is the identification and quantification of errors in the computational model and its solution. In verification activities, the accuracy of a computational solution is primarily measured relative to two types of highly accurate solutions: analytical solutions and highly accurate numerical solutions. Methods for determining the accuracy of numerical solutions are presented and the importance of software testing during verification activities is emphasized. The fundamental strategy of validation is to assess how accurately the computational results compare with the experimental data, with quantified error and uncertainty estimates for both. This strategy employs a hierarchical methodology that segregates and simplifies the physical and coupling phenomena involved in the complex engineering system of interest. A hypersonic cruise missile is used as an example of how this hierarchical structure is formulated. The discussion of validation assessment also encompasses a number of other important topics. A set of guidelines is proposed for designing and conducting validation experiments, supported by an explanation of how validation experiments are different
Sader, Safaa; Wu, Chun
2017-03-01
Amsacrine is an effective topoisomerase II enzyme inhibitor in acute lymphatic leukemia. Previous experimental studies have successfully identified two important mutations (R487K and E571K) conferring 100 and 25 fold resistance to Amsacrine respectively. Although the reduction of the cleavage ligand-DNA-protein ternary complex has been well thought as the major cause of drug resistance, the detailed energetic, structural and dynamic mechanisms remain to be elusive. In this study, we constructed human topoisomerase II alpha (hTop2α) homology model docked with Amsacrine based on crystal structure of human Top2β in complex with etoposide. This wild type complex was used to build the ternary complex with R487K and E571K mutants. Three 500ns molecular dynamics simulations were performed on complex systems of wild type and two mutants. The detailed energetic, structural and dynamic analysis were performed on the simulation data. Our binding data indicated a significant impairment of Amsacrine binding energy in the two mutants compared with the wild type. The order of weakening (R487K>E571K) was in agreement with the order of experimental drug resistance fold (R489K>E571K). Our binding energy decomposition further indicated that weakening of the ligand-protein interaction rather than the ligand-DNA interaction was the major contributor of the binding energy difference between R487K and E571K. In addition, key residues contributing to the binding energy (ΔG) or the decrease of the binding energy (ΔΔG) were identified through the energy decomposition analysis. The change in ligand binding pose, dynamics of protein, DNA and ligand upon the mutations were thoroughly analyzed and discussed. Deciphering the molecular basis of drug resistance is crucial to overcome drug resistance using rational drug design. Copyright © 2017 Elsevier Inc. All rights reserved.
Molecular Science Computing Facility Scientific Challenges: Linking Across Scales
Energy Technology Data Exchange (ETDEWEB)
De Jong, Wibe A.; Windus, Theresa L.
2005-07-01
The purpose of this document is to define the evolving science drivers for performing environmental molecular research at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and to provide guidance associated with the next-generation high-performance computing center that must be developed at EMSL's Molecular Science Computing Facility (MSCF) in order to address this critical research. The MSCF is the pre-eminent computing facility?supported by the U.S. Department of Energy's (DOE's) Office of Biological and Environmental Research (BER)?tailored to provide the fastest time-to-solution for current computational challenges in chemistry and biology, as well as providing the means for broad research in the molecular and environmental sciences. The MSCF provides integral resources and expertise to emerging EMSL Scientific Grand Challenges and Collaborative Access Teams that are designed to leverage the multiple integrated research capabilities of EMSL, thereby creating a synergy between computation and experiment to address environmental molecular science challenges critical to DOE and the nation.
Artificial Intelligence In Computational Fluid Dynamics
Vogel, Alison Andrews
1991-01-01
Paper compares four first-generation artificial-intelligence (Al) software systems for computational fluid dynamics. Includes: Expert Cooling Fan Design System (EXFAN), PAN AIR Knowledge System (PAKS), grid-adaptation program MITOSIS, and Expert Zonal Grid Generation (EZGrid). Focuses on knowledge-based ("expert") software systems. Analyzes intended tasks, kinds of knowledge possessed, magnitude of effort required to codify knowledge, how quickly constructed, performances, and return on investment. On basis of comparison, concludes Al most successful when applied to well-formulated problems solved by classifying or selecting preenumerated solutions. In contrast, application of Al to poorly understood or poorly formulated problems generally results in long development time and large investment of effort, with no guarantee of success.
Lectures series in computational fluid dynamics
International Nuclear Information System (INIS)
Thompson, K.W.
1987-08-01
The lecture notes cover the basic principles of computational fluid dynamics (CFD). They are oriented more toward practical applications than theory, and are intended to serve as a unified source for basic material in the CFD field as well as an introduction to more specialized topics in artificial viscosity and boundary conditions. Each chapter in the text is associated with a videotaped lecture. The basic properties of conservation laws, wave equations, and shock waves are described. The duality of the conservation law and wave representations is investigated, and shock waves are examined in some detail. Finite difference techniques are introduced for the solution of wave equations and conservation laws. Stability analysis for finite difference approximations are presented. A consistent description of artificial viscosity methods are provided. Finally, the problem of nonreflecting boundary conditions are treated
Domain decomposition algorithms and computational fluid dynamics
International Nuclear Information System (INIS)
Chan, T.F.
1988-01-01
In the past several years, domain decomposition has been a very popular topic, partly because of the potential of parallelization. Although numerous theories and algorithms have been developed for model elliptic problems, they are only recently starting to be tested on realistic applications. This paper investigates the application of some of these methods to two model problems in computational fluid dynamics: two-dimensional convection-diffusion problems and the incompressible driven cavity flow problem. The authors approach is the construction and analysis of efficient preconditioners for the interface operator to be used in the iterative solution of the interface solution. For the convection-diffusion problems, they discuss the effect of the convection term and its discretization on the performance of some of the preconditioners. For the driven cavity problem, they discuss the effectiveness of a class of boundary probe preconditioners
Molecular dynamics simulation of nanomaterials using an artificial neural net
Benedict, Mark; Maguire, John F.
2004-11-01
We report a method of conducting molecular dynamics (MD) simulations that uses an artificial neural net (ANN) to significantly increase computational speed. The technique enables dynamical simulation of hard objects with essentially arbitrarily complex geometry and is well suited to the simulation of granular matter over a wide range of densities. In hard systems, binary collisions are well defined and the ANN approach enables an efficient algorithm to determine the time to next collision with high accuracy. The method has been used to enable an MD study of an ensemble of 1800 hard, smooth, impenetrable equilateral triangles in a two-dimensional periodic space. At high packing fraction (0.6translational order but in which there is nearly perfect long-range orientational order. As the packing fraction decreases, the LCP undergoes a transition to a fluid state in which the long-range orientational correlation vanishes but short-range order is retained. Long-lived clusters, notably hexamers, are clearly apparent in the liquid phase and appear to be stabilized by a sort of internal “orientational” osmotic pressure. Insofar as can be inferred from our machine calculations, the transition between the LCP and the liquid occurs around ρ˜0.57 and appears to be second order. At low density, the hard-triangle system undergoes “chattering” collisions in which pairs of triangles collide and become associated, undergoing multiple collisions with each other before colliding with a third particle. The radial distribution function obtained from both molecular dynamics and Monte Carlo calculations shows a weak peak at low packing fraction.
Combining optimal control theory and molecular dynamics for protein folding.
Arkun, Yaman; Gur, Mert
2012-01-01
A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.
Combining optimal control theory and molecular dynamics for protein folding.
Directory of Open Access Journals (Sweden)
Yaman Arkun
Full Text Available A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD. In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.
Computational Fluid Dynamics Modeling of Bacillus anthracis ...
Journal Article Three-dimensional computational fluid dynamics and Lagrangian particle deposition models were developed to compare the deposition of aerosolized Bacillus anthracis spores in the respiratory airways of a human with that of the rabbit, a species commonly used in the study of anthrax disease. The respiratory airway geometries for each species were derived from computed tomography (CT) or µCT images. Both models encompassed airways that extended from the external nose to the lung with a total of 272 outlets in the human model and 2878 outlets in the rabbit model. All simulations of spore deposition were conducted under transient, inhalation-exhalation breathing conditions using average species-specific minute volumes. Four different exposure scenarios were modeled in the rabbit based upon experimental inhalation studies. For comparison, human simulations were conducted at the highest exposure concentration used during the rabbit experimental exposures. Results demonstrated that regional spore deposition patterns were sensitive to airway geometry and ventilation profiles. Despite the complex airway geometries in the rabbit nose, higher spore deposition efficiency was predicted in the upper conducting airways of the human at the same air concentration of anthrax spores. This greater deposition of spores in the upper airways in the human resulted in lower penetration and deposition in the tracheobronchial airways and the deep lung than that predict
Computational Fluid Dynamics - Applications in Manufacturing Processes
Beninati, Maria Laura; Kathol, Austin; Ziemian, Constance
2012-11-01
A new Computational Fluid Dynamics (CFD) exercise has been developed for the undergraduate introductory fluid mechanics course at Bucknell University. The goal is to develop a computational exercise that students complete which links the manufacturing processes course and the concurrent fluid mechanics course in a way that reinforces the concepts in both. In general, CFD is used as a tool to increase student understanding of the fundamentals in a virtual world. A ``learning factory,'' which is currently in development at Bucknell seeks to use the laboratory as a means to link courses that previously seemed to have little correlation at first glance. A large part of the manufacturing processes course is a project using an injection molding machine. The flow of pressurized molten polyurethane into the mold cavity can also be an example of fluid motion (a jet of liquid hitting a plate) that is applied in manufacturing. The students will run a CFD process that captures this flow using their virtual mold created with a graphics package, such as SolidWorks. The laboratory structure is currently being implemented and analyzed as a part of the ``learning factory''. Lastly, a survey taken before and after the CFD exercise demonstrate a better understanding of both the CFD and manufacturing process.
Large-scale molecular dynamics simulations of self-assembling systems.
Klein, Michael L; Shinoda, Wataru
2008-08-08
Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.
Molecular-dynamics simulation of displacement cascades in Cu: analysis of replacement sequences
International Nuclear Information System (INIS)
King, W.E.; Benedek, R.
1981-01-01
Molecular-dynamics computer simulations of displacement cascades in copper have been performed for recoil energies up to 450 eV. Statistical analyses of the atomic replacements are presented. Linear replacement sequence lengths are extremely short on the average. The effect of the cooling phase of the cascade is discussed
Molecular dynamics simulations of bio-nano systems with MBN Explorer
DEFF Research Database (Denmark)
Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.
2013-01-01
We present results of molecular dynamics simulations performed using a multi-purpose computer code MBN Explorer. In particular we consider the process of laser induced acoustic desorption of lysine amino acids from the surface of a nickel foil. We analyze the rate of lysine desorption from the ni...... packages, making MBN Explorer a possible alternative to the available codes....
Molecular-dynamics of water transport through membranes - water from solvent to solute
BERENDSEN, HJC; MARRINK, SJ
1993-01-01
An application of Molecular Dynamics computer simulation (MD) to the process of transport of water through a lipid bilayer membrane is described. The permeation process is far too slow to be modeled by straightforward MD. In stead the inverse of the permeability coefficient is expressed as an
NATO Advanced Study Institute on Methods in Computational Molecular Physics
Diercksen, Geerd
1992-01-01
This volume records the lectures given at a NATO Advanced Study Institute on Methods in Computational Molecular Physics held in Bad Windsheim, Germany, from 22nd July until 2nd. August, 1991. This NATO Advanced Study Institute sought to bridge the quite considerable gap which exist between the presentation of molecular electronic structure theory found in contemporary monographs such as, for example, McWeeny's Methods 0/ Molecular Quantum Mechanics (Academic Press, London, 1989) or Wilson's Electron correlation in moleeules (Clarendon Press, Oxford, 1984) and the realization of the sophisticated computational algorithms required for their practical application. It sought to underline the relation between the electronic structure problem and the study of nuc1ear motion. Software for performing molecular electronic structure calculations is now being applied in an increasingly wide range of fields in both the academic and the commercial sectors. Numerous applications are reported in areas as diverse as catalysi...
Self-diffusion in monodisperse three-dimensional magnetic fluids by molecular dynamics simulations
International Nuclear Information System (INIS)
Dobroserdova, A.B.; Kantorovich, S.S.
2017-01-01
In the present work we study the self-diffusion behaviour in the three-dimensional monodisperse magnetic fluids using the Molecular Dynamics Simulation and Density Functional Theory. The peculiarity of computer simulation is to study two different systems: dipolar and soft sphere ones. In the theoretical method, it is important to choose the approximation for the main structures, which are chains. We compare the theoretical results and the computer simulation data for the self-diffusion coefficient as a function of the particle volume fraction and magnetic dipole-dipole interaction parameter and find the qualitative and quantitative agreement to be good. - Highlights: • The paper deals with the study of the self-diffusion in monodisperse three-dimensional magnetic fluids. • The theoretical approach contains the free energy density functional minimization. • Computer simulations are performed by the molecular dynamics method. • We have a good qualitative and quantitative agreement between the theoretical results and computer simulation data.
Self-diffusion in monodisperse three-dimensional magnetic fluids by molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Dobroserdova, A.B. [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); Kantorovich, S.S., E-mail: alla.dobroserdova@urfu.ru [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); University of Vienna, Sensengasse 8, Vienna (Austria)
2017-06-01
In the present work we study the self-diffusion behaviour in the three-dimensional monodisperse magnetic fluids using the Molecular Dynamics Simulation and Density Functional Theory. The peculiarity of computer simulation is to study two different systems: dipolar and soft sphere ones. In the theoretical method, it is important to choose the approximation for the main structures, which are chains. We compare the theoretical results and the computer simulation data for the self-diffusion coefficient as a function of the particle volume fraction and magnetic dipole-dipole interaction parameter and find the qualitative and quantitative agreement to be good. - Highlights: • The paper deals with the study of the self-diffusion in monodisperse three-dimensional magnetic fluids. • The theoretical approach contains the free energy density functional minimization. • Computer simulations are performed by the molecular dynamics method. • We have a good qualitative and quantitative agreement between the theoretical results and computer simulation data.
Computer aided molecular design with combined molecular modeling and group contribution
DEFF Research Database (Denmark)
Harper, Peter Mathias; Gani, Rafiqul; Kolar, Petr
1999-01-01
Computer-aided molecular design (CAMD) provides a means for determining molecules or mixtures of molecules (CAMMD) having a desirable set of physicochemical properties. The application range of CAMD is restricted due to limitations on the complexity of the generated molecular structures and on th...
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)
In-silico design of computational nucleic acids for molecular information processing.
Ramlan, Effirul Ikhwan; Zauner, Klaus-Peter
2013-05-07
Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing.
Predicting Intersystem Crossing Rates with AIMS-DFT Molecular Dynamics.
Fedorov, Dmitry A; Lykhin, Aleksandr O; Varganov, Sergey A
2018-03-23
Accurate prediction of the intersystem crossing rates is important for many different applications in chemistry, physics, and biology. Recently, we implemented the ab initio multiple spawning (AIMS) molecular dynamics method to describe the intersystem crossing processes, where nonradiative transitions between electronic states with different spin multiplicities are mediated by spin-orbit coupling. Our original implementation of the direct AIMS dynamics used the complete active space self-consistent field (CASSCF) method to describe multiple coupled electronic states on which multidimensional Gaussian wave packets were propagated. In this work, we improve the computational efficiency and versatility of the AIMS dynamics by interfacing it with the density functional theory (DFT). The new AIMS-DFT and the earlier AIMS-CASSCF implementations are used to investigate the effects of electronic structure methods on the predicted intersystem crossing rate constants and the lowest triplet state lifetime in the GeH 2 molecule. We also compare the rates and lifetimes obtained from the AIMS simulations with those predicted by the statistical nonadiabatic transition state theory (NA-TST). In NA-TST, the probabilities of spin transitions are calculated using the Landau-Zener, weak coupling, and Zhu-Nakamura formulas. Convergence of the AIMS rate constants with respect to the simulation time and the number of initial trajectories (Gaussian wave packets) is analyzed. An excellent agreement between AIMS-DFT and AIMS-CASSCF can be explained by cancelation of two effects: higher energy barriers and a stronger spin-orbit coupling in DFT relative to CASSCF. The rate constants obtained with the AIMS-DFT dynamics are about a factor of 2 larger than those predicted by the statistical NA-TST. This is likely due to the importance of the nonlocal interstate transitions missing from the NA-TST description.
Computational Approaches for Probing the Formation of Atmospheric Molecular Clusters
DEFF Research Database (Denmark)
Elm, Jonas
This thesis presents the investigation of atmospheric molecular clusters using computational methods. Previous investigations have focused on solving problems related to atmospheric nucleation, and have not been targeted at the performance of the applied methods. This thesis focuses on assessing...... the performance of computational strategies in order to identify a sturdy methodology, which should be applicable for handling various issues related to atmospheric cluster formation. Density functional theory (DFT) is applied to study individual cluster formation steps. Utilizing large test sets of numerous...
Biomembrane modeling: molecular dynamics simulation of phospholipid monolayers
Energy Technology Data Exchange (ETDEWEB)
Thompson, T.R.
1979-01-01
As a first step toward a computer model of a biomembrane-like bilayer, a dynamic, deterministric model of a phospholipid monolayer has been constructed. The model moves phospholipid-like centers of force according to an integrated law of motion in finite difference form. Forces on each phospholipid analogue are derived from the gradient of the local potential, itself the sum of Coulombic and short-range terms. The Coulombic term is approximated by use of a finite-difference form of Poisson's equation, while the short-range term results from finite-radius, pairwise summation of a Lennard-Jones potential. Boundary potentials are treated in such a way that the model is effectively infinite in extent in the plane of the monolayer. The two-dimensional virial theorem is used to find the surface pressure of the monolayer as a function of molecular area. Pressure-versus-area curves for simulated monolayers are compared to those of real monolayers. Dependence of the simulator's behavior on Lennard-Jones parameters and the specific geometry of the molecular analogue is discussed. Implications for the physical theory of phospholipid monolayers and bilayers are developed.
Enhanced molecular dynamics for simulating porous interphase layers in batteries.
Energy Technology Data Exchange (ETDEWEB)
Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan (Rice University, Houston, TX)
2009-10-01
Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.
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...
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.
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.
Bicanonical ab Initio Molecular Dynamics for Open Systems.
Frenzel, Johannes; Meyer, Bernd; Marx, Dominik
2017-08-08
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.
Multiscale Molecular Dynamics Approach to Energy Transfer in Nanomaterials.
Espinosa-Duran, John M; Sereda, Yuriy V; Abi-Mansour, Andrew; Ortoleva, Peter
2018-02-13
After local transient fluctuations are dissipated, in an energy transfer process, a system evolves to a state where the energy density field varies slowly in time relative to the dynamics of atomic collisions and vibrations. Furthermore, the energy density field remains strongly coupled to the atomic scale processes (collisions and vibrations), and it can serve as the basis of a multiscale theory of energy transfer. Here, a method is introduced to capture the long scale energy density variations as they coevolve with the atomistic state in a way that yields insights into the basic physics and implies an efficient algorithm for energy transfer simulations. The approach is developed based on the N-atom Liouville equation and an interatomic force field and avoids the need for conjectured phenomenological equations for energy transfer and other processes. The theory is demonstrated for sodium chloride and silicon dioxide nanoparticles immersed in a water bath via molecular dynamics simulations of the energy transfer between a nanoparticle and its aqueous host fluid. The energy density field is computed for different sets of symmetric grid densities, and the multiscale theory holds when slowly varying energy densities at the nodes are obtained. Results strongly depend on grid density and nanoparticle constituent material. A nonuniform temperature distribution, larger thermal fluctuations in the nanoparticle than in the bath, and enhancement of fluctuations at the surface, which are expressed due to the atomic nature of the systems, are captured by this method rather than by phenomenological continuum energy transfer models.
Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries.
Sasselli, I R; Moreira, I P; Ulijn, R V; Tuttle, T
2017-08-09
There is significant interest in the use of unmodified self-assembling peptides as building blocks for functional, supramolecular biomaterials. Recently, dynamic peptide libraries (DPLs) have been proposed to select self-assembling materials from dynamically exchanging mixtures of dipeptide inputs in the presence of a nonspecific protease enzyme, where peptide sequences are selected and amplified based on their self-assembling tendencies. It was shown that the results of the DPL of mixed sequences (e.g. starting from a mixture of dileucine, L 2 , and diphenylalanine, F 2 ) did not give the same outcome as the separate L 2 and F 2 libraries (which give rise to the formation of F 6 and L 6 ), implying that interactions between these sequences could disrupt the self-assembly. In this study, coarse grained molecular dynamics (CG-MD) simulations are used to understand the DPL results for F 2 , L 2 and mixed libraries. CG-MD simulations demonstrate that interactions between precursors can cause the low formation yield of hexapeptides in the mixtures of dipeptides and show that this ability to disrupt is influenced by the concentration of the different species in the DPL. The disrupting self-assembly effect between the species in the DPL is an important effect to take into account in dynamic combinatorial chemistry as it affects the possible discovery of new materials. This work shows that combined computational and experimental screening can be used complementarily and in combination providing a powerful means to discover new supramolecular peptide nanostructures.
International Nuclear Information System (INIS)
Kubo, Momoji; Ando, Minako; Sakahara, Satoshi; Jung, Changho; Seki, Kotaro; Kusagaya, Tomonori; Endou, Akira; Takami, Seiichi; Imamura, Akira; Miyamoto, Akira
2004-01-01
Recently, we have proposed a new concept called 'combinatorial computational chemistry' to realize a theoretical, high-throughput screening of catalysts and materials. We have already applied our combinatorial, computational-chemistry approach, mainly based on static first-principles calculations, to various catalysts and materials systems and its applicability to the catalysts and materials design was strongly confirmed. In order to realize more effective and efficient combinatorial, computational-chemistry screening, a high-speed, chemical-reaction-dynamics simulator based on quantum-chemical, molecular-dynamics method is essential. However, to the best of our knowledge, there is no chemical-reaction-dynamics simulator, which has an enough high-speed ability to perform a high-throughput screening. In the present study, we have succeeded in the development of a chemical-reaction-dynamics simulator based on our original, tight-binding, quantum-chemical, molecular-dynamics method, which is more than 5000 times faster than the regular first-principles, molecular-dynamics method. Moreover, its applicability and effectiveness to the atomistic clarification of the methanol-synthesis dynamics at reaction temperature were demonstrated
Close-packed (polytypic) structures in molecular-dynamics simulations
International Nuclear Information System (INIS)
Moody, M.; Ray, J.R.; Rahman, A.
1987-01-01
Molecular-dynamics (MD) computer-simulation studies are used to study close-packed structures found in solid-phase atomic systems interacting via a Morse potential (parametrized to model Ni). A graphical display of particle positions [a (112-bar0) projection] within the parallelepiped forming the MD cell is illustrated. Such a graphic projection allows accurate, complete, and readily visual recognition of the stacking order of close-packed planes and is a much more effective way of identifying polytypes than a study of the pair-distribution function for the structure. These illustrations demonstrate the polytypic nature of previously and newly recognized MD close-packed structures. When assuming compatibility with periodic boundary conditions, as is conventional in MD, only certain polytypes are allowed for an MD simulation system. A discussion of compatibility between close-packed structures and the periodic boundary conditions is presented. The pair coordination numbers, geometrical structure-factor intensities, and potential-energy lattice sums are then calculated for some of these compatible structures. This paper concludes that, through careful consideration, a considerable variety of close-packed physical systems may be appropriately modeled with use of MD computer simulation. Conversely, proper interpretation of the data obtained during such studies may require awareness of the findings presented here
A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.
Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E
2017-06-20
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Efficient stochastic thermostatting of path integral molecular dynamics.
Ceriotti, Michele; Parrinello, Michele; Markland, Thomas E; Manolopoulos, David E
2010-09-28
The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat which exploits an analytic knowledge of the free path integral normal mode frequencies. We also apply a recently developed colored noise thermostat based on a generalized Langevin equation (GLE), which automatically achieves a similar, frequency-optimized sampling. The sampling efficiencies of these thermostats are compared with that of the more conventional Nosé-Hoover chain (NHC) thermostat for a number of physically relevant properties of the liquid water and hydrogen-in-palladium systems. In nearly every case, the new PILE thermostat is found to perform just as well as the NHC thermostat while allowing for a computationally more efficient implementation. The GLE thermostat also proves to be very robust delivering a near-optimum sampling efficiency in all of the cases considered. We suspect that these simple stochastic thermostats will therefore find useful application in many future PIMD simulations.
Mean field ring polymer molecular dynamics for electronically nonadiabatic reaction rates.
Duke, Jessica Ryan; Ananth, Nandini
2016-12-22
We present a mean field ring polymer molecular dynamics method to calculate the rate of electron transfer (ET) in multi-state, multi-electron condensed-phase processes. Our approach involves calculating a transition state theory (TST) estimate to the rate using an exact path integral in discrete electronic states and continuous Cartesian nuclear coordinates. A dynamic recrossing correction to the TST rate is then obtained from real-time dynamics simulations using mean field ring polymer molecular dynamics. We employ two different reaction coordinates in our simulations and show that, despite the use of mean field dynamics, the use of an accurate dividing surface to compute TST rates allows us to achieve remarkable agreement with Fermi's golden rule rates for nonadiabatic ET in the normal regime of Marcus theory. Further, we show that using a reaction coordinate based on electronic state populations allows us to capture the turnover in rates for ET in the Marcus inverted regime.
Animated molecular dynamics simulations of hydrated caesium-smectite interlayers
Sutton, Rebecca; Sposito, Garrison
2002-01-01
Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.
A domain specific language for performance portable molecular dynamics algorithms
Saunders, William Robert; Grant, James; Müller, Eike Hermann
2018-03-01
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.
Animated molecular dynamics simulations of hydrated caesium-smectite interlayers
Directory of Open Access Journals (Sweden)
Sposito Garrison
2002-09-01
Full Text Available Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.
Dynamic control of function by light-driven molecular motors
van Leeuwen, Thomas; Lubbe, Anouk S.; Stacko, Peter; Wezenberg, Sander J.; Feringa, Ben L.
2017-01-01
The field of dynamic functional molecular systems has progressed enormously over the past few decades. By coupling the mechanical properties of molecular switches and motors to chemical and biological processes, exceptional control of function has been attained. Overcrowded alkene-based light-driven
Molecular Dynamics Investigation of Efficient SO2 Absorption by ...
Indian Academy of Sciences (India)
ANIRBAN MONDAL
TMG][L]) that absorbs an equimolar amount of SO2 through chemisorption.12 Subsequently, a sig- ...... Visual molecular dynamics J. Mol. Graphics 14 33. 83. Fiorin G, Klein M L and Hénin J 2013 Using collective variables to drive molecular ...
Directory of Open Access Journals (Sweden)
Juan P. Marcolongo
2018-03-01
Full Text Available In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU, that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
On the computation of molecular auxiliary functions An and Bn
Indian Academy of Sciences (India)
Comment: “On the computation of molecular auxiliary functions An and Bn”. FRANK E HARRIS. Department of Physics, University of Utah, Salt Lake City, UT 84112, USA. Quantum Theory Project, University of Florida, P.O. Box 118435, Gainesville, FL 32611, USA. Email: harris@qtp.ufl.edu. Abstract. Guseinov, Mamedov ...
Quantum computing applied to calculations of molecular energies
Czech Academy of Sciences Publication Activity Database
Pittner, Jiří; Veis, L.
2011-01-01
Roč. 241, - (2011), 151-phys ISSN 0065-7727. [National Meeting and Exposition of the American-Chemical-Society (ACS) /241./. 27.03.2011-31.03.2011, Anaheim] Institutional research plan: CEZ:AV0Z40400503 Keywords : molecular energie * quantum computers Subject RIV: CF - Physical ; Theoretical Chemistry
Computational social dynamic modeling of group recruitment.
Energy Technology Data Exchange (ETDEWEB)
Berry, Nina M.; Lee, Marinna; Pickett, Marc; Turnley, Jessica Glicken (Sandia National Laboratories, Albuquerque, NM); Smrcka, Julianne D. (Sandia National Laboratories, Albuquerque, NM); Ko, Teresa H.; Moy, Timothy David (Sandia National Laboratories, Albuquerque, NM); Wu, Benjamin C.
2004-01-01
The Seldon software toolkit combines concepts from agent-based modeling and social science to create a computationally social dynamic model for group recruitment. The underlying recruitment model is based on a unique three-level hybrid agent-based architecture that contains simple agents (level one), abstract agents (level two), and cognitive agents (level three). This uniqueness of this architecture begins with abstract agents that permit the model to include social concepts (gang) or institutional concepts (school) into a typical software simulation environment. The future addition of cognitive agents to the recruitment model will provide a unique entity that does not exist in any agent-based modeling toolkits to date. We use social networks to provide an integrated mesh within and between the different levels. This Java based toolkit is used to analyze different social concepts based on initialization input from the user. The input alters a set of parameters used to influence the values associated with the simple agents, abstract agents, and the interactions (simple agent-simple agent or simple agent-abstract agent) between these entities. The results of phase-1 Seldon toolkit provide insight into how certain social concepts apply to different scenario development for inner city gang recruitment.
CFDLIB05, Computational Fluid Dynamics Library
International Nuclear Information System (INIS)
Kashiwa, B.A.; Padial, N.T.; Rauenzahn, R.M.; VanderHeyden, W.B.
2007-01-01
1 - Description of program or function: CFDLib05 is the Los Alamos Computational Fluid Dynamics Library. This is a collection of hydro-codes using a common data structure and a common numerical method, for problems ranging from single-field, incompressible flow, to multi-species, multi-field, compressible flow. The data structure is multi-block, with a so-called structured grid in each block. The numerical method is a Finite-Volume scheme employing a state vector that is fully cell-centered. This means that the integral form of the conversation laws is solved on the physical domain that is represented by a mesh of control volumes. The typical control volume is an arbitrary quadrilateral in 2D and an arbitrary hexahedron in 3D. The Finite-Volume scheme is for time-unsteady flow and remains well coupled by means of time and space centered fluxes; if a steady state solution is required, the problem is integrated forward in time until the user is satisfied that the state is stationary. 2 - Methods: Cells-centered Implicit Continuous-fluid Eulerian (ICE) method
Computational fluid dynamics in ventilation: Practical approach
Fontaine, J. R.
The potential of computation fluid dynamics (CFD) for conceiving ventilation systems is shown through the simulation of five practical cases. The following examples are considered: capture of pollutants on a surface treating tank equipped with a unilateral suction slot in the presence of a disturbing air draft opposed to suction; dispersion of solid aerosols inside fume cupboards; performances comparison of two general ventilation systems in a silkscreen printing workshop; ventilation of a large open painting area; and oil fog removal inside a mechanical engineering workshop. Whereas the two first problems are analyzed through two dimensional numerical simulations, the three other cases require three dimensional modeling. For the surface treating tank case, numerical results are compared to laboratory experiment data. All simulations are carried out using EOL, a CFD software specially devised to deal with air quality problems in industrial ventilated premises. It contains many analysis tools to interpret the results in terms familiar to the industrial hygienist. Much experimental work has been engaged to validate the predictions of EOL for ventilation flows.
The use of molecular dynamics for the thermodynamic properties of simple and transition metals
International Nuclear Information System (INIS)
Straub, G.K.
1987-04-01
The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated
Molecular dynamics simulation of supercritical fluids
Branam, Richard D.
Axisymmetric injectors appear in a multitude of applications ranging from rocket engines to biotechnology. While experimentation is limited to larger injectors, much interest has been shown in the micro- and nano-scales as well. Experimentation at these scales can be cost prohibitive if even possible. Often, the operating regime involves supercritical fluids or complex geometries. Molecular dynamics modeling provides a unique way to explore these flow regimes, calculate hard to measure flow parameters accurately, and determine the value of potential improvements before investing in costly experiments or manufacturing. This research effort modeled sub- and supercritical fluid flow in a cylindrical tube being injected into a quiescent chamber. The ability of four wall models to provide an accurate simulation was compared. The simplest model, the diffuse wall, proved useful in getting results quickly but the results for the higher density cases are questionable, especially with respect to velocity profiles and density distributions. The one zone model, three layers of an fcc solid tethered to the lattice sites with a spring, proved very useful for this research primarily because it did not need as many CPU hours to equilibrate. The two zone wall uses springs as a two body potential and has a second stationary zone to hold the wall in place. The most complicated, the three zone wall, employed a reactionary zone, a stochastic zone and a stationary zone using a Lennard-Jones two body potential. Jet simulations were conducted on argon and nitrogen for liquid tube diameters from 20 to 65 A at both sub and supercritical temperatures (Ar: 130 K and 160 K, N2: 120 K and 130 K). The simulations focused on pressures above the critical pressure (Ar: 6 MPa, N2: 4 MPa). The diffusive wall showed some variation from the analytical velocity profile in the tube while the atomistically modeled walls performed very well. The walls were all able to maintain system temperature to reach
Computer Programme for the Dynamic Analysis of Tall Regular ...
African Journals Online (AJOL)
The traditional method of dynamic analysis of tall rigid frames assumes the shear frame model. Models that allow joint rotations with/without the inclusion of the column axial loads give improved results but pose much more computational difficulty. In this work a computer program Natfrequency that determines the dynamic ...
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...
Molecular dynamics study of two- and three-dimensional classical ...
Indian Academy of Sciences (India)
Abstract. We have carried out a molecular dynamics simulation of two- and three- dimensional double Yukawa fluids near the triple point. We have compared some of the static and dynamic correlation functions with those of Lennard–Jones, when parameters occurring in double Yukawa potential are chosen to fit ...
Interfacial Properties of an Ionic Liquid by Molecular Dynamics
Heggen, B.; Zhao, W.; Leroy, F.; Dammers, A.T.; Müller-Plathe, F.
2010-01-01
We studied the influence of a liquid-vapor interface on dynamic properties like reorientation and diffusion as well as the surface tension of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) by molecular dynamics simulations. In the interfacial region, reorientation of
HTTR plant dynamic simulation using a hybrid computer
International Nuclear Information System (INIS)
Shimazaki, Junya; Suzuki, Katsuo; Nabeshima, Kunihiko; Watanabe, Koichi; Shinohara, Yoshikuni; Nakagawa, Shigeaki.
1990-01-01
A plant dynamic simulation of High-Temperature Engineering Test Reactor has been made using a new-type hybrid computer. This report describes a dynamic simulation model of HTTR, a hybrid simulation method for SIMSTAR and some results obtained from dynamics analysis of HTTR simulation. It concludes that the hybrid plant simulation is useful for on-line simulation on account of its capability of computation at high speed, compared with that of all digital computer simulation. With sufficient accuracy, 40 times faster computation than real time was reached only by changing an analog time scale for HTTR simulation. (author)
Optimal control of molecular motion expressed through quantum fluid dynamics
Dey, Bijoy K.; Rabitz, Herschel; Askar, Attila
2000-04-01
A quantum fluid-dynamic (QFD) control formulation is presented for optimally manipulating atomic and molecular systems. In QFD the control quantum system is expressed in terms of the probability density ρ and the quantum current j. This choice of variables is motivated by the generally expected slowly varying spatial-temporal dependence of the fluid-dynamical variables. The QFD approach is illustrated for manipulation of the ground electronic state dynamics of HCl induced by an external electric field.
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
Analyzing machupo virus-receptor binding by molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Austin G. Meyer
2014-02-01
Full Text Available In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein–protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host–virus protein–protein interface. We use steered molecular dynamics (SMD to computationally pull the machupo virus (MACV spike glycoprotein (GP1 away from the human transferrin receptor (hTfR1. We then approximate affinity using the maximum applied force of separation and the area under the force-versus-distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-crystal structure shows two large hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein–protein interactions.
Analyzing machupo virus-receptor binding by molecular dynamics simulations
Sawyer, Sara L.; Ellington, Andrew D.; Wilke, Claus O.
2014-01-01
In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein–protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host–virus protein–protein interface. We use steered molecular dynamics (SMD) to computationally pull the machupo virus (MACV) spike glycoprotein (GP1) away from the human transferrin receptor (hTfR1). We then approximate affinity using the maximum applied force of separation and the area under the force-versus-distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-crystal structure shows two large hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein–protein interactions. PMID:24624315
International Nuclear Information System (INIS)
Washizu, Hitoshi; Sanda, Shuzo; Hyodo, Shi-aki; Ohmori, Toshihide; Nishino, Noriaki; Suzuki, Atsushi
2007-01-01
Friction control of machine elements on a molecular level is a challenging subject in vehicle technology. We describe the molecular dynamics studies of friction in two significant lubrication regimes. As a case of elastohydrodynamic lubrication, we introduce the mechanism of momentum transfer related to the molecular structure of the hydrocarbon fluids, phase transition of the fluids under high pressure, and a submicron thickness simulation of the oil film using a tera-flops computer. For boundary lubrication, the dynamic behavior of water molecules on hydrophilic and hydrophobic silicon surfaces under a shear condition is studied. The dynamic structure of the hydrogen bond network on the hydrophilic surface is related to the low friction of the diamond-like carbon containing silicon (DLC-Si) coating
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)
Jójárt, Balázs; Márki, Arpád
2007-01-01
In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone-human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the molecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research.
Dynamic leaching test of personal computer components.
Li, Yadong; Richardson, Jay B; Niu, Xiaojun; Jackson, Ollie J; Laster, Jeremy D; Walker, Aaron K
2009-11-15
A dynamic leaching test (DLT) was developed and used to evaluate the leaching of toxic substances for electronic waste in the environment. The major components in personal computers (PCs) including motherboards, hard disc drives, floppy disc drives, and compact disc drives were tested. The tests lasted for 2 years for motherboards and 1.5 year for the disc drives. The extraction fluids for the standard toxicity characteristic leaching procedure (TCLP) and synthetic precipitation leaching procedure (SPLP) were used as the DLT leaching solutions. A total of 18 elements including Ag, Al, As, Au, Ba, Be, Cd, Cr, Cu, Fe, Ga, Ni, Pd, Pb, Sb, Se, Sn, and Zn were analyzed in the DLT leachates. Only Al, Cu, Fe, Ni, Pb, and Zn were commonly found in the DLT leachates of the PC components. Their leaching levels were much higher in TCLP extraction fluid than in SPLP extraction fluid. The toxic heavy metal Pb was found to continuously leach out of the components over the entire test periods. The cumulative amounts of Pb leached out of the motherboards in TCLP extraction fluid reached 2.0 g per motherboard over the 2-year test period, and that in SPLP extraction fluid were 75-90% less. The leaching rates or levels of Pb were largely affected by the content of galvanized steel in the PC components. The higher was the steel content, the lower the Pb leaching rate would be. The findings suggest that the obsolete PCs disposed of in landfills or discarded in the environment continuously release Pb for years when subjected to landfill leachate or rains.
Shen, Lin; Yang, Weitao
2018-03-13
Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of
Quantum Computation and Quantum Spin Dynamics
Raedt, Hans De; Michielsen, Kristel; Hams, Anthony; Miyashita, Seiji; Saito, Keiji
2001-01-01
We analyze the stability of quantum computations on physically realizable quantum computers by simulating quantum spin models representing quantum computer hardware. Examples of logically identical implementations of the controlled-NOT operation are used to demonstrate that the results of a quantum
Dynamic computed tomography findings in cerebrovascular diseases
International Nuclear Information System (INIS)
Araki, Yutaka; Tomoda, Kaname; Kariya, Mitsumasa; Mori, Shigeru; Mitomo, Masanori.
1988-01-01
Dynamic CT was performed with 41 patients with the clinically diagnosed cerebrovascular diseases. A visual evaluation based on the dynamic CT images classified six patterns of brain parenchymal enhancement, especially four patterns of which could only be detected by dynamic CT technique. Dynamic CT was proved of great value in detecting regional cerebral tissue filled by collaterals in retrograde fashion because of the occlusion of main arteries, namely brain tissue perfusion of internal carotid occlusion disease and moyamoya disease was best understood by dynamic CT with adequate resolution. (author)
VUV studies of molecular photofragmentation dynamics
Energy Technology Data Exchange (ETDEWEB)
White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)
1993-12-01
State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.
Design of Carborane Molecular Architectures via Electronic Structure Computations
International Nuclear Information System (INIS)
Oliva, J.M.; Serrano-Andres, L.; Klein, D.J.; Schleyer, P.V.R.; Mich, J.
2009-01-01
Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of poly carborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photo energy processes.
Molecular determinants of epidermal growth factor binding: a molecular dynamics study.
Directory of Open Access Journals (Sweden)
Jeffrey M Sanders
Full Text Available The epidermal growth factor receptor (EGFR is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of
Constructing Scientific Arguments Using Evidence from Dynamic Computational Climate Models
Pallant, Amy; Lee, Hee-Sun
2015-04-01
Modeling and argumentation are two important scientific practices students need to develop throughout school years. In this paper, we investigated how middle and high school students ( N = 512) construct a scientific argument based on evidence from computational models with which they simulated climate change. We designed scientific argumentation tasks with three increasingly complex dynamic climate models. Each scientific argumentation task consisted of four parts: multiple-choice claim, openended explanation, five-point Likert scale uncertainty rating, and open-ended uncertainty rationale. We coded 1,294 scientific arguments in terms of a claim's consistency with current scientific consensus, whether explanations were model based or knowledge based and categorized the sources of uncertainty (personal vs. scientific). We used chi-square and ANOVA tests to identify significant patterns. Results indicate that (1) a majority of students incorporated models as evidence to support their claims, (2) most students used model output results shown on graphs to confirm their claim rather than to explain simulated molecular processes, (3) students' dependence on model results and their uncertainty rating diminished as the dynamic climate models became more and more complex, (4) some students' misconceptions interfered with observing and interpreting model results or simulated processes, and (5) students' uncertainty sources reflected more frequently on their assessment of personal knowledge or abilities related to the tasks than on their critical examination of scientific evidence resulting from models. These findings have implications for teaching and research related to the integration of scientific argumentation and modeling practices to address complex Earth systems.
International Nuclear Information System (INIS)
Kashiwagi, H.
1982-01-01
A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience. (orig.)
Molecular-dynamics analysis of the diffusion of molecular hydrogen in all-silica sodalite
Van den Berg, A.W.C.; Bromley, S.T.; Flikkema, E.; Wojdel, J.; Maschmeyer, T.; Jansen, J.C.
2004-01-01
In order to investigate the technical feasibility of crystalline porous silicates as hydrogen storage materials, the self-diffusion of molecular hydrogen in all-silica sodalite is modeled using large-scale classical molecular-dynamics simulations employing full lattice flexibility. In the
Simplistic Coulomb Forces in Molecular Dynamics
DEFF Research Database (Denmark)
Hansen, Jesper Schmidt; Schrøder, Thomas; Dyre, J. C.
2012-01-01
salt model the SF approximation overall reproduces the structural and dynamical properties as accurately as does the Wolf method. It is shown that the optimal Wolf damping parameter depends on the property in focus and that neither the potential energy nor the radial distribution function are useful...
In Silico Dynamics: computer simulation in a Virtual Embryo ...
Abstract: Utilizing cell biological information to predict higher order biological processes is a significant challenge in predictive toxicology. This is especially true for highly dynamical systems such as the embryo where morphogenesis, growth and differentiation require precisely orchestrated interactions between diverse cell populations. In patterning the embryo, genetic signals setup spatial information that cells then translate into a coordinated biological response. This can be modeled as ‘biowiring diagrams’ representing genetic signals and responses. Because the hallmark of multicellular organization resides in the ability of cells to interact with one another via well-conserved signaling pathways, multiscale computational (in silico) models that enable these interactions provide a platform to translate cellular-molecular lesions perturbations into higher order predictions. Just as ‘the Cell’ is the fundamental unit of biology so too should it be the computational unit (‘Agent’) for modeling embryogenesis. As such, we constructed multicellular agent-based models (ABM) with ‘CompuCell3D’ (www.compucell3d.org) to simulate kinematics of complex cell signaling networks and enable critical tissue events for use in predictive toxicology. Seeding the ABMs with HTS/HCS data from ToxCast demonstrated the potential to predict, quantitatively, the higher order impacts of chemical disruption at the cellular or biochemical level. This is demonstrate
Energy Technology Data Exchange (ETDEWEB)
Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)
2015-06-28
In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible
Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations
Levine, Zachary Alan
Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant
Computational fluid dynamics on a massively parallel computer
Jespersen, Dennis C.; Levit, Creon
1989-01-01
A finite difference code was implemented for the compressible Navier-Stokes equations on the Connection Machine, a massively parallel computer. The code is based on the ARC2D/ARC3D program and uses the implicit factored algorithm of Beam and Warming. The codes uses odd-even elimination to solve linear systems. Timings and computation rates are given for the code, and a comparison is made with a Cray XMP.
Hybrid nonnegative and computational dynamical systems
Directory of Open Access Journals (Sweden)
Wassim M. Haddad
2002-01-01
Full Text Available Nonnegative and Compartmental dynamical systems are governed by conservation laws and are comprised of homogeneous compartments which exchange variable nonnegative quantities of material via intercompartmental flow laws. These systems typically possess hierarchical (and possibly hybrid structures and are remarkably effective in capturing the phenomenological features of many biological and physiological dynamical systems. In this paper we develop several results on stability and dissipativity of hybrid nonnegative and Compartmental dynamical systems. Specifically, using linear Lyapunov functions we develop sufficient conditions for Lyapunov and asymptotic stability for hybrid nonnegative dynamical systems. In addition, using linear and nonlinear storage functions with linear hybrid supply rates we develop new notions of dissipativity theory for hybrid nonnegative dynamical systems. Finally, these results are used to develop general stability criteria for feedback interconnections of hybrid nonnegative dynamical systems.
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.
Computational Exploration of Molecular Scaffolds in Medicinal Chemistry.
Hu, Ye; Stumpfe, Dagmar; Bajorath, Jürgen
2016-05-12
The scaffold concept is widely applied in medicinal chemistry. Scaffolds are mostly used to represent core structures of bioactive compounds. Although the scaffold concept has limitations and is often viewed differently from a chemical and computational perspective, it has provided a basis for systematic investigations of molecular cores and building blocks, going far beyond the consideration of individual compound series. Over the past 2 decades, alternative scaffold definitions and organization schemes have been introduced and scaffolds have been studied in a variety of ways and increasingly on a large scale. Major applications of the scaffold concept include the generation of molecular hierarchies, structural classification, association of scaffolds with biological activities, and activity prediction. This contribution discusses computational approaches for scaffold generation and analysis, with emphasis on recent developments impacting medicinal chemistry. A variety of scaffold-based studies are discussed, and a perspective on scaffold methods is provided.
Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase
Directory of Open Access Journals (Sweden)
Beata Szefler
2016-10-01
Full Text Available Glucose oxidase (GOx is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2. GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI. The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD study of the PEI ligand (C14N8_07_B22 and the GOx enzyme (3QVR was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1 of −5.8 kcal/mol and (LIG2 of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1 and on its surface (LIG2 were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.
International Nuclear Information System (INIS)
Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M
2010-01-01
Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives
Propagation of Computer Virus under Human Intervention: A Dynamical Model
Chenquan Gan; Xiaofan Yang; Wanping Liu; Qingyi Zhu; Xulong Zhang
2012-01-01
This paper examines the propagation behavior of computer virus under human intervention. A dynamical model describing the spread of computer virus, under which a susceptible computer can become recovered directly and an infected computer can become susceptible directly, is proposed. Through a qualitative analysis of this model, it is found that the virus-free equilibrium is globally asymptotically stable when the basic reproduction number R0≤1, whereas the viral equilibrium is globally asympt...
Application of Connection in Molecular Dynamics
Sun, Xin
2018-03-01
The evolution of electronic states in molecule has two origins: dynamical one produced by Schrödinger equation and kinematical one caused by base transformation due to nuclear motion. In current theories, the former gets analytic expression; the latter depends on heavy numerical calculation, which contains uncertainty. By using connection of fiber bundles, this paper establishes an analytic formula for the latter, and the numerical work is simplified. It shows the mathematical structure of molecule is fiber bundle.
Numerical Simulations for Large Deformation of Geomaterials Using Molecular Dynamics
Directory of Open Access Journals (Sweden)
Ziyang Zhao
2018-01-01
Full Text Available From the microperspective, this paper presents a model based on a new type of noncontinuous theoretical mechanical method, molecular dynamics (MD, to simulate the typical soil granular flow. The Hertzian friction formula and viscous damping force are introduced in the MD governing equations to model the granular flow. To show the validity of the proposed approach, a benchmark problem of 2D viscous material flow is simulated. The calculated final flow runout distance of the viscous material agrees well with the result of constrained interpolated profile (CIP method as reported in the literature. Numerical modeling of the propagation of the collapse of three-dimensional axisymmetric sand columns is performed by the application of MD models. Comparison of the MD computational runout distance and the obtained distance by experiment shows a high degree of similarity. This indicates that the proposed MD model can accurately represent the evolution of the granular flow. The model developed may thus find applications in various problems involving dense granular flow and large deformations, such as landslides and debris flow. It provides a means for predicting fluidization characteristics of soil large deformation flow disasters and for identification and design of appropriate protective measures.
Unraveling Mg2+-RNA binding with atomistic molecular dynamics.
Cunha, Richard A; Bussi, Giovanni
2017-05-01
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We report here a detailed molecular dynamics study of all the possible binding sites for Mg 2+ on an RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle sampling issues, we develop a modified version of bias-exchange metadynamics, which allows us to simultaneously compute affinities with previously unreported statistical accuracy. Results correctly reproduce trends observed in crystallographic databases. Based on this, we simulate a carefully chosen set of models that allows us to quantify the effects of competition with monovalent cations, RNA flexibility, and RNA hybridization. Our simulations reproduce the decrease and increase of Mg 2+ affinity due to ion competition and hybridization, respectively, and predict that RNA flexibility has a site-dependent effect. This suggests a nontrivial interplay between RNA conformational entropy and divalent cation binding. © 2017 Cunha and Bussi; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
MOLECULAR DYNAMICS SIMULATIONS OF DISPLACEMENT CASCADES IN MOLYBDENUM
International Nuclear Information System (INIS)
Smith, Richard Whiting
2003-01-01
Molecular dynamics calculations have been employed to simulate displacement cascades in neutron irradiated Mo. A total of 90 simulations were conducted for PKA energies between 1 and 40 keV and temperatures from 298 to 923K. The results suggest very little effect of temperature on final defect count and configuration, but do display a temperature effect on peak defect generation prior to cascade collapse. Cascade efficiency, relative to the NRT model, is computed to lie between 1/4 and 1/3 in agreement with simulations performed on previous systems. There is a tendency for both interstitials and vacancies to cluster together following cascade collapse producing vacancy rich regions surrounded by interstitials. Although coming to rest in close proximity, the point defects comprising the clusters generally do not lie within the nearest neighbor positions of one another, except for the formation of dumbbell di-interstitials. Cascades produced at higher PKA energies (20 or 40 keV) exhibit the formation of subcascades
Green’s function molecular dynamics meets discrete dislocation plasticity
Venugopalan, Syam P.; Müser, Martin H.; Nicola, Lucia
2017-09-01
Metals deform plastically at the asperity level when brought in contact with a counter body even when the nominal contact pressure is small. Modeling the plasticity of solids with rough surfaces is challenging due to the multi-scale nature of surface roughness and the length-scale dependence of plasticity. While discrete-dislocation plasticity (DDP) simulations capture size-dependent plasticity by keeping track of the motion of individual dislocations, only simple two-dimensional surface geometries have so far been studied with DDP. The main computational bottleneck in contact problems modeled by DDP is the calculation of the dislocation image fields. We address this issue by combining two-dimensional DDP with Green’s function molecular dynamics. The resulting method allows for an efficient boundary-value-method based treatment of elasticity in the presence of dislocations. We demonstrate that our method captures plasticity quantitatively from single to many dislocations and that it scales more favorably with system size than conventional methods. We also derive the relevant Green’s functions for elastic slabs of finite width allowing arbitrary boundary conditions on top and bottom surface to be simulated.
Computational studies of protein-ligand molecular recognition
Gillies, M.B.
2001-01-01
Structure-based drug design is made possible by our understanding of molecular recognition. The utility of this approach was apparent in the development of the clinically e V ective HIV-1 PR inhibitors, where crystal structures of complexes of HIV-1 protease and inhibitors gave pivotal information. Computational methods drawing upon structural data are of increasing relevance to the drug design process. Nonetheless, these methods are quite rudimentary and signicant improvements are needed. Th...
Computing Bisectors in a Dynamic Geometry Environment
Botana, Francisco
2013-01-01
In this note, an approach combining dynamic geometry and automated deduction techniques is used to study the bisectors between points and curves. Usual teacher constructions for bisectors are discussed, showing that inherent limitations in dynamic geometry software impede their thorough study. We show that the interactive sketching of bisectors…
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.
Computable Analysis with Applications to Dynamic Systems
P.J. Collins (Pieter)
2010-01-01
htmlabstractIn this article we develop a theory of computation for continuous mathematics. The theory is based on earlier developments of computable analysis, especially that of the school of Weihrauch, and is presented as a model of intuitionistic type theory. Every effort has been made to keep the
Studying Interactions by Molecular Dynamics Simulations at High Concentration
Directory of Open Access Journals (Sweden)
Federico Fogolari
2012-01-01
Full Text Available Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.
Driving Ordering Processes in Molecular-Dynamics Simulations
Dittmar, Harro; Kusalik, Peter G.
2014-05-01
Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized.
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
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.
Computing the Ediz eccentric connectivity index of discrete dynamic structures
Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei
2017-06-01
From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.
Molecular Dynamics and Spectra. II. Diatomic Raman.
1981-02-01
in, /he C’omputer .Simi/e-awn of ondeImed Mc’dha, edited by 1). (eperely (National Resource f~or Computation in C’hemisry. Berke- ley , 1980)) p. 13. 21...Quantum Mec /tanocs, 10 o1 , luondamnewals ( W. A. Benjamiin . Nes% )i fork. 1966) pp. 66-74. 256-264. 56. K. F. I loldy, L. C. Kiot/. and K. R. Wilson...Sets (Academic Press, New York. 1959) 61 J . A. Koni ngstein . hitroductfioo fo the Thecory of the( Rainan lei (I) Reidel, Do)1rdi cclhi. 1972) 62 It
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
Electron trapping in amorphous silicon: A quantum molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
Yang, Lin H.; Kalia, R.K.; Vashishta, P.
1990-12-01
Quantum molecular dynamics (QMD) simulations provide the real-time dynamics of electrons and ions through numerical solutions of the time-dependent Schrodinger and Newton equations, respectively. Using the QMD approach we have investigated the localization behavior of an excess electron in amorphous silicon at finite temperatures. For time scales on the order of a few picoseconds, we find the excess electron is localized inside a void of radius {approximately}3 {Angstrom} at finite temperatures. 12 refs.
Automated Computational Fluid Dynamics Design With Shape Optimization, Phase II
National Aeronautics and Space Administration — Computational fluid dynamics (CFD) is used as an analysis tool to help the designer gain greater understanding of the fluid flow phenomena involved in the components...
Validation of Computational Fluid Dynamics Simulations for Realistic Flows (Preprint)
National Research Council Canada - National Science Library
Davoudzadeh, Farhad
2007-01-01
Strategies used to verify and validate computational fluid dynamics (CFD) calculations are described via case studies of realistic flow simulations, each representing a complex flow physics and complex geometry...
ADDRESSING ENVIRONMENTAL ENGINEERING CHALLENGES WITH COMPUTATIONAL FLUID DYNAMICS
This paper discusses the status and application of Computational Fluid Dynamics )CFD) models to address environmental engineering challenges for more detailed understanding of air pollutant source emissions, atmospheric dispersion and resulting human exposure. CFD simulations ...
Automated Computational Fluid Dynamics Design With Shape Optimization, Phase I
National Aeronautics and Space Administration — Computational fluid dynamics (CFD) is used as an analysis tool to help the designer gain greater understanding of the fluid flow phenomena involved in the components...
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.
Dynamic Reconfiguration for Adaptive Computing Systems (DRACS)
National Research Council Canada - National Science Library
Zaino, John
2002-01-01
...) driven and one additional host-driven demonstration. This report describes how these can be used to develop a "virtual co-processor" that supports multiple reconfigurable computing applications residing in a single piece of hardware...
Computational modeling of turn-taking dynamics in spoken conversations
Chowdhury, Shammur Absar
2017-01-01
The study of human interaction dynamics has been at the center for multiple research disciplines in- cluding computer and social sciences, conversational analysis and psychology, for over decades. Recent interest has been shown with the aim of designing computational models to improve human-machine interaction system as well as support humans in their decision-making process. Turn-taking is one of the key aspects of conversational dynamics in dyadic conversations and is an integral part of hu...
Computer architecture evaluation for structural dynamics computations: Project summary
Standley, Hilda M.
1989-01-01
The intent of the proposed effort is the examination of the impact of the elements of parallel architectures on the performance realized in a parallel computation. To this end, three major projects are developed: a language for the expression of high level parallelism, a statistical technique for the synthesis of multicomputer interconnection networks based upon performance prediction, and a queueing model for the analysis of shared memory hierarchies.
Molecular circuits for dynamic noise filtering.
Zechner, Christoph; Seelig, Georg; Rullan, Marc; Khammash, Mustafa
2016-04-26
The invention of the Kalman filter is a crowning achievement of filtering theory-one that has revolutionized technology in countless ways. By dealing effectively with noise, the Kalman filter has enabled various applications in positioning, navigation, control, and telecommunications. In the emerging field of synthetic biology, noise and context dependency are among the key challenges facing the successful implementation of reliable, complex, and scalable synthetic circuits. Although substantial further advancement in the field may very well rely on effectively addressing these issues, a principled protocol to deal with noise-as provided by the Kalman filter-remains completely missing. Here we develop an optimal filtering theory that is suitable for noisy biochemical networks. We show how the resulting filters can be implemented at the molecular level and provide various simulations related to estimation, system identification, and noise cancellation problems. We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using flow cytometry measurements of a light-inducible circuit in Escherichia coli.
Medders, Gregory R; Paesani, Francesco
2015-03-10
Vibrational spectroscopy is a powerful technique to probe the structure and dynamics of water. However, deriving an unambiguous molecular-level interpretation of the experimental spectral features remains a challenge due to the complexity of the underlying hydrogen-bonding network. In this contribution, we present an integrated theoretical and computational framework (named many-body molecular dynamics or MB-MD) that, by systematically removing uncertainties associated with existing approaches, enables a rigorous modeling of vibrational spectra of water from quantum dynamical simulations. Specifically, we extend approaches used to model the many-body expansion of interaction energies to develop many-body representations of the dipole moment and polarizability of water. The combination of these "first-principles" representations with centroid molecular dynamics simulations enables the simulation of infrared and Raman spectra of liquid water under ambient conditions that, without relying on any ad hoc parameters, are in good agreement with the corresponding experimental results. Importantly, since the many-body energy, dipole, and polarizability surfaces employed in the simulations are derived independently from accurate fits to correlated electronic structure data, MB-MD allows for a systematic analysis of the calculated spectra in terms of both electronic and dynamical contributions. The present analysis suggests that, while MB-MD correctly reproduces both the shifts and the shapes of the main spectroscopic features, an improved description of quantum dynamical effects possibly combined with a dissociable water potential may be necessary for a quantitative representation of the OH stretch band.
Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.
Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro
2015-01-01
Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Correlations and symmetry of interactions influence collective dynamics of molecular motors
International Nuclear Information System (INIS)
Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B
2015-01-01
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)
Prospects for Computational Fluid Dynamics in Room Air Contaminant Control
DEFF Research Database (Denmark)
Nielsen, Peter V.
The fluid dynamics research is strongly influenced by the increasing computer power which has been available for the last decades. This development is obvious from the curve in figure 1 which shows the computation cost as a function of years. It is obvious that the cost for a given job...
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, hi...
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...
Hydration of Cd(II): molecular dynamics study | M. Mohammed ...
African Journals Online (AJOL)
The inclusion of the three-body correction was found to be crucial for the description of the system, and results thus obtained are in good agreement with experimental values. Radial ... KEY WORDS: Molecular dynamics, Umbrella sampling, Hydration structure, Cd(II), Water exchange, Three-body corrections. Bull. Chem.
Projector augmented wave method: ab initio molecular dynamics ...
Indian Academy of Sciences (India)
Unknown
The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. .... In that case the muffin–tin approximation is used solely to define the basis set. ..... functions probe the local character of the auxiliary wave function in the atomic region. Examples ...
Active site modeling in copper azurin molecular dynamics simulations
Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R
Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the
CF3+ etching silicon surface: A molecular dynamics study
Zhao, C.; Lu, X.; He, P.; Zhang, P.; Sun, W.; Zhang, Jingwei; Chen, F.; Gou, F.
2012-01-01
In this study, a molecular dynamics simulation method has been employed to investigate CF3 + ions, bombarding Si surface with the energy of 100, 200, 300 and 400 eV and an incident angle of 45 degrees with respect to the normal. The simulation results show that when CF3+ ions approach the Si surface
Molecular dynamics simulations and free energy profile of ...
Indian Academy of Sciences (India)
Molecular dynamics simulations and free energy profile of Paracetamol in DPPC and DMPC lipid bilayers. YOUSEF NADEMIa, SEPIDEH AMJAD IRANAGHb, ABBAS YOUSEFPOURa,. SEYEDEH ZAHRA MOUSAVIa and HAMID MODARRESSa,∗. aDepartment of Chemical Engineering, bDepartment of Chemistry, ...
Molecular Dynamics and Bioactivity of a Novel Mutated Human ...
African Journals Online (AJOL)
Purpose: To design and evaluate a novel human parathyroid hormone (hPTH) analog. Methods: Mutation stability prediction was processed on hPTH, docked the mutant hPTH with its receptor, and then proceeded with molecular dynamics using Discovery Studio 3.5 software package for the complex. The bioactivity of the ...
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 ...
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...
Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations
Bulacu, Monica; Goga, Nicolae; Zhao, Wei; Rossi, Giulia; Monticelli, Luca; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.
Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules.
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...
A molecular dynamics study of SiSe2 glass
International Nuclear Information System (INIS)
Antonio, G.A.; Kalia, R.K.; Vashishta, P.
1988-10-01
We report the results of a molecular dynamics study of molten and glassy SiSe 2 using an effective interparticle interaction. Results for the partial pair-correlation functions, partial structure factors, bond-angle distributions and statistics of rings are reported. Results are in good agreement with the neutron diffraction experiments. 11 refs., 6 figs
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.
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
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 ...
Molecular dynamics simulations of phase transformations in niti bicrystals
Srinivasan, P.; Nicola, L.; Simone, A.; Floryan, J.M.; Tvergaard, V.; van Campen, D.
2016-01-01
The influence of grain boundaries and grain misorientation on the nucleation and growth of martensite in an equi-atomic nickeltitanium (NiTi) shape memory alloy (SMA) is investigated by performing molecular dynamics (MD) simulations on bicrystals with a modified embedded atom method (MEAM)
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
Coarse – grained molecular dynamics simulation of cross – linking ...
African Journals Online (AJOL)
Coarse – grained molecular dynamics simulation of cross – linking of DGEBA epoxy resin and estimation of the adhesive strength. ... The PDF file you selected should load here if your Web browser has a PDF reader plug-in installed (for example, a recent version of Adobe Acrobat Reader). If you would like more ...
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.
Unsteady computational fluid dynamics in aeronautics
Tucker, P G
2014-01-01
The field of Large Eddy Simulation (LES) and hybrids is a vibrant research area. This book runs through all the potential unsteady modelling fidelity ranges, from low-order to LES. The latter is probably the highest fidelity for practical aerospace systems modelling. Cutting edge new frontiers are defined. One example of a pressing environmental concern is noise. For the accurate prediction of this, unsteady modelling is needed. Hence computational aeroacoustics is explored. It is also emerging that there is a critical need for coupled simulations. Hence, this area is also considered and the tensions of utilizing such simulations with the already expensive LES. This work has relevance to the general field of CFD and LES and to a wide variety of non-aerospace aerodynamic systems (e.g. cars, submarines, ships, electronics, buildings). Topics treated include unsteady flow techniques; LES and hybrids; general numerical methods; computational aeroacoustics; computational aeroelasticity; coupled simulations and...
(U) Computation acceleration using dynamic memory
Energy Technology Data Exchange (ETDEWEB)
Hakel, Peter [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2014-10-24
Many computational applications require the repeated use of quantities, whose calculations can be expensive. In order to speed up the overall execution of the program, it is often advantageous to replace computation with extra memory usage. In this approach, computed values are stored and then, when they are needed again, they are quickly retrieved from memory rather than being calculated again at great cost. Sometimes, however, the precise amount of memory needed to store such a collection is not known in advance, and only emerges in the course of running the calculation. One problem accompanying such a situation is wasted memory space in overdimensioned (and possibly sparse) arrays. Another issue is the overhead of copying existing values to a new, larger memory space, if the original allocation turns out to be insufficient. In order to handle these runtime problems, the programmer therefore has the extra task of addressing them in the code.
The Molecular Electronic Device and the Biochip Computer: Present Status
Haddon, R. C.; Lamola, A. A.
1985-04-01
The idea that a single molecule might function as a self-contained electronic device has been of interest for some time. However, a fully integrated version--the biochip or the biocomputer, in which both production and assembly of molecular electronic components is achieved through biotechnology--is a relatively new concept that is currently attracting attention both within the scientific community and among the general public. In the present article we draw together some of the approaches being considered for the construction of such devices and delineate the revolutionary nature of the current proposals for molecular electronic devices (MEDs) and biochip computers (BCCs). With the silicon semiconductor industry already in place and in view of the continuing successes of the lithographic process it seems appropriate to ask why the highly speculative MED or BCC has engendered such interest. In some respects the answer is paradigmatic as much as it is real. It is perhaps best stated as the promise of the realm of the molecular. Thus it is envisioned that devices will be constructed by assembly of individual molecular electronic components into arrays, thereby engineering from small upward rather than large downward as do current lithographic techniques. An important corollary of the construction technique is that the functional elements of such an array would be individual molecules rather than macroscopic ensembles. These two aspects of the MED/BCC--assembly of molecular arrays and individually accessible functional molecular units--are truly revolutionary. Both require scientific breakthroughs and the necessary principles, quite apart from the technology, remain essentially unknown. It is concluded that the advent of the MED/BCC still lies well before us. The twin criteria of utilization of individual molecules as functional elements and the assembly of such elements remains as elusive as ever. Biology engineers structures on the molecular scale but biomolecules
Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.
2018-04-01
Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.
Computational fluid dynamics for sport simulation
2009-01-01
All over the world sport plays a prominent role in society: as a leisure activity for many, as an ingredient of culture, as a business and as a matter of national prestige in such major events as the World Cup in soccer or the Olympic Games. Hence, it is not surprising that science has entered the realm of sports, and, in particular, that computer simulation has become highly relevant in recent years. This is explored in this book by choosing five different sports as examples, demonstrating that computational science and engineering (CSE) can make essential contributions to research on sports topics on both the fundamental level and, eventually, by supporting athletes’ performance.
Spatiotemporal Dynamics and Reliable Computations in Recurrent Spiking Neural Networks
Pyle, Ryan; Rosenbaum, Robert
2017-01-01
Randomly connected networks of excitatory and inhibitory spiking neurons provide a parsimonious model of neural variability, but are notoriously unreliable for performing computations. We show that this difficulty is overcome by incorporating the well-documented dependence of connection probability on distance. Spatially extended spiking networks exhibit symmetry-breaking bifurcations and generate spatiotemporal patterns that can be trained to perform dynamical computations under a reservoir computing framework.
Benjamin, Ilan; Pohorille, Andrew
1993-01-01
The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.
Modeling molecular boiling points using computed interaction energies.
Peterangelo, Stephen C; Seybold, Paul G
2017-12-20
The noncovalent van der Waals interactions between molecules in liquids are typically described in textbooks as occurring between the total molecular dipoles (permanent, induced, or transient) of the molecules. This notion was tested by examining the boiling points of 67 halogenated hydrocarbon liquids using quantum chemically calculated molecular dipole moments, ionization potentials, and polarizabilities obtained from semi-empirical (AM1 and PM3) and ab initio Hartree-Fock [HF 6-31G(d), HF 6-311G(d,p)], and density functional theory [B3LYP/6-311G(d,p)] methods. The calculated interaction energies and an empirical measure of hydrogen bonding were employed to model the boiling points of the halocarbons. It was found that only terms related to London dispersion energies and hydrogen bonding proved significant in the regression analyses, and the performances of the models generally improved at higher levels of quantum chemical computation. An empirical estimate for the molecular polarizabilities was also tested, and the best models for the boiling points were obtained using either this empirical polarizability itself or the polarizabilities calculated at the B3LYP/6-311G(d,p) level, along with the hydrogen-bonding parameter. The results suggest that the cohesive forces are more appropriately described as resulting from highly localized interactions rather than interactions between the global molecular dipoles.
Molecular Dynamics and Docking of Biphenyl: A Potential ...
African Journals Online (AJOL)
by computational molecular modeling and docking is that it is a truthful and precise rational drug design approach. The present study serves as a motivation of pursue for an attachment inhibitor against HIV-1 gp120 glycoprotein to complement the currently. 0. 1. 2. 3. 4. 5. 6. 0. 1000. 2000. 3000. 4000. 5000. R. MSD. /Å.
Structure and dynamics of alkali borate glasses: a molecular dynamics study
Verhoef, A.H; den Hartog, H. W.
Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at
Dynamic traffic assignment on parallel computers
Energy Technology Data Exchange (ETDEWEB)
Nagel, K.; Frye, R.; Jakob, R.; Rickert, M.; Stretz, P.
1998-12-01
The authors describe part of the current framework of the TRANSIMS traffic research project at the Los Alamos National Laboratory. It includes parallel implementations of a route planner and a microscopic traffic simulation model. They present performance figures and results of an offline load-balancing scheme used in one of the iterative re-planning runs required for dynamic route assignment.
Dynamic grid adaptation for computational magnetohydrodynamics
Keppens, R.; Nool, M.; Zegeling, P. A.; Goedbloed, J. P.; Bubak, M.; Williams, R.; Afsarmanesh, H.; Hertzberger, B.
2000-01-01
In many plasma physical and astrophysical problems, both linear and nonlinear effects can lead to global dynamics that induce, or occur simultaneously with, local phenomena. For example, a magnetically confined plasma column can potentially posses global magnetohydrodynamic (MHD) eigenmodes with an
Vibrational frequencies in Car-Parrinello molecular dynamics.
Ong, Sheau Wei; Tok, Eng Soon; Kang, Hway Chuan
2010-12-07
Car-Parrinello molecular dynamics (CPMD) are widely used to investigate the dynamical properties of molecular systems. An important issue in such applications is the dependence of dynamical quantities such as molecular vibrational frequencies upon the fictitious orbital mass μ. Although it is known that the correct Born-Oppenheimer dynamics are recovered at zero μ, it is not clear how these dynamical quantities are to be rigorously extracted from CPMD calculations. Our work addresses this issue for vibrational frequencies. We show that when the system is sufficiently close to the ground state the calculated ionic vibrational frequencies are ω(M) = ω(0M)[1 -C(μ/M)] for small μ/M, where ω(0M) is the Born-Oppenheimer ionic frequency, M the ionic mass, and C a constant that depends upon the ion-orbital coupling force constants. Our analysis also provides a quantitative understanding of the orbital oscillation amplitudes, leading to a relationship between the adiabaticity of a system and the ion-orbital coupling constants. In particular, we show that there is a significant systematic dependence of calculated vibrational frequencies upon how close the CPMD trajectory is to the Born-Oppenheimer surface. We verify our analytical results with numerical simulations for N(2), Sn(2), and H/Si(100)-(2×1).
Computational fluid dynamics investigation of turbulent separated ...
African Journals Online (AJOL)
user
This aims to contribute to the physics of flow separation, by computing the pressure coefficients ... model belongs to the class of two-equation models, in which model transport equations are solved for two turbulence quantities k and ε. ... model two other equations are required, namely the transport equations for k and ε :.
Computational Fluid Dynamics and Ventilation Airflow
DEFF Research Database (Denmark)
Nielsen, Peter Vilhelm
2014-01-01
the principle behind CFD, the development in numerical schemes and computer size since the 1970s. Special attention is given to the selection of the correct governing equations, to the understanding of low turbulent flow, to the selection of turbulence models, and to addressing situations with more steady...
Nonlinear dynamics of the bimodal optical computer
Caulfield, H. John
1999-03-01
In the bimodal optical computer, linear and nonlinear acts occur in rapid succession generating solutions to Ax equals b. Both chaos and stochastic resonance can appear in some cases. This is the first observation of such complexity effects in optical processors.
Statistical properties of dynamical systems – Simulation and abstract computation
International Nuclear Information System (INIS)
Galatolo, Stefano; Hoyrup, Mathieu; Rojas, Cristóbal
2012-01-01
Highlights: ► A survey on results about computation and computability on the statistical properties of dynamical systems. ► Computability and non-computability results for invariant measures. ► A short proof for the computability of the convergence speed of ergodic averages. ► A kind of “constructive” version of the pointwise ergodic theorem. - Abstract: We survey an area of recent development, relating dynamics to theoretical computer science. We discuss some aspects of the theoretical simulation and computation of the long term behavior of dynamical systems. We will focus on the statistical limiting behavior and invariant measures. We present a general method allowing the algorithmic approximation at any given accuracy of invariant measures. The method can be applied in many interesting cases, as we shall explain. On the other hand, we exhibit some examples where the algorithmic approximation of invariant measures is not possible. We also explain how it is possible to compute the speed of convergence of ergodic averages (when the system is known exactly) and how this entails the computation of arbitrarily good approximations of points of the space having typical statistical behaviour (a sort of constructive version of the pointwise ergodic theorem).
Thermal conductivity of MgO periclase from equilibrium first principles molecular dynamics.
de Koker, Nico
2009-09-18
A method is presented by which the lattice thermal conductivity can be computed from first principles using relatively small system sizes and simulation times. The method uses the relation for thermal conductivity of a kinetic gas, with phonon lifetimes and frequencies determined by combining equilibrium first principles molecular dynamics and first principles lattice dynamics. To illustrate the method, the lattice conductivity is computed for MgO periclase. For individual wave vectors and vibrational modes, phonon lifetimes in periclase are found to be inversely proportional to temperature, with optic modes shorter lived than acoustic modes, contributing only approximately 5% to the lattice conductivity. Computed thermal conductivity values show excellent agreement with experimental measurements, and suggest that the radiative contribution to thermal transport in periclase starts playing a role above approximately 1500 K.
A molecular dynamics study of lithium-containing aprotic heterocyclic ionic liquid electrolytes
Lourenço, Tuanan C.; Zhang, Yong; Costa, Luciano T.; Maginn, Edward J.
2018-05-01
Classical molecular dynamics simulations were performed on twelve different ionic liquids containing aprotic heterocyclic anions doped with Li+. These ionic liquids have been shown to be promising electrolytes for lithium ion batteries. Self-diffusivities, lithium transference numbers, densities, and free volumes were computed as a function of lithium concentration. The dynamics and free volume decreased with increasing lithium concentration, and the trends were rationalized by examining the changes to the liquid structure. Of those examined in the present work, it was found that (methyloxymethyl)triethylphosphonium triazolide ionic liquids have the overall best performance.
A complex systems approach to computational molecular biology
Energy Technology Data Exchange (ETDEWEB)
Lapedes, A. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States)
1993-09-01
We report on the containing research program at Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here are the use of co-evolving adaptive neutral networks for determining predictable protein structure classifications, and the use of information theory to elucidate protein structure and function. A ``snapshot`` of the current state of research in these two topics is presented, representing the present state of two major research thrusts in the program of Genetic Data and Sequence Analysis at the Santa Fe Institute.
Eirín-López, José M
2013-01-01
The study of chromatin constitutes one of the most active research fields in life sciences, being subject to constant revisions that continuously redefine the state of the art in its knowledge. As every other rapidly changing field, chromatin biology requires clear and straightforward educational strategies able to efficiently translate such a vast body of knowledge to the classroom. With this aim, the present work describes a multidisciplinary computer lab designed to introduce undergraduate students to the dynamic nature of chromatin, within the context of the one semester course "Chromatin: Structure, Function and Evolution." This exercise is organized in three parts including (a) molecular evolutionary biology of histone families (using the H1 family as example), (b) histone structure and variation across different animal groups, and (c) effect of histone diversity on nucleosome structure and chromatin dynamics. By using freely available bioinformatic tools that can be run on common computers, the concept of chromatin dynamics is interactively illustrated from a comparative/evolutionary perspective. At the end of this computer lab, students are able to translate the bioinformatic information into a biochemical context in which the relevance of histone primary structure on chromatin dynamics is exposed. During the last 8 years this exercise has proven to be a powerful approach for teaching chromatin structure and dynamics, allowing students a higher degree of independence during the processes of learning and self-assessment. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.
DEFF Research Database (Denmark)
Galliero, Guillaume; Medvedev, Oleg; Shapiro, Alexander
2005-01-01
A 322 (2004) 151). In the current study, a fast molecular dynamics scheme has been developed to determine the values of the penetration lengths in Lennard-Jones binary systems. Results deduced from computations provide a new insight into the concept of penetration lengths. It is shown for four different...... binary liquid mixtures of non-polar components that computed penetration lengths, for various temperatures and compositions, are consistent with those deduced from experiments in the framework of the formalism of the fluctuation theory. Moreover, the mutual diffusion coefficients obtained from a coupled...
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
2014-01-01
Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585
A simple nonlinear dynamical computing device
International Nuclear Information System (INIS)
Miliotis, Abraham; Murali, K.; Sinha, Sudeshna; Ditto, William L.; Spano, Mark L.
2009-01-01
We propose and characterize an iterated map whose nonlinearity has a simple (i.e., minimal) electronic implementation. We then demonstrate explicitly how all the different fundamental logic gates can be implemented and morphed using this nonlinearity. These gates provide the full set of gates necessary to construct a general-purpose, reconfigurable computing device. As an example of how such chaotic computing devices can be exploited, we use an array of these maps to encode data and to process information. Each map can store one of M items, where M is variable and can be large. This nonlinear hardware stores data naturally in different bases or alphabets. We also show how this method of storing information can serve as a preprocessing tool for exact or inexact pattern-matching searches.
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.
Exponential rise of dynamical complexity in quantum computing through projections.
Burgarth, Daniel Klaus; Facchi, Paolo; Giovannetti, Vittorio; Nakazato, Hiromichi; Pascazio, Saverio; Yuasa, Kazuya
2014-10-10
The ability of quantum systems to host exponentially complex dynamics has the potential to revolutionize science and technology. Therefore, much effort has been devoted to developing of protocols for computation, communication and metrology, which exploit this scaling, despite formidable technical difficulties. Here we show that the mere frequent observation of a small part of a quantum system can turn its dynamics from a very simple one into an exponentially complex one, capable of universal quantum computation. After discussing examples, we go on to show that this effect is generally to be expected: almost any quantum dynamics becomes universal once 'observed' as outlined above. Conversely, we show that any complex quantum dynamics can be 'purified' into a simpler one in larger dimensions. We conclude by demonstrating that even local noise can lead to an exponentially complex dynamics.
An improved version of the Green's function molecular dynamics method
Kong, Ling Ti; Denniston, Colin; Müser, Martin H.
2011-02-01
This work presents an improved version of the Green's function molecular dynamics method (Kong et al., 2009; Campañá and Müser, 2004 [1,2]), which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only atoms near the surface. In the previous implementation, the effective elastic coefficients measured at the Γ-point were altered to reduce finite size effects: their eigenvalues corresponding to the acoustic modes were set to zero. This scheme was found to work well for simple Bravais lattices as long as only atoms within the last layer were treated as Green's function atoms. However, it failed to function as expected in all other cases. It turns out that a violation of the acoustic sum rule for the effective elastic coefficients at Γ (Kong, 2010 [3]) was responsible for this behavior. In the new version, the acoustic sum rule is enforced by adopting an iterative procedure, which is found to be physically more meaningful than the previous one. In addition, the new algorithm allows one to treat lattices with bases and the Green's function slab is no longer confined to one layer. New version program summaryProgram title: FixGFC/FixGFMD v1.12 Catalogue identifier: AECW_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECW_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 206 436 No. of bytes in distributed program, including test data, etc.: 4 314 850 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Yes. Code has been parallelized using MPI directives. RAM: Depends on the problem Classification: 7.7 External routines: LAMMPS ( http://lammps.sandia.gov/), MPI ( http
Fluid dynamics applications of the Illiac IV computer
Maccormack, R. W.; Stevens, K. G., Jr.
1976-01-01
The Illiac IV is a parallel-structure computer with computing power an order of magnitude greater than that of conventional computers. It can be used for experimental tasks in fluid dynamics which can be simulated more economically, for simulating flows that cannot be studied by experiment, and for combining computer and experimental simulations. The architecture of Illiac IV is described, and the use of its parallel operation is demonstrated on the example of its solution of the one-dimensional wave equation. For fluid dynamics problems, a special FORTRAN-like vector programming language was devised, called CFD language. Two applications are described in detail: (1) the determination of the flowfield around the space shuttle, and (2) the computation of transonic turbulent separated flow past a thick biconvex airfoil.
A general-purpose coarse-grained molecular dynamics program
Aoyagi, Takeshi; Sawa, Fumio; Shoji, Tatsuya; Fukunaga, Hiroo; Takimoto, Jun-ichi; Doi, Masao
2002-05-01
In this article, we describe a general-purpose coarse-grained molecular dynamics program COGNAC ( COarse Grained molecular dynamics program by NAgoya Cooperation). COGNAC has been developed for general molecular dynamics simulation, especially for coarse-grained polymer chain models. COGNAC can deal with general molecular models, in which each molecule consists of coarse-grained atomic units connected by chemical bonds. The chemical bonds are specified by bonding potentials for the stretching, bending and twisting of the bonds, each of which are the functions of the position coordinates of the two, three and four atomic units. COGNAC can deal with both isotropic and anisotropic interactions between the non-bonded atomic units. As an example, the Gay-Berne potential is implemented. New potential functions can be added to the list of existing potential functions by users. COGNAC can do simulations for various situations such as under constant temperature, under constant pressure, under shear and elongational deformation, etc. Some new methods are implemented in COGNAC for modeling multiphase structures of polymer blends and block copolymers. A density biased Monte Carlo method and a density biased potential method can generate equilibrium chain configurations from the results of the self-consistent field calculations. Staggered reflective boundary conditions can generate interfacial structures with smaller system size compared with those of periodic boundary conditions.
Energy Technology Data Exchange (ETDEWEB)
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul, E-mail: paul.tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig–Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)
2015-03-14
Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10{sup 3}-10{sup 5} molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.
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.
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
Energy Technology Data Exchange (ETDEWEB)
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-03-14
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Stretching siloxanes: An ab initio molecular dynamics study
Lupton, E. M.; Nonnenberg, C.; Frank, I.; Achenbach, F.; Weis, J.; Bräuchle, C.
2005-10-01
We present an ab initio molecular dynamics study of siloxane elastomers placed under tensile stress for comparison with single molecule AFM experiments. Of particular interest is stress-induced chemical bond breaking in the high force regime, where a description of the molecular electronic structure is essential to determine the rupture mechanism. We predict an ionic mechanism for the bond breaking process with a rupture force of 4.4 nN for an isolated siloxane decamer pulled at a rate of 27.3 m/s and indicate lower values at experimental polymer lengths and pulling rates.
Spectra modelling combining molecular dynamics and quantum mechanics
Czech Academy of Sciences Publication Activity Database
Novák, Vít; Bouř, Petr
2015-01-01
Roč. 22, č. 1 (2015), s. 48 ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /13./. 19.03.2015-21.03.2015, Nové Hrady] R&D Projects: GA ČR GAP208/11/0105; GA ČR GA15-09072S Grant - others:GA MŠk(CZ) LM2010005; GA MŠk(CZ) ED3.2.00/08.0144 Institutional support: RVO:61388963 Keywords : Raman scattering * molecular dynamics * autocorrelation function Subject RIV: CF - Physical ; Theoretical Chemistry
Adversarial Threshold Neural Computer for Molecular de Novo Design.
Putin, Evgeny; Asadulaev, Arip; Vanhaelen, Quentin; Ivanenkov, Yan; Aladinskaya, Anastasia V; Aliper, Alex; Zhavoronkov, Alex
2018-03-30
In this article, we propose the deep neural network Adversarial Threshold Neural Computer (ATNC). The ATNC model is intended for the de novo design of novel small-molecule organic structures. The model is based on generative adversarial network architecture and reinforcement learning. ATNC uses a Differentiable Neural Computer as a generator and has a new specific block, called adversarial threshold (AT). AT acts as a filter between the agent (generator) and the environment (discriminator + objective reward functions). Furthermore, to generate more diverse molecules we introduce a new objective reward function named Internal Diversity Clustering (IDC). In this work, ATNC is tested and compared with the ORGANIC model. Both models were trained on the SMILES string representation of the molecules, using four objective functions (internal similarity, Muegge druglikeness filter, presence or absence of sp 3 -rich fragments, and IDC). The SMILES representations of 15K druglike molecules from the ChemDiv collection were used as a training data set. For the different functions, ATNC outperforms ORGANIC. Combined with the IDC, ATNC generates 72% of valid and 77% of unique SMILES strings, while ORGANIC generates only 7% of valid and 86% of unique SMILES strings. For each set of molecules generated by ATNC and ORGANIC, we analyzed distributions of four molecular descriptors (number of atoms, molecular weight, logP, and tpsa) and calculated five chemical statistical features (internal diversity, number of unique heterocycles, number of clusters, number of singletons, and number of compounds that have not been passed through medicinal chemistry filters). Analysis of key molecular descriptors and chemical statistical features demonstrated that the molecules generated by ATNC elicited better druglikeness properties. We also performed in vitro validation of the molecules generated by ATNC; results indicated that ATNC is an effective method for producing hit compounds.
Molecular states of HeH+. Energies and dynamical couplings
International Nuclear Information System (INIS)
Macias, A.; Riera, A.; Yanez, M.
1983-01-01
We complete the molecular results reported in a previous paper by presenting additional energies (for /sup 1,3/μ states) and radial couplings (between 'μ states) of the HeH + system. These results are needed to treat elastic and inelastic charge-exchange processes when full account is taken of momentum-transfer problems. We also present a formalism to calculate radial couplings between wave functions computed with the use of different variational methods and basis sets. The detailed form of the radial couplings is discussed and related to the Barat-Lichten correlation diagram. The effect of using finite basis sets in calculatig degenerate molecular energies is also discussed
Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction
Lynch, Diane L.; Hurst, Dow P.; Shore, Derek M.; Pitman, Mike C.; Reggio, Patricia H.
2018-01-01
The cannabinoid type 1 and 2 G-protein-coupled receptors are currently important pharmacological targets with significant drug discovery potential. These receptors have been shown to display functional selectivity or biased agonism, a property currently thought to have substantial therapeutic potential. Although recent advances in crystallization techniques have provided a wealth of structural information about this important class of membrane-embedded proteins, these structures lack dynamical information. In order to fully understand the interplay of structure and function for this important class of proteins, complementary techniques that address the dynamical aspects of their function are required such as NMR as well as a variety of other spectroscopies. Complimentary to these experimental approaches is molecular dynamics, which has been effectively used to help unravel, at the atomic level, the dynamics of ligand binding and activation of these membrane-bound receptors. Here, we discuss and present several representative examples of the application of molecular dynamics simulations to the understanding of the signatures of ligand-binding and -biased signaling at the cannabinoid type 1 and 2 receptors. PMID:28750815
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)
Stone, John E; McGreevy, Ryan; Isralewitz, Barry; Schulten, Klaus
2014-01-01
Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally-determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithms vis-à-vis existing tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods.
Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy
Ocaya, R. O.; Terblans, J. J.
2017-10-01
Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.
Interface between computational fluid dynamics (CFD) and plant analysis computer codes
International Nuclear Information System (INIS)
Coffield, R.D.; Dunckhorst, F.F.; Tomlinson, E.T.; Welch, J.W.
1993-01-01
Computational fluid dynamics (CFD) can provide valuable input to the development of advanced plant analysis computer codes. The types of interfacing discussed in this paper will directly contribute to modeling and accuracy improvements throughout the plant system and should result in significant reduction of design conservatisms that have been applied to such analyses in the past
Directory of Open Access Journals (Sweden)
Qixin Liu
2014-07-01
Full Text Available This paper presents studies on the characteristics of gas molecular mean freepath in nanopores by molecular dynamics simulation. Our study results indicate that themean free path of all molecules in nanopores depend on both the radius of the nanoporeand the gas-solid interaction strength. Besides mean free path of all molecules in thenanopore, this paper highlights the gas molecular mean free path at different positions ofthe nanopore and the anisotropy of the gas molecular mean free path at nanopores. Themolecular mean free path varies with the molecule’s distance from the center of thenanopore. The least value of the mean free path occurs at the wall surface of the nanopore.The present paper found that the gas molecular mean free path is anisotropic when gas isconfined in nanopores. The radial gas molecular mean free path is much smaller than themean free path including all molecular collisions occuring in three directions. Our studyresults also indicate that when gas is confined in nanopores the gas molecule number densitydoes not affect the gas molecular mean free path in the same way as it does for the gas inunbounded space. These study results may bring new insights into understanding the gasflow’s characteristic at nanoscale.
Dynamics and control of trajectory tubes theory and computation
Kurzhanski, Alexander B
2014-01-01
This monograph presents theoretical methods involving the Hamilton–Jacobi–Bellman formalism in conjunction with set-valued techniques of nonlinear analysis to solve significant problems in dynamics and control. The emphasis is on issues of reachability, feedback control synthesis under complex state constraints, hard or double bounds on controls, and performance in finite time. Guaranteed state estimation, output feedback control, and hybrid dynamics are also discussed. Although the focus is on systems with linear structure, the authors indicate how to apply each approach to nonlinear and nonconvex systems. The main theoretical results lead to computational schemes based on extensions of ellipsoidal calculus that provide complete solutions to the problems. These computational schemes in turn yield software tools that can be applied effectively to high-dimensional systems. Dynamics and Control of Trajectory Tubes: Theory and Computation will interest graduate and senior undergraduate students, as well as...
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
Molecular Dynamics and Electron Density Studies of Siderophores and Peptides.
Fidelis, Krzysztof Andrzej
1990-08-01
The dissertation comprises three separate studies of siderophores and peptides. In the first of these studies the relative potential energies for a series of diastereomers of a siderophore neocoprogen I are evaluated with molecular mechanics force field methods. Charges on the hydroxamate moiety are determined with a synthetic model siderophore compound using valence population refinements, and alternatively, with the theoretical ab initio/ESP calculations. The single diastereomer found in the crystal structure is among four characterized by the low potential energy, while prevalence of Delta vs. Lambda configuration about the iron is found to be a property of the entire series. In the second study the crystal structure of a ferrichrome siderophore ferrirhodin is reported. The crystal structure conformation of the molecular backbone as well as the iron coordination geometry compare well with other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using the methods of molecular mechanics. The third study a 300 ps, 300 K, in vacuo molecular dynamics simulation of didemnin A and B yields distinct molecular conformers, which are different from the one found in the crystal structure or modeled in solution, using the Nuclear Overhauser Effect data. Evaluations of the relative potential energy are performed with short 10 ps simulations in solution. Didemnins are natural depsipeptides isolated from a Caribbean tunicate and characterized by particularly potent antiproliferative and immunomodulatory activity. Conformationally rigid and flexible regions of the molecule are described. A short review of the molecular mechanics methodology is given in the introduction.
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
Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates
International Nuclear Information System (INIS)
Zhang Junfang; Rivero, Mayela; Choi, S K
2007-01-01
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
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.
Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar
) in water and organic solvents. The effects of solvent on structural and dynamical enzyme properties are studied, and special attention is given to how enzyme properties in organic solvents are affected by the hydration level, which is shown to be related to the water activity. In experimental studies...... 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......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...
Fluid dynamics parallel computer development at NASA Langley Research Center
Townsend, James C.; Zang, Thomas A.; Dwoyer, Douglas L.
1987-01-01
To accomplish more detailed simulations of highly complex flows, such as the transition to turbulence, fluid dynamics research requires computers much more powerful than any available today. Only parallel processing on multiple-processor computers offers hope for achieving the required effective speeds. Looking ahead to the use of these machines, the fluid dynamicist faces three issues: algorithm development for near-term parallel computers, architecture development for future computer power increases, and assessment of possible advantages of special purpose designs. Two projects at NASA Langley address these issues. Software development and algorithm exploration is being done on the FLEX/32 Parallel Processing Research Computer. New architecture features are being explored in the special purpose hardware design of the Navier-Stokes Computer. These projects are complementary and are producing promising results.
Thermal Transport in Fullerene Derivatives Using Molecular Dynamics Simulations
Chen, Liang; Wang, Xiaojia; Kumar, Satish
2015-01-01
In order to study the effects of alkyl chain on the thermal properties of fullerene derivatives, we perform molecular dynamics (MD) simulations to predict the thermal conductivity of fullerene (C60) and its derivative phenyl-C61-butyric acid methyl ester (PCBM). The results of non-equilibrium MD simulations show a length-dependent thermal conductivity for C60 but not for PCBM. The thermal conductivity of C60, obtained from the linear extrapolation of inverse conductivity vs. inverse length cu...
Spin dynamics of an ultra-small nanoscale molecular magnet
Directory of Open Access Journals (Sweden)
Ciftja Orion
2007-01-01
Full Text Available AbstractWe present mathematical transformations which allow us to calculate the spin dynamics of an ultra-small nanoscale molecular magnet consisting of a dimer system of classical (high Heisenberg spins. We derive exact analytic expressions (in integral form for the time-dependent spin autocorrelation function and several other quantities. The properties of the time-dependent spin autocorrelation function in terms of various coupling parameters and temperature are discussed in detail.
Molecular dynamics simulations of freezing of water and salt solutions
Czech Academy of Sciences Publication Activity Database
Vrbka, Luboš; Jungwirth, Pavel
2007-01-01
Roč. 134, č. 1 (2007), s. 64-70 ISSN 0167-7322 R&D Projects: GA MŠk LC512; GA ČR(CZ) GD203/05/H001 Institutional research plan: CEZ:AV0Z40550506 Keywords : ice freezing * salt ions * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.982, year: 2007
Advances in computational dynamics of particles, materials and structures a unified approach
Har, Jason
2012-01-01
Computational methods for the modeling and simulation of the dynamic response and behavior of particles, materials and structural systems have had a profound influence on science, engineering and technology. Complex science and engineering applications dealing with complicated structural geometries and materials that would be very difficult to treat using analytical methods have been successfully simulated using computational tools. With the incorporation of quantum, molecular and biological mechanics into new models, these methods are poised to play an even bigger role in the future. Ad
Liang, Jie; Qian, Hong
2010-01-01
Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand “complex behavior” and complexity theory, and from which important biological insight can be gained. PMID:24999297
Computational Fluid and Particle Dynamics in the Human Respiratory System
Tu, Jiyuan; Ahmadi, Goodarz
2013-01-01
Traditional research methodologies in the human respiratory system have always been challenging due to their invasive nature. Recent advances in medical imaging and computational fluid dynamics (CFD) have accelerated this research. This book compiles and details recent advances in the modelling of the respiratory system for researchers, engineers, scientists, and health practitioners. It breaks down the complexities of this field and provides both students and scientists with an introduction and starting point to the physiology of the respiratory system, fluid dynamics and advanced CFD modeling tools. In addition to a brief introduction to the physics of the respiratory system and an overview of computational methods, the book contains best-practice guidelines for establishing high-quality computational models and simulations. Inspiration for new simulations can be gained through innovative case studies as well as hands-on practice using pre-made computational code. Last but not least, students and researcher...
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.
A Molecular Dynamics Simulation of the Turbulent Couette Minimal Flow Unit
Smith, Edward
2016-11-01
What happens to turbulent motions below the Kolmogorov length scale? In order to explore this question, a 300 million molecule Molecular Dynamics (MD) simulation is presented for the minimal Couette channel in which turbulence can be sustained. The regeneration cycle and turbulent statistics show excellent agreement to continuum based computational fluid dynamics (CFD) at Re=400. As MD requires only Newton's laws and a form of inter-molecular potential, it captures a much greater range of phenomena without requiring the assumptions of Newton's law of viscosity, thermodynamic equilibrium, fluid isotropy or the limitation of grid resolution. The fundamental nature of MD means it is uniquely placed to explore the nature of turbulent transport. A number of unique insights from MD are presented, including energy budgets, sub-grid turbulent energy spectra, probability density functions, Lagrangian statistics and fluid wall interactions. EPSRC Post Doctoral Prize Fellowship.
Molecular dynamics study of the ternary Cu50Ti25Zr25 bulk glass forming alloy
Directory of Open Access Journals (Sweden)
Celtek M.
2011-05-01
Full Text Available The structure and thermodynamic properties of a ternary Cu50Ti25Zr25 metallic glass forming alloy in solid-liquid to glass phases were studied using molecular dynamics (MD method based on tight-binding (TB potentials. An atomic description of the melting, glass formation and crystallization process has been analyzed using different heating and cooling rates. The computed Glass Forming Ability (GFA parameters are in good agreement with experimental data. The structure analysis of the Cu50Ti25Zr25 based on molecular dynamics simulation will be also presented and compared with available MD results. We have also discussed the crystallization transition with two different interatomic potentials used in this work
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.
Computational fluid dynamics open a new world for designers
International Nuclear Information System (INIS)
Mitsuda, Masahiko; Hosokawa, Yoshiyuki; Oda, Tsuyoshi; Kobayashi, Toshiyuki; Akamatsu, Hiroshi; Yamada, Hitoshi
2001-01-01
As a result of recent improvements in computer performance, practical applications of computational fluid dynamics (CFD) are becoming increasingly common. No longer is the macroscopic flow field merely visualized. It has now become possible to closely investigate boundary issues such as the flow force, the heat transfer, the solid-gas-liquid interface motion. Detailed fluid phenomena is now available to designers and this promises great future developments for various processes. This paper discusses these exciting new developments. (author)
Computational Fluid Dynamics. [numerical methods and algorithm development
1992-01-01
This collection of papers was presented at the Computational Fluid Dynamics (CFD) Conference held at Ames Research Center in California on March 12 through 14, 1991. It is an overview of CFD activities at NASA Lewis Research Center. The main thrust of computational work at Lewis is aimed at propulsion systems. Specific issues related to propulsion CFD and associated modeling will also be presented. Examples of results obtained with the most recent algorithm development will also be presented.
Improved Pyrolysis Micro reactor Design via Computational Fluid Dynamics Simulations
2017-05-23
NUMBER (Include area code) 23 May 2017 Briefing Charts 25 April 2017 - 23 May 2017 Improved Pyrolysis Micro-reactor Design via Computational Fluid... PYROLYSIS MICRO-REACTOR DESIGN VIA COMPUTATIONAL FLUID DYNAMICS SIMULATIONS Ghanshyam L. Vaghjiani* DISTRIBUTION A: Approved for public release...Approved for public release, distribution unlimited. PA Clearance 17247 Chen-Source (>240 references from SciFinder as of 5/1/17): Flash pyrolysis
Molecular dynamics coupled with a virtual system for effective conformational sampling.
Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi
2018-02-21
An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Molecular-dynamics simulations of urea nucleation from aqueous solution
Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele
2015-01-01
Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete. PMID:25492932
Maldonado, E; Roth, M W; Gray, Paul A
2009-06-01
We present and discuss the results of molecular dynamics computer simulations of crude oil confined between graphene planes. The crude oil is represented as a mixture of alkanes having 6 method of separating alkane mixtures at temperatures significantly different from those of conventional refining processes.
Bulacu, M; van der Giessen, E
2005-01-01
Extensive molecular-dynamics simulations have been performed to study the effect of chain conformational rigidity, controlled by bending and torsion potentials, on self-diffusion in polymer melts. The polymer model employs a novel torsion potential that avoids computational singularities without the
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
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......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...
MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.
Directory of Open Access Journals (Sweden)
Mikhail Shugay
2017-05-01
Full Text Available Unique molecular identifiers (UMIs show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants. Using an extensive set of benchmark datasets including gold-standard biological samples with known variant frequencies, cell-free DNA from tumor patient blood samples and publicly available UMI-encoded datasets we demonstrate that our method is both robust and efficient in calling rare variants. The versatility of our software is supported by accurate results obtained for both tumor DNA and viral RNA samples in datasets prepared using three different UMI-based protocols.
Large scale molecular dynamics simulations of nuclear pasta
Horowitz, C. J.; Berry, D.; Briggs, C.; Chapman, M.; Clark, E.; Schneider, A.
2014-09-01
We report large-scale molecular dynamics simulations of nuclear pasta using from 50,000 to more than 3,000,000 nucleons. We use a simple phenomenological two-nucleon potential that reproduces nuclear saturation. We find a complex ``nuclear waffle'' phase in addition to more conventional rod, plate, and sphere phases. We also find long-lived topological defects involving screw like dislocations that may reduce the electrical conductivity and thermal conductivity of lasagna phases. From MD trajectories we calculate a variety of quantities including static structure factor, dynamical response function, shear modulus and breaking strain. We report large-scale molecular dynamics simulations of nuclear pasta using from 50,000 to more than 3,000,000 nucleons. We use a simple phenomenological two-nucleon potential that reproduces nuclear saturation. We find a complex ``nuclear waffle'' phase in addition to more conventional rod, plate, and sphere phases. We also find long-lived topological defects involving screw like dislocations that may reduce the electrical conductivity and thermal conductivity of lasagna phases. From MD trajectories we calculate a variety of quantities including static structure factor, dynamical response function, shear modulus and breaking strain. Supported in parts by DOE Grants No. DE-FG02-87ER40365 (Indiana University) and No. DE-SC0008808 (NUCLEI SciDAC Collaboration).
The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering
Zaccai, Giuseppe; Natali, Francesca; Peters, Judith; Řihová, Martina; Zimmerman, Ella; Ollivier, J.; Combet, J.; Maurel, Marie-Christine; Bashan, Anat; Yonath, Ada
2016-11-01
Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.
The dynamics of molecular evolution over 60,000 generations.
Good, Benjamin H; McDonald, Michael J; Barrick, Jeffrey E; Lenski, Richard E; Desai, Michael M
2017-11-02
The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. However, it is difficult to observe these dynamics directly over long periods and across entire genomes. Here we analyse the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation intervals through sixty thousand generations. Although the rate of fitness gain declines over time, molecular evolution is characterized by signatures of rapid adaptation throughout the duration of the experiment, with multiple beneficial variants simultaneously competing for dominance in each population. Interactions between ecological and evolutionary processes play an important role, as long-term quasi-stable coexistence arises spontaneously in most populations, and evolution continues within each clade. We also present evidence that the targets of natural selection change over time, as epistasis and historical contingency alter the strength of selection on different genes. Together, these results show that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed.
Giorgino, Toni
2014-03-01
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED’s rich syntax to define collective variables (CVs) and VMD’s chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving reference snapshots used for RMSD or native contacts calculations, can be built through dialogs that provide a synoptic view of the available options. Scripts can be either exported for use in simulation programs, or evaluated on the currently loaded molecular trajectories. Script development takes place without leaving VMD, thus enabling an incremental try-see-modify development model for molecular metrics.
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.
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
A rotary nano ion pump: a molecular dynamics study.
Lohrasebi, A; Feshanjerdi, M
2012-09-01
The dynamics of a rotary nano ion pump, inspired by the F (0) part of the F(0)F(1)-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation.
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
International Nuclear Information System (INIS)
Lerbret, A.; Affouard, F.; Bordat, P.; Hedoux, A.; Guinet, Y.; Descamps, M.
2008-01-01
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
Dynamics of dissipative systems and computational physics
International Nuclear Information System (INIS)
Adam, Gh.; Scutaru, H.; Ixaru, L.; Adam, S.; Rizea, M.; Stefanescu, E.; Mihalache, D.; Mazilu, D.; Crasovan, L.
2002-01-01
During the first year of research activity in the frame of this project there have been investigated two main topics: I. Dynamics of systems of fermions in complex dissipative media; II. Solitons with topologic charge in dissipative systems. An essential problem of the quantum information systems is the controllability and observability of the quantum states, generally described by Lindblad's master equation with phenomenological coefficients. In its usual form, this equation describes a decay of the mean-values, but not necessarily the expected decaying transitions. The basic and very difficult problem of a dissipative quantum theory is to project the evolution of the total system (the system of interest + the environment) on the space of the system of interest. In this case, one obtains a quantum master equation where the system evolution is described by two terms: 1) a Hamiltonian term for the processes with energy conservation, and 2) a non-Hamiltonian term with coefficients depending on the dissipative coupling. That means that a master equation is based on some approximations enabling the replacement of the operators of the dissipative environment with average value coefficients. It is often assumed that the evolution operators of the dissipative system define a semigroup, not a group as in the case of an isolated system. In this framework, Lindblad obtained a quantum master equation in agreement with all the quantum-mechanical principles. However, the Lindblad master equation was unable to secure a correct description of the decaying states. To do that, one has to take into account the transition operators between the system eigenstates with appropriate coefficients. Within this investigation, we have obtained an equation obeying to this requirement, giving the ρ(t) time derivative in terms of creation-annihilation operators of the single-particle states |i>, and λ ij , representing the dissipative coefficients, the microscopic expressions of which are
Computational fluid dynamics simulations of light water reactor flows
International Nuclear Information System (INIS)
Tzanos, C.P.; Weber, D.P.
1999-01-01
Advances in computational fluid dynamics (CFD), turbulence simulation, and parallel computing have made feasible the development of three-dimensional (3-D) single-phase and two-phase flow CFD codes that can simulate fluid flow and heat transfer in realistic reactor geometries with significantly reduced reliance, especially in single phase, on empirical correlations. The objective of this work was to assess the predictive power and computational efficiency of a CFD code in the analysis of a challenging single-phase light water reactor problem, as well as to identify areas where further improvements are needed
Morphing-Based Shape Optimization in Computational Fluid Dynamics
Rousseau, Yannick; Men'Shov, Igor; Nakamura, Yoshiaki
In this paper, a Morphing-based Shape Optimization (MbSO) technique is presented for solving Optimum-Shape Design (OSD) problems in Computational Fluid Dynamics (CFD). The proposed method couples Free-Form Deformation (FFD) and Evolutionary Computation, and, as its name suggests, relies on the morphing of shape and computational domain, rather than direct shape parameterization. Advantages of the FFD approach compared to traditional parameterization are first discussed. Then, examples of shape and grid deformations by FFD are presented. Finally, the MbSO approach is illustrated and applied through an example: the design of an airfoil for a future Mars exploration airplane.
Dynamic computer simulation of the Fort St. Vrain steam turbines
International Nuclear Information System (INIS)
Conklin, J.C.
1983-01-01
A computer simulation is described for the dynamic response of the Fort St. Vrain nuclear reactor regenerative intermediate- and low-pressure steam turbines. The fundamental computer-modeling assumptions for the turbines and feedwater heaters are developed. A turbine heat balance specifying steam and feedwater conditions at a given generator load and the volumes of the feedwater heaters are all that are necessary as descriptive input parameters. Actual plant data for a generator load reduction from 100 to 50% power (which occurred as part of a plant transient on November 9, 1981) are compared with computer-generated predictions, with reasonably good agreement
Computational Psychometrics for Modeling System Dynamics during Stressful Disasters
Directory of Open Access Journals (Sweden)
Pietro Cipresso
2017-08-01
Full Text Available Disasters can be very stressful events. However, computational models of stress require data that might be very difficult to collect during disasters. Moreover, personal experiences are not repeatable, so it is not possible to collect bottom-up information when building a coherent model. To overcome these problems, we propose the use of computational models and virtual reality integration to recreate disaster situations, while examining possible dynamics in order to understand human behavior and relative consequences. By providing realistic parameters associated with disaster situations, computational scientists can work more closely with emergency responders to improve the quality of interventions in the future.