Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton
2017-03-28
Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.
Force-Field Functor Theory: Classical Force-Fields which Reproduce Equilibrium Quantum Distributions
Directory of Open Access Journals (Sweden)
Ryan eBabbush
2013-10-01
Full Text Available Feynman and Hibbs were the first to variationally determine an effective potential whose associated classical canonical ensemble approximates the exact quantum partition function. We examine the existence of a map between the local potential and an effective classical potential which matches the exact quantum equilibrium density and partition function. The usefulness of such a mapping rests in its ability to readily improve Born-Oppenheimer potentials for use with classical sampling. We show that such a map is unique and must exist. To explore the feasibility of using this result to improve classical molecular mechanics, we numerically produce a map from a library of randomly generated one-dimensional potential/effective potential pairs then evaluate its performance on independent test problems. We also apply the map to simulate liquid para-hydrogen, finding that the resulting radial pair distribution functions agree well with path integral Monte Carlo simulations. The surprising accessibility and transferability of the technique suggest a quantitative route to adapting Born-Oppenheimer potentials, with a motivation similar in spirit to the powerful ideas and approximations of density functional theory.
Thermodynamic properties for applications in chemical industry via classical force fields.
Guevara-Carrion, Gabriela; Hasse, Hans; Vrabec, Jadran
2012-01-01
Thermodynamic properties of fluids are of key importance for the chemical industry. Presently, the fluid property models used in process design and optimization are mostly equations of state or G (E) models, which are parameterized using experimental data. Molecular modeling and simulation based on classical force fields is a promising alternative route, which in many cases reasonably complements the well established methods. This chapter gives an introduction to the state-of-the-art in this field regarding molecular models, simulation methods, and tools. Attention is given to the way modeling and simulation on the scale of molecular force fields interact with other scales, which is mainly by parameter inheritance. Parameters for molecular force fields are determined both bottom-up from quantum chemistry and top-down from experimental data. Commonly used functional forms for describing the intra- and intermolecular interactions are presented. Several approaches for ab initio to empirical force field parameterization are discussed. Some transferable force field families, which are frequently used in chemical engineering applications, are described. Furthermore, some examples of force fields that were parameterized for specific molecules are given. Molecular dynamics and Monte Carlo methods for the calculation of transport properties and vapor-liquid equilibria are introduced. Two case studies are presented. First, using liquid ammonia as an example, the capabilities of semi-empirical force fields, parameterized on the basis of quantum chemical information and experimental data, are discussed with respect to thermodynamic properties that are relevant for the chemical industry. Second, the ability of molecular simulation methods to describe accurately vapor-liquid equilibrium properties of binary mixtures containing CO(2) is shown.
Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.
Matthews, James F; Beckham, Gregg T; Bergenstråhle-Wohlert, Malin; Brady, John W; Himmel, Michael E; Crowley, Michael F
2012-02-14
Molecular dynamics simulations of cellulose have recently become more prevalent due to increased interest in renewable energy applications, and many atomistic and coarse-grained force fields exist that can be applied to cellulose. However, to date no systematic comparison between carbohydrate force fields has been conducted for this important system. To that end, we present a molecular dynamics simulation study of hydrated, 36-chain cellulose Iβ microfibrils at room temperature with three carbohydrate force fields (CHARMM35, GLYCAM06, and Gromos 45a4) up to the near-microsecond time scale. Our results indicate that each of these simulated microfibrils diverge from the cellulose Iβ crystal structure to varying degrees under the conditions tested. The CHARMM35 and GLYCAM06 force fields eventually result in structures similar to those observed at 500 K with the same force fields, which are consistent with the experimentally observed high-temperature behavior of cellulose I. The third force field, Gromos 45a4, produces behavior significantly different from experiment, from the other two force fields, and from previously reported simulations with this force field using shorter simulation times and constrained periodic boundary conditions. For the GLYCAM06 force field, initial hydrogen-bond conformations and choice of electrostatic scaling factors significantly affect the rate of structural divergence. Our results suggest dramatically different time scales for convergence of properties of interest, which is important in the design of computational studies and comparisons to experimental data. This study highlights that further experimental and theoretical work is required to understand the structure of small diameter cellulose microfibrils typical of plant cellulose.
Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán
2018-04-05
Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.
All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model
Savelyev, Alexey; MacKerell, Alexander D.
2014-01-01
Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978
Riniker, Sereina
2018-03-26
In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.
Interaction between benzenedithiolate and gold: Classical force field for chemical bonding
Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.
2005-06-01
We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.
Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7
Directory of Open Access Journals (Sweden)
A. V. Sulimov
2017-01-01
Full Text Available Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.
Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.
Sulimov, A V; Kutov, D C; Katkova, E V; Sulimov, V B
2017-01-01
Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.
Lemkul, Justin A; MacKerell, Alexander D
2017-05-09
Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.
Quantum mechanical force fields for condensed phase molecular simulations
Giese, Timothy J.; York, Darrin M.
2017-09-01
Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.
The MARTINI force field : Coarse grained model for biomolecular simulations
Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge; Tieleman, D. Peter; de Vries, Alex H.
2007-01-01
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To
Communication: Multiple atomistic force fields in a single enhanced sampling simulation
Energy Technology Data Exchange (ETDEWEB)
Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)
2015-07-14
The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.
Villa, Alessandra; Fan, Hao; Wassenaar, Tsjerk; Mark, Alan E.
2007-01-01
The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ
Artificial force fields for multi-agent simulations of maritime traffic and risk estimation
Xiao, F.; Ligteringen, H.; Van Gulijk, C.; Ale, B.J.M.
2012-01-01
A probabilistic risk model is designed to estimate probabilities of collisions for shipping accidents in busy waterways. We propose a method based on multi-agent simulation that uses an artificial force field to model ship maneuvers. The artificial force field is calibrated by AIS data (Automatic
Low-energy oxygen bombardment of silicon by MD simulations making use of a reactive force field
International Nuclear Information System (INIS)
Philipp, P.; Briquet, L.; Wirtz, T.; Kieffer, J.
2011-01-01
In the field of Secondary Ion Mass Spectrometry (SIMS), ion-matter interactions have been largely investigated by numerical simulations. For MD simulations related to inorganic samples, mostly classical force fields assuming stable bonding structure have been used. In materials science, level-three force fields capable of simulating the breaking and formation of chemical bonds have recently been conceived. One such force field has been developed by John Kieffer . This potential includes directional covalent bonds, Coulomb and dipolar interaction terms, dispersion terms, etc. Important features of this force field for simulating systems that undergo significant structural reorganization are (i) the ability to account for the redistribution of electron density upon ionization, formation, or breaking of bonds, through a charge transfer term, and (ii) the fact that the angular constraints dynamically adjust when a change in the coordination number of an atom occurs. In this paper, the modification of the force field to allow for an exact description of the sputtering process, the influence of this modification on previous results obtained for phase transitions in glasses as well as properties of particles sputtered at 250-1000 eV from a mono-crystalline silicon sample will be presented. The simulation results agree qualitatively with predictions from experiments or models. Most atoms are sputtered from the first monolayer: for an impact energy of 250 eV up to 86% of the atoms are sputtered from the first monolayer and for 750 eV, this percentage drops to 61%, with 89% of the atoms being sputtered from the first two monolayers. For sputtering yields, 250 and 500 eV results agree with experimental data, but for 750 eV sub-channelling in the pristine sample becomes more important than in experiments where samples turn amorphous under ion bombardment.
Cole, Daniel J; Payne, Mike C; Csányi, Gábor; Spearing, S Mark; Colombi Ciacchi, Lucio
2007-11-28
We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidized Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO(2) polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress, and interactions with single water molecules of a natively oxidized Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidized and amorphous silica surfaces of 97 and 90 mJm(2), respectively, at a water adsorption coverage of approximately 1 ML. The difference arises from the stronger interaction of the natively oxidized surface with liquid water, resulting in a higher heat of immersion (203 vs 166 mJm(2)), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller densities with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account.
Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).
Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.
Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui
2016-03-05
The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
Lee, M.W.; Meuwly, M.
2013-01-01
The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.
Lee, Kuo Hao; Chen, Jianhan
2017-06-15
Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.
Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele
2015-10-01
It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.
Miller, Mark S.; Lay, Wesley K.
2016-01-01
Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide. PMID:27052117
Polarization effects in molecular mechanical force fields
Energy Technology Data Exchange (ETDEWEB)
Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)
2009-08-19
The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)
Intermolecular Force Field Parameters Optimization for Computer Simulations of CH4 in ZIF-8
Directory of Open Access Journals (Sweden)
Phannika Kanthima
2016-01-01
Full Text Available The differential evolution (DE algorithm is applied for obtaining the optimized intermolecular interaction parameters between CH4 and 2-methylimidazolate ([C4N2H5]− using quantum binding energies of CH4-[C4N2H5]− complexes. The initial parameters and their upper/lower bounds are obtained from the general AMBER force field. The DE optimized and the AMBER parameters are then used in the molecular dynamics (MD simulations of CH4 molecules in the frameworks of ZIF-8. The results show that the DE parameters are better for representing the quantum interaction energies than the AMBER parameters. The dynamical and structural behaviors obtained from MD simulations with both sets of parameters are also of notable differences.
International Nuclear Information System (INIS)
Pacaud, Fabien
2016-01-01
as result of the nuclear waste vitrification, the knowledge and understanding of the dynamic and structural properties of glasses, including the behavior of radionuclides, is important (in liquid and solid phases). It can influence the glass waste properties, the lifetime of the vitrification process and the amount of radionuclides introduced in the glass matrix. Molecular dynamic simulations have been done to study the influence of the glass matrix composition into the structural and dynamic properties of the glass. a simplified glass, with 3 major oxides of the R7T7 glass such as SiO_2, B_2O_3 and Na_2O, have been used to simulate the R7T7 industrial nuclear glass (a 30 oxides glass). The inclusion of La_2O_3 allows us to simulate the impact of fission products and minor actinides into the properties of the glass matrix. Both systems, the SiO_2-B_2O_3-Na_2O and SiO_2-B_2O_3-Na_2O-La_2O_3, allow us to study the sodium and lanthanum effect on the properties of the glass. During this work, a polarizable force field has been developed to do these simulations. The results obtained at room temperature let us reproduce the experimental results of the structure, the distribution of BIII/BIV and the density. a study has been done on the viscosity and electrical conductivity of the liquid. The distribution BIV/BIII and the influence of the structural changes on the density along with the temperature have also been observed with thermal quenching. The current limits of this approach are also described. (author) [fr
Czech Academy of Sciences Publication Activity Database
Nezbeda, Ivo; Moučka, F.; Smith, W.R.
2016-01-01
Roč. 114, č. 11 (2016), s. 1665-1690 ISSN 0026-8976 R&D Projects: GA ČR GA15-19542S Grant - others:NSERC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : force fields * chemical potentials * aqueous electrolytes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.870, year: 2016
Müller, Erich A; Jackson, George
2014-01-01
A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.
Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.
2018-05-01
Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.
Energy Technology Data Exchange (ETDEWEB)
MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu [Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801 (United States); Kashyap, Hemant K. [Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); DeVane, Russell H. [Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069 (United States); Shinoda, Wataru [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Klauda, Jeffery B. [Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)
2015-12-28
The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.
Snyder, James A; Abramyan, Tigran; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A
2012-12-01
Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.
Energy Technology Data Exchange (ETDEWEB)
Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)
2014-04-07
We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.
Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F; Harger, Matthew; Torabifard, Hedieh; Cisneros, G Andrés; Schnieders, Michael J; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y; Ponder, Jay W; Piquemal, Jean-Philip
2018-01-28
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over
International Nuclear Information System (INIS)
Abdoli, A; Mirzaee, I; Purmahmod, N; Anvari, A
2008-01-01
Among all active flow control methods, EHD, MHD and EMHD are the only methods which operate on the basis of body force induction on flow field. The EHD plasma actuator is the proper method which has been used in various flow control applications recently. In this paper, the effects of different body force fields on different domains have been studied for separation control on NACA 0021 and the results have been discussed. The airflow velocity has been assumed to be 35 m s -1 at a post-stall angle of attack of 23 deg. Three different domains have been used around the airfoil to investigate body forces with different strengths and directions and those which give the best result in separation control have been obtained for each domain. It has been shown that the results could be used for optimizing the plasma actuator by manipulating its electrode configuration. Two non-dimensional numbers, A b and D c , have been obtained and validated by different applied body forces. These numbers have been defined for plasma actuators to show their efficiency in different applications
Energy Technology Data Exchange (ETDEWEB)
Abdoli, A; Mirzaee, I; Purmahmod, N [Faculty of Engineering, Urmia University, Urmia (Iran, Islamic Republic of); Anvari, A [Department of Physics, Sharif University of Technology, Tehran (Iran, Islamic Republic of)], E-mail: ab.abdoli@gmail.com
2008-09-07
Among all active flow control methods, EHD, MHD and EMHD are the only methods which operate on the basis of body force induction on flow field. The EHD plasma actuator is the proper method which has been used in various flow control applications recently. In this paper, the effects of different body force fields on different domains have been studied for separation control on NACA 0021 and the results have been discussed. The airflow velocity has been assumed to be 35 m s{sup -1} at a post-stall angle of attack of 23 deg. Three different domains have been used around the airfoil to investigate body forces with different strengths and directions and those which give the best result in separation control have been obtained for each domain. It has been shown that the results could be used for optimizing the plasma actuator by manipulating its electrode configuration. Two non-dimensional numbers, A{sub b} and D{sub c}, have been obtained and validated by different applied body forces. These numbers have been defined for plasma actuators to show their efficiency in different applications.
DEFF Research Database (Denmark)
Siani, Pablo; de Souza, R M; Dias, L G
2016-01-01
our new data of all-atom and coarse-grained simulations of hydroperoxidized lipid monolayer and bilayer systems and (iii) provide a comparison of the MARTINI and ELBA coarse grained force fields for lipid bilayer systems. We show that the better electrostatic treatment of interactions in ELBA is able...
Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field
Directory of Open Access Journals (Sweden)
Longhua Yang
2016-09-01
Full Text Available Cytochrome c oxidase (CcO is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8 Å X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F, we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
Qi, Yifei; Ingolfsson, Helgi I.; Cheng, Xi; Lee, Jumin; Marrink, Siewert J.; Im, Wonpil
Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed
Ervik, Åsmund; Serratos, Guadalupe Jiménez; Müller, Erich A.
2017-03-01
We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT- γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid-liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.
Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor
2018-03-01
The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.
Pang, Yujia; Li, Wenliang; Zhang, Jingping
2017-09-15
A novel type of porous organic frameworks, based on Mg-porphyrin, with diamond-like topology, named POF-Mgs is computationally designed, and the gas uptakes of CO 2 , H 2 , N 2 , and H 2 O in POF-Mgs are investigated by Grand canonical Monte Carlo simulations based on first-principles derived force fields (FF). The FF, which describes the interactions between POF-Mgs and gases, are fitted by dispersion corrected double-hybrid density functional theory, B2PLYP-D3. The good agreement between the obtained FF and the first-principle energies data confirms the reliability of the FF. Furthermore our simulation shows the presence of a small amount of H 2 O (≤ 0.01 kPa) does not much affect the adsorption quantity of CO 2 , but the presence of higher partial pressure of H 2 O (≥ 0.1 kPa) results in the CO 2 adsorption decrease significantly. The good performance of POF-Mgs in the simulation inspires us to design novel porous materials experimentally for gas adsorption and purification. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
The Martini Coarse-Grained Force Field
Periole, X.; Marrink, S.J.; Monticelli, Luca; Salonen, Emppu
2013-01-01
The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical
Energy Technology Data Exchange (ETDEWEB)
Raiteri, Paolo; Gale, Julian D [Nanochemistry Research Institute, Department of Chemistry, Curtin University, GPO Box 1987, Perth, WA 6845 (Australia); Bussi, Giovanni, E-mail: paolo@ivec.org, E-mail: julian@ivec.org [Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste (Italy)
2011-08-24
A new reactive force field to describe proton diffusion within the solid oxide fuel cell material BaZrO{sub 3} has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO{sub 3} have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.
International Nuclear Information System (INIS)
Nayebi, Payman; Zaminpayma, Esmaeil
2016-01-01
In this paper, we performed molecular dynamic simulations by Reax force field to study the mechanical properties of graphene–polythiophene nanocomposite. By computing elastic constant, breaking stress, breaking strain and Young's modulus from the stress–strain curve for the nanocomposites, we investigated effects of tension orientation, graphene loading to the polymer, temperature of nanocomposite and defect of graphene on these mechanical characters. It is found that mechanical characters of tension along the zigzag orientation are higher than other directions. Also, by increasing the weight concentration of graphene in composite, the Young's modulus and breaking strain increase. Our results showed that the Young's modulus decreased with increasing temperature. Finally by applying defect on graphene structure, we found that one atom missing defect has lower Young's modulus. Also, by increasing the defects concentration, elastic modulus decreases gradually. - Highlights: • We studied mechanical properties of graphene–polythiophene nanocomposite. • Mechanical characters of tension along the zigzag are higher than other directions. • By increasing the weight concentration of graphene in composite, the Young's modulus increases. • Young's modulus decreased with increasing temperature. • By increasing the defects concentration, elastic modulus decreases gradually.
International Nuclear Information System (INIS)
Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof
2015-01-01
A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities
Savelyev, Alexey; MacKerell, Alexander D.
2015-01-01
In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte so...
Can quantum imaging be classically simulated?
D'Angelo, Milena; Shih, Yanhua
2003-01-01
Quantum imaging has been demonstrated since 1995 by using entangled photon pairs. The physics community named these experiments "ghost image", "quantum crypto-FAX", "ghost interference", etc. Recently, Bennink et al. simulated the "ghost" imaging experiment by two co-rotating k-vector correlated lasers. Did the classical simulation simulate the quantum aspect of the "ghost" image? We wish to provide an answer. In fact, the simulation is very similar to a historical model of local realism. The...
Czech Academy of Sciences Publication Activity Database
Beššeová, Ivana; Banáš, Pavel; Kührová, P.; Košinová, P.; Otyepka, Michal; Šponer, Jiří
Roč. 116, č. 33 ( 2012 ), s. 9899-9916 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034; GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476 Grant - others:GA AV ČR(CZ) GPP301/11/P558 Program:GP Institutional research plan: CEZ:AV0Z50040702 Keywords : A-RNA * molecular dynamics * force field Subject RIV: BO - Biophysics Impact factor: 3.607, year: 2012
Perspective: Ab initio force field methods derived from quantum mechanics
Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.
2018-03-01
It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.
Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi
2017-12-01
Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH 2 ). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD 3 CD in H 2 O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.
Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi
2017-12-01
Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD3CD in H2O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.
Pacaud, Fabien; Delaye, Jean-Marc; Charpentier, Thibault; Cormier, Laurent; Salanne, Mathieu
2017-10-28
Sodium borosilicate glasses Na 2 O-B 2 O 3 -SiO 2 (NBS) are complex systems from a structural point of view. Three main building units are present: tetrahedral SiO 4 and BO 4 (B IV ) and triangular BO 3 (B III ). One of the salient features of these compounds is the change of the B III /B IV ratio with the alkali concentration, which is very difficult to capture in force fields-based molecular dynamics simulations. In this work, we develop a polarizable force field that is able to reproduce the boron coordination and more generally the structure of several NBS systems in the glass and in the melt. The parameters of the potential are fitted from density functional theory calculations only, in contrast with the existing empirical potentials for NBS systems. This ensures a strong improvement on the transferability of the parameters from one composition to another. Using this new force field, the structure of NBS systems is validated against neutron diffraction and nuclear magnetic resonance experiments. A special focus is given to the distribution of B III /B IV with respect to the composition and the temperature.
Duboué-Dijon, Elise; Mason, Philip E; Fischer, Henry E; Jungwirth, Pavel
2018-04-05
Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H 2 O and D 2 O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg 2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing quantitatively.
Directory of Open Access Journals (Sweden)
Jörg Grunenberg
2016-03-01
Full Text Available We propose several new and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational space in terms of a the isolated and b the ribosomal bound state. In a first step, an all-atom model of the bacterial ribosome consisting of nearly 1600 atoms was constructed and evaluated. The conformational space of 30 different ribosomal/oxazolidinone complexes was scanned by stochastic methods, followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants. The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way.
Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali
2009-02-17
A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.
Das, Arya; Ali, Sk. Musharaf
2018-02-01
Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0-1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP-TiAP and TiAP-dodecane molecules. Further, shear viscosity has been computed by
Das, Arya; Ali, Sk Musharaf
2018-02-21
Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0-1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP-TiAP and TiAP-dodecane molecules. Further, shear viscosity has been computed by
Rapid parameterization of small molecules using the Force Field Toolkit.
Mayne, Christopher G; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C
2013-12-15
The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). Copyright © 2013 Wiley Periodicals, Inc.
Raju, Muralikrishna
The interaction of dense fluids (water, polar organic solvents, room temperature ionic liquids, etc.) with solid substrates controls many chemical processes encountered in nature and industry. The key features of fluid-solid interfaces (FSIs) are the high mobility and often reactivity of the fluid phase, and the structural control provided by the solid phase. In this dissertation we apply molecular modeling methods to study FSIs in the following systems: 1. Dissociation of water on titania surfaces. We studied the adsorption and dissociation of water at 300 K on the following TiO2 surfaces: anatase (101), (100), (112), (001) and rutile (110) at various water coverages, using a recently developed ReaxFF reactive force field. The molecular and dissociative adsorption configurations predicted by ReaxFF for various water coverages agree with previous theoretical studies and experiment. 2. Mechanisms of Oriented Attachment in TiO2 nanocrystals. Oriented attachment (OA) of nanocrystals is now widely recognized as a key process in the solution-phase growth of hierarchical nanostructures. However, the microscopic origins of OA remain unclear. Using the same ReaxFF Ti/O/H reactive force field employed in the previous study, we perform molecular dynamics simulations to study the aggregation of various titanium dioxide (anatase) nanocrystals in vacuum and humid environments. 3. Li interactions in carbon based materials. Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length/time-scales and Li-ion concentrations. In this study we describe development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon based materials using atomistic simulations. We develop force-field parameters for Li-C systems using van
Savelyev, Alexey; MacKerell, Alexander D.
2015-01-01
In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions. PMID:25751286
Böckmann, Marcus; Doltsinis, Nikos L; Marx, Dominik
2015-06-09
An extended Lagrangian formalism that allows for a smooth transition between two different descriptions of interactions during a molecular dynamics simulation is presented. This time-adaptive method is particularly useful in the context of multiscale simulation as it provides a sound recipe to switch on demand between different hierarchical levels of theory, for instance between ab initio ("QM") and force field ("MM") descriptions of a given (sub)system in the course of a molecular dynamics simulation. The equations of motion can be integrated straightforwardly using the usual propagators, such as the Verlet algorithm. First test cases include a bath of harmonic oscillators, of which a subset is switched to a different force constant and/or equilibrium position, as well as an all-MM to QM/MM transition in a hydrogen-bonded water dimer. The method is then applied to a smectic 8AB8 liquid crystal and is shown to be able to switch dynamically a preselected 8AB8 molecule from an all-MM to a QM/MM description which involves partition boundaries through covalent bonds. These examples show that the extended Lagrangian approach is not only easy to implement into existing code but that it is also efficient and robust. The technique moreover provides easy access to a conserved energy quantity, also in cases when Nosé-Hoover chain thermostatting is used throughout dynamical switching. A simple quadratic driving potential proves to be sufficient to guarantee a smooth transition whose time scale can be easily tuned by varying the fictitious mass parameter associated with the auxiliary variable used to extend the Lagrangian. The method is general and can be applied to time-adaptive switching on demand between two different levels of theory within the framework of hybrid scale-bridging simulations.
Classical molecular dynamics simulation of nuclear fuels
International Nuclear Information System (INIS)
Devanathan, R.; Krack, M.; Bertolus, M.
2015-01-01
Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)
Development of a reactive force field for iron-oxyhydroxide systems.
Aryanpour, Masoud; van Duin, Adri C T; Kubicki, James D
2010-06-03
We adopt a classical force field methodology, ReaxFF, which is able to reproduce chemical reactions, and train its parameters for the thermodynamics of iron oxides as well as energetics of a few iron redox reactions. Two parametrizations are developed, and their results are compared with quantum calculations or experimental measurements. In addition to training, two test cases are considered: the lattice parameters of a selected set of iron minerals, and the molecular dynamics simulation of a model for alpha-FeOOH (goethite)-water interaction. Reliability and limitations of the developed force fields in predicting structure and energetics are discussed.
Machine learning of accurate energy-conserving molecular force fields
Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert
2017-01-01
Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076
Explicit polarization: a quantum mechanical framework for developing next generation force fields.
Gao, Jiali; Truhlar, Donald G; Wang, Yingjie; Mazack, Michael J M; Löffler, Patrick; Provorse, Makenzie R; Rehak, Pavel
2014-09-16
Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples
Optimal Classical Simulation of State-Independent Quantum Contextuality
Cabello, Adán; Gu, Mile; Gühne, Otfried; Xu, Zhen-Peng
2018-03-01
Simulating quantum contextuality with classical systems requires memory. A fundamental yet open question is what is the minimum memory needed and, therefore, the precise sense in which quantum systems outperform classical ones. Here, we make rigorous the notion of classically simulating quantum state-independent contextuality (QSIC) in the case of a single quantum system submitted to an infinite sequence of measurements randomly chosen from a finite QSIC set. We obtain the minimum memory needed to simulate arbitrary QSIC sets via classical systems under the assumption that the simulation should not contain any oracular information. In particular, we show that, while classically simulating two qubits tested with the Peres-Mermin set requires log224 ≈4.585 bits, simulating a single qutrit tested with the Yu-Oh set requires, at least, 5.740 bits.
Classical simulations of heavy-ion fusion reactions and weakly
Indian Academy of Sciences (India)
2014-04-30
Apr 30, 2014 ... Heavy-ion collision simulations in various classical models are discussed. ... are also simulated in a 3-stage classical molecular dynamics (3S-CMD) ... considered as a weakly-bound cluster of deuteron and 4He nuclei, thus, ...
Consistent force fields for saccharides
DEFF Research Database (Denmark)
Rasmussen, Kjeld
1999-01-01
Consistent force fields for carbohydrates were hitherto developed by extensive optimization ofpotential energy function parameters on experimental data and on ab initio results. A wide range of experimental data is used: internal structures obtained from gas phase electron diffraction and from x......-anomeric effects are accounted for without addition of specific terms. The work is done in the framework of the Consistent Force Field which originatedin Israel and was further developed in Denmark. The actual methods and strategies employed havebeen described previously. Extensive testing of the force field...
Hybrid classical/quantum simulation for infrared spectroscopy of water
Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro
2018-05-01
We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.
Classical diffusion: theory and simulation codes
International Nuclear Information System (INIS)
Grad, H.; Hu, P.N.
1978-03-01
A survey is given of the development of classical diffusion theory which arose from the observation of Grad and Hogan that the Pfirsch-Schluter and Neoclassical theories are very special and frequently inapplicable because they require that plasma mass flow be treated as transport rather than as a state variable of the plasma. The subsequent theory, efficient numerical algorithms, and results of various operating codes are described
Ensemble simulations with discrete classical dynamics
DEFF Research Database (Denmark)
Toxværd, Søren
2013-01-01
For discrete classical Molecular dynamics (MD) obtained by the "Verlet" algorithm (VA) with the time increment $h$ there exist a shadow Hamiltonian $\\tilde{H}$ with energy $\\tilde{E}(h)$, for which the discrete particle positions lie on the analytic trajectories for $\\tilde{H}$. $\\tilde......{E}(h)$ is employed to determine the relation with the corresponding energy, $E$ for the analytic dynamics with $h=0$ and the zero-order estimate $E_0(h)$ of the energy for discrete dynamics, appearing in the literature for MD with VA. We derive a corresponding time reversible VA algorithm for canonical dynamics...
Simulation of molecular transitions using classical trajectories
Energy Technology Data Exchange (ETDEWEB)
Donoso, A.; Martens, C. C. [University of California, California (United States)
2001-03-01
In the present work, we describe the implementation of a semiclassical method to study physical-chemical processes in molecular systems where electronic state transitions and quantum coherence play a dominant role. The method is based on classical trajectory propagation on the underlying coupled electronic surfaces and is derived from the semiclassical limit of the quantum Liouville equation. Unlike previous classical trajectory-based methods, quantum electronic coherence are treated naturally within this approach as complex weighted trajectory ensembles propagating on the average electronic surfaces. The method is tested on a model problem consisting of one-dimensional motion on two crossing electronic surfaces. Excellent agreement is obtained when compared to the exact results obtained by wave packet propagation. The method is applied to model quantum wave packet interferometry, where two wave packets, differing only in a relative phase, collide in the region where the two electronic surfaces cross. The dependence of the resulting population transfer on the initial relative phase of the wave packets is perfectly captured by our classical trajectory method. Comparison with an alternative method, surface hopping, shows that our approach is appropriate for modelling quantum interference phenomena. [Spanish] En este trabajo se describe la implementacion de un metodo semiclasico para estudiar procesos fisicos-quimicos en sistemas moleculares donde las transiciones entre estados electronicos y las coherencias cuanticas juegan un papel predominante. El metodo se basa en la propagacion de trayectorias clasicas sobre las correspondientes superficies electronicas acopladas y se deriva a partir del limite semiclasico de la ecuacion cuantica de Liouville. A diferencia de metodos previos basados en trayectoria clasica, dentro de este esquema, las coherencias electronicas cuanticas son tratadas de manera natural como ensamble de trayectorias con pesos complejos, moviendose en
Czech Academy of Sciences Publication Activity Database
Krepl, Miroslav; Zgarbová, M.; Stadlbauer, Petr; Otyepka, M.; Banáš, P.; Koča, J.; Cheatham III, T.E.; Jurečka, P.; Šponer, Jiří
2012-01-01
Roč. 8, č. 7 (2012), s. 2506-2520 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GBP305/12/G034 Institutional research plan: CEZ:AV0Z50040702 Keywords : refinement of empirical force fields * DNA * Z-DNA backbone Subject RIV: BO - Biophysics Impact factor: 5.389, year: 2012
ATK-ForceField: a new generation molecular dynamics software package
Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt
2017-12-01
ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.
Approximate photochemical dynamics of azobenzene with reactive force fields
Li, Yan; Hartke, Bernd
2013-12-01
We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis→trans- and trans→cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work).
Preface: Special Topic: From Quantum Mechanics to Force Fields
Piquemal, Jean-Philip; Jordan, Kenneth D.
2017-10-01
This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.
Deriving force field parameters for coordination complexes
DEFF Research Database (Denmark)
Norrby, Per-Ola; Brandt, Peter
2001-01-01
The process of deriving molecular mechanics force fields for coordination complexes is outlined. Force field basics are introduced with an emphasis on special requirements for metal complexes. The review is then focused on how to set up the initial model, define the target, refine the parameters......, and validate the final force field, Alternatives to force field derivation are discussed briefly....
Kato, Rodrigo B; Silva, Frederico T; Pappa, Gisele L; Belchior, Jadson C
2015-01-28
We report the use of genetic algorithms (GA) as a method to refine force field parameters in order to determine RNA energy. Quantum-mechanical (QM) calculations are carried out for the isolated canonical ribonucleosides (adenosine, guanosine, cytidine and uridine) that are taken as reference data. In this particular study, the dihedral and electrostatic energies are reparametrized in order to test the proposed approach, i.e., GA coupled with QM calculations. Overall, RMSE comparison with recent published results for ribonucleosides energies shows an improvement, on average, of 50%. Finally, the new reparametrized potential energy function is used to determine the spatial structure of RNA (PDB code ) that was not taken into account in the parametrization process. This structure was improved about 82% comparable with previously published results.
Harmonic force field for nitro compounds.
Bellido, Edson P; Seminario, Jorge M
2012-06-01
Molecular simulations leading to sensors for the detection of explosive compounds require force field parameters that can reproduce the mechanical and vibrational properties of energetic materials. We developed precise harmonic force fields for alanine polypeptides and glycine oligopeptides using the FUERZA procedure that uses the Hessian tensor (obtained from ab initio calculations) to calculate precise parameters. In this work, we used the same procedure to calculate generalized force field parameters of several nitro compounds. We found a linear relationship between force constant and bond distance. The average angle in the nitro compounds was 116°, excluding the 90° angle of the carbon atoms in the octanitrocubane. The calculated parameters permitted the accurate molecular modeling of nitro compounds containing many functional groups. Results were acceptable when compared with others obtained using methods that are specific for one type of molecule, and much better than others obtained using methods that are too general (these ignore the chemical effects of surrounding atoms on the bonding and therefore the bond strength, which affects the mechanical and vibrational properties of the whole molecule).
Classical and quantum simulations of many-body systems
Energy Technology Data Exchange (ETDEWEB)
Murg, Valentin
2008-04-07
This thesis is devoted to recent developments in the fields of classical and quantum simulations of many-body systems. We describe new classical algorithms that overcome problems apparent in conventional renormalization group and Monte Carlo methods. These algorithms make possible the detailed study of finite temperature properties of 2-D classical and 1-D quantum systems, the investigation of ground states of 2-D frustrated or fermionic systems and the analysis of time evolutions of 2-D quantum systems. Furthermore, we propose new 'analog' quantum simulators that are able to realize interesting models such as a Tonks-Girardeau gas or a frustrated spin-1/2 XY model on a trigonal lattice. These quantum simulators make use of optical lattices and trapped ions and are technically feasible. In fact, the Tonks-Girardeau gas has been realized experimentally and we provide a detailed comparison between the experimental data and the theoretical predictions. (orig.)
Classical and quantum simulations of many-body systems
International Nuclear Information System (INIS)
Murg, Valentin
2008-01-01
This thesis is devoted to recent developments in the fields of classical and quantum simulations of many-body systems. We describe new classical algorithms that overcome problems apparent in conventional renormalization group and Monte Carlo methods. These algorithms make possible the detailed study of finite temperature properties of 2-D classical and 1-D quantum systems, the investigation of ground states of 2-D frustrated or fermionic systems and the analysis of time evolutions of 2-D quantum systems. Furthermore, we propose new ''analog'' quantum simulators that are able to realize interesting models such as a Tonks-Girardeau gas or a frustrated spin-1/2 XY model on a trigonal lattice. These quantum simulators make use of optical lattices and trapped ions and are technically feasible. In fact, the Tonks-Girardeau gas has been realized experimentally and we provide a detailed comparison between the experimental data and the theoretical predictions. (orig.)
Positive Wigner functions render classical simulation of quantum computation efficient.
Mari, A; Eisert, J
2012-12-07
We show that quantum circuits where the initial state and all the following quantum operations can be represented by positive Wigner functions can be classically efficiently simulated. This is true both for continuous-variable as well as discrete variable systems in odd prime dimensions, two cases which will be treated on entirely the same footing. Noting the fact that Clifford and Gaussian operations preserve the positivity of the Wigner function, our result generalizes the Gottesman-Knill theorem. Our algorithm provides a way of sampling from the output distribution of a computation or a simulation, including the efficient sampling from an approximate output distribution in the case of sampling imperfections for initial states, gates, or measurements. In this sense, this work highlights the role of the positive Wigner function as separating classically efficiently simulable systems from those that are potentially universal for quantum computing and simulation, and it emphasizes the role of negativity of the Wigner function as a computational resource.
Classical Simulation of Intermediate-Size Quantum Circuits
Chen, Jianxin; Zhang, Fang; Chen, Mingcheng; Huang, Cupjin; Newman, Michael; Shi, Yaoyun
2018-01-01
We introduce a distributed classical simulation algorithm for general quantum circuits, and present numerical results for calculating the output probabilities of universal random circuits. We find that we can simulate more qubits to greater depth than previously reported using the cluster supported by the Data Infrastructure and Search Technology Division of the Alibaba Group. For example, computing a single amplitude of an $8\\times 8$ qubit circuit with depth $40$ was previously beyond the r...
Classical simulations of heavy-ion fusion reactions and weakly ...
Indian Academy of Sciences (India)
82, No. 5. — journal of. May 2014 physics pp. 879–891. Classical simulations of heavy-ion fusion reactions and weakly-bound projectile breakup reactions ... on the collision energy and the moment of inertia of the deformed nucleus. ... where each individual nucleus consists of a number of protons and neutrons, in some.
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...
Energy Technology Data Exchange (ETDEWEB)
Vlcek, Lukas [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Uhlik, Filip [Charles Univ., Prague (Czech Republic); Moucka, Filip [Purkinje Univ. (Czech Republic); Nezbeda, Ivo [Purkinje Univ. (Czech Republic); Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Chialvo, Ariel A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
2015-12-16
We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ion hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.
Liu, Z.; Ensing, B.; Moore, P.B.
2011-01-01
The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (phi-psi) conformational space. The FES is obtained from metadynamics simulations with five commonly used
Computational Physics Simulation of Classical and Quantum Systems
Scherer, Philipp O. J
2010-01-01
This book encapsulates the coverage for a two-semester course in computational physics. The first part introduces the basic numerical methods while omitting mathematical proofs but demonstrating the algorithms by way of numerous computer experiments. The second part specializes in simulation of classical and quantum systems with instructive examples spanning many fields in physics, from a classical rotor to a quantum bit. All program examples are realized as Java applets ready to run in your browser and do not require any programming skills.
Computational physics. Simulation of classical and quantum systems
Energy Technology Data Exchange (ETDEWEB)
Scherer, Philipp O.J. [TU Muenchen (Germany). Physikdepartment T38
2010-07-01
This book encapsulates the coverage for a two-semester course in computational physics. The first part introduces the basic numerical methods while omitting mathematical proofs but demonstrating the algorithms by way of numerous computer experiments. The second part specializes in simulation of classical and quantum systems with instructive examples spanning many fields in physics, from a classical rotor to a quantum bit. All program examples are realized as Java applets ready to run in your browser and do not require any programming skills. (orig.)
Computational physics simulation of classical and quantum systems
Scherer, Philipp O J
2017-01-01
This textbook presents basic numerical methods and applies them to a large variety of physical models in multiple computer experiments. Classical algorithms and more recent methods are explained. Partial differential equations are treated generally comparing important methods, and equations of motion are solved by a large number of simple as well as more sophisticated methods. Several modern algorithms for quantum wavepacket motion are compared. The first part of the book discusses the basic numerical methods, while the second part simulates classical and quantum systems. Simple but non-trivial examples from a broad range of physical topics offer readers insights into the numerical treatment but also the simulated problems. Rotational motion is studied in detail, as are simple quantum systems. A two-level system in an external field demonstrates elementary principles from quantum optics and simulation of a quantum bit. Principles of molecular dynamics are shown. Modern bounda ry element methods are presented ...
The ambiguity of simplicity in quantum and classical simulation
Aghamohammadi, Cina; Mahoney, John R.; Crutchfield, James P.
2017-04-01
A system's perceived simplicity depends on whether it is represented classically or quantally. This is not so surprising, as classical and quantum physics are descriptive frameworks built on different assumptions that capture, emphasize, and express different properties and mechanisms. What is surprising is that, as we demonstrate, simplicity is ambiguous: the relative simplicity between two systems can change sign when moving between classical and quantum descriptions. Here, we associate simplicity with small model-memory. We see that the notions of absolute physical simplicity at best form a partial, not a total, order. This suggests that appeals to principles of physical simplicity, via Ockham's Razor or to the ;elegance; of competing theories, may be fundamentally subjective. Recent rapid progress in quantum computation and quantum simulation suggest that the ambiguity of simplicity will strongly impact statistical inference and, in particular, model selection.
Evaluating amber force fields using computed NMR chemical shifts.
Koes, David R; Vries, John K
2017-10-01
NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.
The ambiguity of simplicity in quantum and classical simulation
International Nuclear Information System (INIS)
Aghamohammadi, Cina; Mahoney, John R.; Crutchfield, James P.
2017-01-01
Highlights: • Simplicity depends on whether a system is represented classically or quantally. • We demonstrate that simplicity is unavoidably ambiguous. • Relative simplicity changes order moving between classical and quantum descriptions. • Ambiguity of simplicity bears directly on model selection. - Abstract: A system's perceived simplicity depends on whether it is represented classically or quantally. This is not so surprising, as classical and quantum physics are descriptive frameworks built on different assumptions that capture, emphasize, and express different properties and mechanisms. What is surprising is that, as we demonstrate, simplicity is ambiguous: the relative simplicity between two systems can change sign when moving between classical and quantum descriptions. Here, we associate simplicity with small model-memory. We see that the notions of absolute physical simplicity at best form a partial, not a total, order. This suggests that appeals to principles of physical simplicity, via Ockham's Razor or to the “elegance” of competing theories, may be fundamentally subjective. Recent rapid progress in quantum computation and quantum simulation suggest that the ambiguity of simplicity will strongly impact statistical inference and, in particular, model selection.
The ambiguity of simplicity in quantum and classical simulation
Energy Technology Data Exchange (ETDEWEB)
Aghamohammadi, Cina, E-mail: caghamohammadi@ucdavis.edu; Mahoney, John R., E-mail: jrmahoney@ucdavis.edu; Crutchfield, James P., E-mail: chaos@ucdavis.edu
2017-04-11
Highlights: • Simplicity depends on whether a system is represented classically or quantally. • We demonstrate that simplicity is unavoidably ambiguous. • Relative simplicity changes order moving between classical and quantum descriptions. • Ambiguity of simplicity bears directly on model selection. - Abstract: A system's perceived simplicity depends on whether it is represented classically or quantally. This is not so surprising, as classical and quantum physics are descriptive frameworks built on different assumptions that capture, emphasize, and express different properties and mechanisms. What is surprising is that, as we demonstrate, simplicity is ambiguous: the relative simplicity between two systems can change sign when moving between classical and quantum descriptions. Here, we associate simplicity with small model-memory. We see that the notions of absolute physical simplicity at best form a partial, not a total, order. This suggests that appeals to principles of physical simplicity, via Ockham's Razor or to the “elegance” of competing theories, may be fundamentally subjective. Recent rapid progress in quantum computation and quantum simulation suggest that the ambiguity of simplicity will strongly impact statistical inference and, in particular, model selection.
A Kirkwood-Buff derived force field for alkaline earth halide salts
Naleem, Nawavi; Bentenitis, Nikolaos; Smith, Paul E.
2018-06-01
The activity and function of many macromolecules in cellular environments are coupled with the binding of divalent ions such as calcium or magnesium. In principle, computer simulations can be used to understand the molecular level aspects of how many important macromolecules interact with ions. However, most of the force fields currently available often fail to accurately reproduce the properties of divalent ions in aqueous environments. Here we develop classical non-polarizable force fields for the aqueous alkaline earth metal halides (MX2), where M = Mg2+, Ca2+, Sr2+, Ba2+ and X = Cl-, Br-, I-, which can be used in bimolecular simulations and which are compatible with the Simple Point Charge/Extended (SPC/E) water model. The force field parameters are specifically developed to reproduce the experimental Kirkwood-Buff integrals for aqueous solutions and thereby the experimental activity derivatives, partial molar volumes, and excess coordination numbers. This ensures that a reasonable balance between ion-ion, ion-water, and water-water distributions is obtained. However, this requires a scaling of the cation to water oxygen interaction strength in order to accurately reproduce the integrals. The scaling factors developed for chloride salts are successfully transferable to the bromide and iodide salts. Use of these new models leads to reasonable diffusion constants and dielectric decrements. However, the performance of the models decreases with increasing salt concentration (>4m), and simulations of the pure crystals exhibited unstable behavior.
MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields
Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.
2011-01-01
We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689
Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
Savelyev, Alexey; MacKerell, Alexander D.
2014-01-01
Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and...
A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics
International Nuclear Information System (INIS)
Morante, S.; Rossi, G.C.
2017-01-01
We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.
Multipolar Force Fields and Their Effects on Solvent Dynamics around Simple Solutes
DEFF Research Database (Denmark)
Jakobsen, Sofie; Bereau, Tristan; Meuwly, Markus
2015-01-01
The performance of multipole (MTP) and point charge (PC) force fields in classical molecular dynamics (MD) simulations of condensed-phase systems for both equilibrium and dynamical quantities is compared. MTP electrostatics provides an improved description of the anisotropic electrostatic potential......, which is especially important to describe key, challenging interactions, such as lone pairs, π-interactions, and hydrogen bonds. These chemical environments are probed by focusing on the hydration properties of two molecules: N-methylacetamide and phenyl bromide. Both, equilibrium and dynamical...
A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics
Energy Technology Data Exchange (ETDEWEB)
Morante, S., E-mail: morante@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Rossi, G.C., E-mail: rossig@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Compendio del Viminale, Piazza del Viminale 1, I-00184 Rome (Italy)
2017-02-15
We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.
Computational physics simulation of classical and quantum systems
Scherer, Philipp O J
2013-01-01
This textbook presents basic and advanced computational physics in a very didactic style. It contains very-well-presented and simple mathematical descriptions of many of the most important algorithms used in computational physics. Many clear mathematical descriptions of important techniques in computational physics are given. The first part of the book discusses the basic numerical methods. A large number of exercises and computer experiments allows to study the properties of these methods. The second part concentrates on simulation of classical and quantum systems. It uses a rather general concept for the equation of motion which can be applied to ordinary and partial differential equations. Several classes of integration methods are discussed including not only the standard Euler and Runge Kutta method but also multistep methods and the class of Verlet methods which is introduced by studying the motion in Liouville space. Besides the classical methods, inverse interpolation is discussed, together with the p...
Classical molecular dynamics simulation of electronically non-adiabatic processes.
Miller, William H; Cotton, Stephen J
2016-12-22
Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).
Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D
2015-07-15
Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.
Indian Academy of Sciences (India)
2013-11-11
Nov 11, 2013 ... Polanyi's classic paper, co-authored by Henry Eyring, reproduced in this ... spatial conf guration of the atoms in terms of the energy function of the diatomic .... The present communication deals with the construction of such .... These three contributions are complemented by a fourth term if one takes into.
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...
Are current atomistic force fields accurate enough to study proteins in crowded environments?
Directory of Open Access Journals (Sweden)
Drazen Petrov
2014-05-01
Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields
Transition States from Empirical Force Fields
DEFF Research Database (Denmark)
Jensen, Frank; Norrby, Per-Ola
2003-01-01
This is an overview of the use of empirical force fields in the study of reaction mechanisms. EVB-type methods (including RFF and MCMM) produce full reaction surfaces by mixing, in the simplest case, known force fields describing reactants and products. The SEAM method instead locates approximate...
Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo
2016-01-21
Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.
Fernando L. Dri; Xiawa Wu; Robert J. Moon; Ashlie Martini; Pablo D. Zavattieri
2015-01-01
Molecular dynamics simulation is commonly used to study the properties of nanocellulose-based materials at the atomic scale. It is well known that the accuracy of these simulations strongly depends on the force field that describes energetic interactions. However, since there is no force field developed specifically for cellulose, researchers utilize models...
Force field refinement from NMR scalar couplings
Energy Technology Data Exchange (ETDEWEB)
Huang Jing [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland); Meuwly, Markus, E-mail: m.meuwly@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland)
2012-03-02
Graphical abstract: We show that two classes of H-bonds are sufficient to quantitatively describe scalar NMR coupling constants in small proteins. Highlights: Black-Right-Pointing-Pointer We present force field refinements based on explicit MD simulations using scalar couplings across hydrogen bonds. Black-Right-Pointing-Pointer This leads to {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings to within 0.03 Hz at best compared to experiment. Black-Right-Pointing-Pointer A classification of H-bonds according to secondary structure is not sufficiently robust. Black-Right-Pointing-Pointer Grouping H-bonds into two classes and reparametrization yields an RMSD of 0.07 Hz. Black-Right-Pointing-Pointer This is an improvement of 50. - Abstract: NMR observables contain valuable information about the protein dynamics sampling a high-dimensional potential energy surface. Depending on the observable, the dynamics is sensitive to different time-windows. Scalar coupling constants {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} reflect the pico- to nanosecond motions associated with the intermolecular hydrogen bond network. Including an explicit H-bond in the molecular mechanics with proton transfer (MMPT) potential allows us to reproduce experimentally determined {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings to within 0.02 Hz at best for ubiquitin and protein G. This is based on taking account of the chemically changing environment by grouping the H-bonds into up to seven classes. However, grouping them into two classes already reduces the RMSD between computed and observed {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings by almost 50%. Thus, using ensemble-averaged data with two classes of H-bonds leads to substantially improved scalar couplings from simulations with accurate force fields.
Simulation of unilateral contact problems departing from the classical boundary problems
International Nuclear Information System (INIS)
Frey, S.L.; Sampaio, R.; Gama, R.M.S. da.
1989-08-01
A numerical algorithm is proposed for simulating unilateral contact problems under the classical elasticity point of view. This simple algorithm may be employed by engineers with a minimum knowledge on classical elasticity. (A.C.A.S.) [pt
Martini Force Field Parameters for Glycolipids
Lopez, Cesar A.; Sovova, Zofie; van Eerden, Floris J.; de Vries, Alex H.; Marrink, Siewert J.
We present an extension of the Martini coarse-grained force field to glycolipids. The glycolipids considered here are the glycoglycerolipids monogalactosyldiacylglycerol (MGDG), sulfoquinovosyldiacylglycerol (SQDG), digalactosyldiacylglycerol (DGDG), and phosphatidylinositol (PI) and its
Improved Parameters for the Martini Coarse-Grained Protein Force Field
de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew; Arnarez, Clement; Wassenaar, Tsjerk A.; Schafer, Lars V.; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.
The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too
Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters
Directory of Open Access Journals (Sweden)
Kenichi Dedachi
2013-01-01
Full Text Available Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials and electrostatic and Lennard-Jones potentials between the amino acid units. In this study, the SAAP force field (SAAPFF parameters were improved, and classical canonical Monte Carlo (MC simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model. Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin. The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides. A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.
Energy Technology Data Exchange (ETDEWEB)
Wen, Jialin; Ma, Tianbao [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Zhang, Weiwei; Psofogiannakis, George; Duin, Adri C.T. van [Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, PA 16802 (United States); Chen, Lei; Qian, Linmao [Tribology Research Institute, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031 (China); Hu, Yuanzhong [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Lu, Xinchun, E-mail: xclu@tsinghua.edu.cn [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China)
2016-12-30
Highlights: • New ReaxFF reactive force field was applied to simulate the tribochemical wear process at Si/SiO{sub 2} interface. • Wear of silicon atoms is due to the breaking of Si–O–Si bonds and Si–Si–O–Si bond chains on the Si substrate. • Interfacial bridge bonds play an important role during the tribochemical wear process. • Higher pressures applied to the silica phase can cause more Si atoms to be removed by forming more interfacial bridge bonds. • Water plays an opposing role in the wear process because of its both chemical and mechanical effects. - Abstract: In this work, the atomic mechanism of tribochemical wear of silicon at the Si/SiO{sub 2} interface in aqueous environment was investigated using ReaxFF molecular dynamics (MD) simulations. Two types of Si atom removal pathways were detected in the wear process. The first is caused by the destruction of stretched Si–O–Si bonds on the Si substrate surface and is assisted by the attachment of H atoms on the bridging oxygen atoms of the bonds. The other is caused by the rupture of Si–Si bonds in the stretched Si–Si–O–Si bond chains at the interface. Both pathways effectively remove Si atoms from the silicon surface via interfacial Si–O–Si bridge bonds. Our simulations also demonstrate that higher pressures applied to the silica phase can cause more Si atoms to be removed due to the formation of increased numbers of interfacial Si–O–Si bridge bonds. Besides, water plays a dual role in the wear mechanism, by oxidizing the Si substrate surface as well as by preventing the close contact of the surfaces. This work shows that the removal of Si atoms from the substrate is a result of both chemical reaction and mechanical effects and contributes to the understanding of tribochemical wear behavior in the microelectromechanical systems (MEMS) and Si chemical mechanical polishing (CMP) process.
Software Process Improvement Using Force Field Analysis ...
African Journals Online (AJOL)
An improvement plan is then drawn and implemented. This paper studied the state of Nigerian software development organizations based on selected attributes. Force field analysis is used to partition the factors obtained into driving and restraining forces. An attempt was made to improve the software development process ...
Simulating quantum systems on classical computers with matrix product states
International Nuclear Information System (INIS)
Kleine, Adrian
2010-01-01
In this thesis, the numerical simulation of strongly-interacting many-body quantum-mechanical systems using matrix product states (MPS) is considered. Matrix-Product-States are a novel representation of arbitrary quantum many-body states. Using quantum information theory, it is possible to show that Matrix-Product-States provide a polynomial-sized representation of one-dimensional quantum systems, thus allowing an efficient simulation of one-dimensional quantum system on classical computers. Matrix-Product-States form the conceptual framework of the density-matrix renormalization group (DMRG). After a general introduction in the first chapter of this thesis, the second chapter deals with Matrix-Product-States, focusing on the development of fast and stable algorithms. To obtain algorithms to efficiently calculate ground states, the density-matrix renormalization group is reformulated using the Matrix-Product-States framework. Further, time-dependent problems are considered. Two different algorithms are presented, one based on a Trotter decomposition of the time-evolution operator, the other one on Krylov subspaces. Finally, the evaluation of dynamical spectral functions is discussed, and a correction vector-based method is presented. In the following chapters, the methods presented in the second chapter, are applied to a number of different physical problems. The third chapter deals with the existence of chiral phases in isotropic one-dimensional quantum spin systems. A preceding analytical study based on a mean-field approach indicated the possible existence of those phases in an isotropic Heisenberg model with a frustrating zig-zag interaction and a magnetic field. In this thesis, the existence of the chiral phases is shown numerically by using Matrix-Product-States-based algorithms. In the fourth chapter, we propose an experiment using ultracold atomic gases in optical lattices, which allows a well controlled observation of the spin-charge separation (of
Simulating quantum systems on classical computers with matrix product states
Energy Technology Data Exchange (ETDEWEB)
Kleine, Adrian
2010-11-08
In this thesis, the numerical simulation of strongly-interacting many-body quantum-mechanical systems using matrix product states (MPS) is considered. Matrix-Product-States are a novel representation of arbitrary quantum many-body states. Using quantum information theory, it is possible to show that Matrix-Product-States provide a polynomial-sized representation of one-dimensional quantum systems, thus allowing an efficient simulation of one-dimensional quantum system on classical computers. Matrix-Product-States form the conceptual framework of the density-matrix renormalization group (DMRG). After a general introduction in the first chapter of this thesis, the second chapter deals with Matrix-Product-States, focusing on the development of fast and stable algorithms. To obtain algorithms to efficiently calculate ground states, the density-matrix renormalization group is reformulated using the Matrix-Product-States framework. Further, time-dependent problems are considered. Two different algorithms are presented, one based on a Trotter decomposition of the time-evolution operator, the other one on Krylov subspaces. Finally, the evaluation of dynamical spectral functions is discussed, and a correction vector-based method is presented. In the following chapters, the methods presented in the second chapter, are applied to a number of different physical problems. The third chapter deals with the existence of chiral phases in isotropic one-dimensional quantum spin systems. A preceding analytical study based on a mean-field approach indicated the possible existence of those phases in an isotropic Heisenberg model with a frustrating zig-zag interaction and a magnetic field. In this thesis, the existence of the chiral phases is shown numerically by using Matrix-Product-States-based algorithms. In the fourth chapter, we propose an experiment using ultracold atomic gases in optical lattices, which allows a well controlled observation of the spin-charge separation (of
International Nuclear Information System (INIS)
Bauduceau, O.; Pons, P.; Romero, L.; Fayolle, M.; Campana, F.; Bollet, M.
2005-01-01
Purpose. - To compare conventional 2D simulation and virtual simulation on 14 patients with breast cancer. Patients and methods. - Patients were simulated for treatment using standard procedure. They subsequently underwent CT scan in the treatment position. The CTV was defined as breast tissue. The PTV was obtained by adding a 3D margin of 1 cm around CTV. Organs at risk (lungs and heart) were outlined. Ballistics and dose distribution obtained with the two planning methods were compared. Results. - With conventional simulation, 95% of CTV received 95% of the dose prescribed. Virtual simulation significantly improved dosimetric coverage of PTV without increasing irradiation volume of lung and heart. In 2D simulation, using three slices allowed optimisation by adjusting wedge angle. The five-slice plan was a much better predictor of the maximum dose regions when compared to the three-slice plan. Using entire CT data did not give any benefit. Conclusion. - Variations in CTV delineation and PTV definition limit interest of virtual simulation. In classic simulation, a 5 CT slice-plan can be used to optimise dose distribution. (author)
Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E
2013-10-31
A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row).
Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme
Buck, Matthias; Bouguet-Bonnet, Sabine; Pastor, Richard W.; MacKerell, Alexander D.
2005-01-01
The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.
Classical and quantum computing with C++ and Java simulations
Hardy, Y
2001-01-01
Classical and Quantum computing provides a self-contained, systematic and comprehensive introduction to all the subjects and techniques important in scientific computing. The style and presentation are readily accessible to undergraduates and graduates. A large number of examples, accompanied by complete C++ and Java code wherever possible, cover every topic. Features and benefits: - Comprehensive coverage of the theory with many examples - Topics in classical computing include boolean algebra, gates, circuits, latches, error detection and correction, neural networks, Turing machines, cryptography, genetic algorithms - For the first time, genetic expression programming is presented in a textbook - Topics in quantum computing include mathematical foundations, quantum algorithms, quantum information theory, hardware used in quantum computing This book serves as a textbook for courses in scientific computing and is also very suitable for self-study. Students, professionals and practitioners in computer...
Solitons in a random force field
International Nuclear Information System (INIS)
Bass, F.G.; Konotop, V.V.; Sinitsyn, Y.A.
1985-01-01
We study the dynamics of a soliton of the sine-Gordon equation in a random force field in the adiabatic approximation. We obtain an Einstein-Fokker equation and find the distribution function for the soliton parameters which we use to evaluate its statistical characteristics. We derive an equation for the averaged functions of the soliton parameters. We determine the limits of applicability of the delta-correlated in time random field approximation
Charm production and the confining force field
International Nuclear Information System (INIS)
Andersson, B.; Bengtsson, H.-U.; Gustafson, G.
1983-03-01
We show that charm production at SPS energies can be understood simply from O(α 2 sub (s)) QCD processes when combined with fragmentation of the colour fields stretched by the final state partons. The tension of the confining force field responsible for particle production is found to pull the charmed particles away from the reaction centre, giving rise to a harder x sub (F)-spectrum than would be expected from the bare QCD matrix elements. (Authors)
A quantum-classical simulation of a multi-surface multi-mode ...
Indian Academy of Sciences (India)
Multi surface multi mode quantum dynamics; parallelized quantum classical approach; TDDVR method. 1. ... cal simulation on molecular system is a great cha- llenge for ..... on a multiple core cluster with shared memory using. OpenMP based ...
Computer simulation of mixed classical-quantum systems
International Nuclear Information System (INIS)
Kalia, R.K.; Vashishta, P.
1988-11-01
We briefly review three important methods that are currently used in the simulation of mixed systems. Two of these techniques, path integral Monte Carlo or molecular dynamics and dynamical simulated annealing, have the limitation that they can only describe the structural properties in the ground state. The third so-called quantum molecular dynamics (QMD) method can provide not only the static properties but also the real-time dynamics of a quantum particle at finite temperatures. 10 refs
Microcanonical simulations in classical and quantum field theory
International Nuclear Information System (INIS)
Olson, D.P.
1988-01-01
In the first part of this thesis, a stochastic adaptation of the microcanonical simulation method is applied to the numerical simulation of the Su-Schrieffer-Heeger Hamiltonian for polyacetylene, a one-dimensional polymer were fermion-boson interactions play a dominant role in the dynamics of the system. The pure microcanonical simulation method fails in the marginally ergodic case and a stochastic adaptation, the hybrid microcanonical method, is employed to resolve problems with ergodicity. The hybrid method is shown to be an efficient method for higher dimensional fermionic quantum systems. In the second part of this thesis, a numerical simulation of the evolution of a network of global cosmic strings is an expanding Robertson-Walker universe is carried out. The system is quenched through an order-disorder phase transition and the nature of the string distribution is examined. While the string distribution observed at the phase transition is in good agreement with earlier estimates, the simulation reveals that the dynamics of the strings are suppressed by interactions with the Goldstone field. The network decays by topological annihilation and no spatial correlations are observed at any point in the simulation
Effects of Force Field Selection on the Computational Ranking of MOFs for CO2 Separations.
Dokur, Derya; Keskin, Seda
2018-02-14
Metal-organic frameworks (MOFs) have been considered as highly promising materials for adsorption-based CO 2 separations. The number of synthesized MOFs has been increasing very rapidly. High-throughput molecular simulations are very useful to screen large numbers of MOFs in order to identify the most promising adsorbents prior to extensive experimental studies. Results of molecular simulations depend on the force field used to define the interactions between gas molecules and MOFs. Choosing the appropriate force field for MOFs is essential to make reliable predictions about the materials' performance. In this work, we performed two sets of molecular simulations using the two widely used generic force fields, Dreiding and UFF, and obtained adsorption data of CO 2 /H 2 , CO 2 /N 2 , and CO 2 /CH 4 mixtures in 100 different MOF structures. Using this adsorption data, several adsorbent evaluation metrics including selectivity, working capacity, sorbent selection parameter, and percent regenerability were computed for each MOF. MOFs were then ranked based on these evaluation metrics, and top performing materials were identified. We then examined the sensitivity of the MOF rankings to the force field type. Our results showed that although there are significant quantitative differences between some adsorbent evaluation metrics computed using different force fields, rankings of the top MOF adsorbents for CO 2 separations are generally similar: 8, 8, and 9 out of the top 10 most selective MOFs were found to be identical in the ranking for CO 2 /H 2 , CO 2 /N 2 , and CO 2 /CH 4 separations using Dreiding and UFF. We finally suggested a force field factor depending on the energy parameters of atoms present in the MOFs to quantify the robustness of the simulation results to the force field selection. This easily computable factor will be highly useful to determine whether the results are sensitive to the force field type or not prior to performing computationally demanding
A new force field including charge directionality for TMAO in aqueous solution
International Nuclear Information System (INIS)
Usui, Kota; Nagata, Yuki; Hunger, Johannes; Bonn, Mischa; Sulpizi, Marialore
2016-01-01
We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O TMAO ) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O TMAO to mimic the O TMAO lone pairs and we migrate the negative charge on the O TMAO to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.
A new force field including charge directionality for TMAO in aqueous solution
Energy Technology Data Exchange (ETDEWEB)
Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes; Bonn, Mischa [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Sulpizi, Marialore, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de [Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz (Germany)
2016-08-14
We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O{sub TMAO}) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O{sub TMAO} to mimic the O{sub TMAO} lone pairs and we migrate the negative charge on the O{sub TMAO} to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.
Lay, Wesley K; Miller, Mark S; Elcock, Adrian H
2016-04-12
GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to optimize force fields.
A test on reactive force fields for the study of silica dimerization reactions
Energy Technology Data Exchange (ETDEWEB)
Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T.; Åstrand, Per-Olof; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117, 7491 Trondheim (Norway)
2015-11-14
We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method.
Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.
Zheng, Mo; Li, Xiaoxia; Guo, Li
2013-04-01
Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. Copyright © 2013 Elsevier Inc. All rights reserved.
Simulation of classical thermal states on a quantum computer: A transfer-matrix approach
International Nuclear Information System (INIS)
Yung, Man-Hong; Nagaj, Daniel; Whitfield, James D.; Aspuru-Guzik, Alan
2010-01-01
We present a hybrid quantum-classical algorithm to simulate thermal states of classical Hamiltonians on a quantum computer. Our scheme employs a sequence of locally controlled rotations, building up the desired state by adding qubits one at a time. We identified a class of classical models for which our method is efficient and avoids potential exponential overheads encountered by Grover-like or quantum Metropolis schemes. Our algorithm also gives an exponential advantage for two-dimensional Ising models with magnetic field on a square lattice, compared with the previously known Zalka's algorithm.
Three-stage classical molecular dynamics model for simulation of heavy-ion fusion
Directory of Open Access Journals (Sweden)
Godre Subodh S.
2015-01-01
Full Text Available A three-stage Classical Molecular Dynamics (3S-CMD approach for heavy-ion fusion is developed. In this approach the Classical Rigid-Body Dynamics simulation for heavy-ion collision involving light deformed nucleus is initiated on their Rutherford trajectories at very large initial separation. Collision simulation is then followed by relaxation of the rigid-body constrains for one or both the colliding nuclei at distances close to the barrier when the trajectories of all the nucleons are obtained in a Classical Molecular Dynamics approach. This 3S-CMD approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but also the internal vibrational excitations of one or both the nuclei at distances close to the barrier. The results of the dynamical simulation for 24Mg+208Pb collision show significant modification of the fusion barrier and calculated fusion cross sections due to internal excitations.
A transferable force field for CdS-CdSe-PbS-PbSe solid systems
Fan, Zhaochuan; Koster, Rik S.; Wang, Shuaiwei; Fang, Changming; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; van Huis, Marijn A.; Vlugt, Thijs J. H.
2014-12-01
A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.
A transferable force field for CdS-CdSe-PbS-PbSe solid systems
Energy Technology Data Exchange (ETDEWEB)
Fan, Zhaochuan; Vlugt, Thijs J. H., E-mail: t.j.h.vlugt@tudelft.nl [Process and Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft,The Netherlands (Netherlands); Koster, Rik S.; Fang, Changming; Huis, Marijn A. van [Debye Institute for Nanomaterials Science and Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC Utrecht (Netherlands); Wang, Shuaiwei [Institute of Nanostructured Functional Materials, Huanghe Science and Technology College, Zhengzhou, Henan 450006 (China); Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W. [Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft (Netherlands)
2014-12-28
A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., “Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth,” Nano Lett. 14, 3661–3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.
Reactive Force Field for Liquid Hydrazoic Acid with Applications to Detonation Chemistry
Furman, David; Dubnikova, Faina; van Duin, Adri; Zeiri, Yehuda; Kosloff, Ronnie
The development of a reactive force field (ReaxFF formalism) for Hydrazoic acid (HN3), a highly sensitive liquid energetic material, is reported. The force field accurately reproduces results of density functional theory (DFT) calculations. The quality and performance of the force field are examined by detailed comparison with DFT calculations related to uni, bi and trimolecular thermal decomposition routes. Reactive molecular dynamics (RMD) simulations are performed to reveal the initial chemical events governing the detonation chemistry of liquid HN3. The outcome of these simulations compares very well with recent results of tight-binding DFT molecular dynamics and thermodynamic calculations. Based on our RMD simulations, predictions were made for the activation energies and volumes in a broad range of temperatures and initial material compressions. Work Supported by The Center of Excellence for Explosives Detection, Mitigation and Response, Department of Homeland Security.
Building machine learning force fields for nanoclusters
Zeni, Claudio; Rossi, Kevin; Glielmo, Aldo; Fekete, Ádám; Gaston, Nicola; Baletto, Francesca; De Vita, Alessandro
2018-06-01
We assess Gaussian process (GP) regression as a technique to model interatomic forces in metal nanoclusters by analyzing the performance of 2-body, 3-body, and many-body kernel functions on a set of 19-atom Ni cluster structures. We find that 2-body GP kernels fail to provide faithful force estimates, despite succeeding in bulk Ni systems. However, both 3- and many-body kernels predict forces within an ˜0.1 eV/Å average error even for small training datasets and achieve high accuracy even on out-of-sample, high temperature structures. While training and testing on the same structure always provide satisfactory accuracy, cross-testing on dissimilar structures leads to higher prediction errors, posing an extrapolation problem. This can be cured using heterogeneous training on databases that contain more than one structure, which results in a good trade-off between versatility and overall accuracy. Starting from a 3-body kernel trained this way, we build an efficient non-parametric 3-body force field that allows accurate prediction of structural properties at finite temperatures, following a newly developed scheme [A. Glielmo et al., Phys. Rev. B 95, 214302 (2017)]. We use this to assess the thermal stability of Ni19 nanoclusters at a fractional cost of full ab initio calculations.
International Nuclear Information System (INIS)
Garcia-Vela, A.
2002-01-01
A new quantum-type phase-space distribution is proposed in order to sample initial conditions for classical trajectory simulations. The phase-space distribution is obtained as the modulus of a quantum phase-space state of the system, defined as the direct product of the coordinate and momentum representations of the quantum initial state. The distribution is tested by sampling initial conditions which reproduce the initial state of the Ar-HCl cluster prepared by ultraviolet excitation, and by simulating the photodissociation dynamics by classical trajectories. The results are compared with those of a wave packet calculation, and with a classical simulation using an initial phase-space distribution recently suggested. A better agreement is found between the classical and the quantum predictions with the present phase-space distribution, as compared with the previous one. This improvement is attributed to the fact that the phase-space distribution propagated classically in this work resembles more closely the shape of the wave packet propagated quantum mechanically
Efficient classical simulation of the Deutsch-Jozsa and Simon's algorithms
Johansson, Niklas; Larsson, Jan-Åke
2017-09-01
A long-standing aim of quantum information research is to understand what gives quantum computers their advantage. This requires separating problems that need genuinely quantum resources from those for which classical resources are enough. Two examples of quantum speed-up are the Deutsch-Jozsa and Simon's problem, both efficiently solvable on a quantum Turing machine, and both believed to lack efficient classical solutions. Here we present a framework that can simulate both quantum algorithms efficiently, solving the Deutsch-Jozsa problem with probability 1 using only one oracle query, and Simon's problem using linearly many oracle queries, just as expected of an ideal quantum computer. The presented simulation framework is in turn efficiently simulatable in a classical probabilistic Turing machine. This shows that the Deutsch-Jozsa and Simon's problem do not require any genuinely quantum resources, and that the quantum algorithms show no speed-up when compared with their corresponding classical simulation. Finally, this gives insight into what properties are needed in the two algorithms and calls for further study of oracle separation between quantum and classical computation.
Energy Technology Data Exchange (ETDEWEB)
Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr; Meier, Christoph [Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse (France); Falvo, Cyril [Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay (France)
2016-08-07
We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the “surfaces” for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.
Molecular dynamics simulations of classical sound absorption in a monatomic gas
Ayub, M.; Zander, A. C.; Huang, D. M.; Cazzolato, B. S.; Howard, C. Q.
2018-05-01
Sound wave propagation in argon gas is simulated using molecular dynamics (MD) in order to determine the attenuation of acoustic energy due to classical (viscous and thermal) losses at high frequencies. In addition, a method is described to estimate attenuation of acoustic energy using the thermodynamic concept of exergy. The results are compared against standing wave theory and the predictions of the theory of continuum mechanics. Acoustic energy losses are studied by evaluating various attenuation parameters and by comparing the changes in behavior at three different frequencies. This study demonstrates acoustic absorption effects in a gas simulated in a thermostatted molecular simulation and quantifies the classical losses in terms of the sound attenuation constant. The approach can be extended to further understanding of acoustic loss mechanisms in the presence of nanoscale porous materials in the simulation domain.
Implications of confining force field structures in hard hadronic processes
International Nuclear Information System (INIS)
Bengtsson, H.-U.
1983-04-01
This thesis is centered on the study of confining force field structures in hard scattering processes. Perturbative QCD provides the means of calculating any process on the parton level, but to be able accurately to describe the actual outcome of an event, one still needs a phenomenological model for how quarks and gluons transform into observable hadrons. One such model is based on the assumption that the particles are produced by the confining fields stretched between the partons. The actual particle distributions will then depend on the topology of the confining fields. We have developed a Monte Carlo program to simulate complete events in hard scattering, and we use this to study the properties of the confining field in different trigger situations. We further look at the amount of hard processes that can be expected in experiments that trigger on transverse energy sum (calorimeter experiments). Finally, we investigate charm production within our model. (author)
Simulating spontaneous parametric down-conversion using classical light: Conference paper
CSIR Research Space (South Africa)
Zhang, Y
2014-08-01
Full Text Available We present a simple way of simulating Spontaneous parametric down-conversion (SPDC) by modulating a classical laser beam with two spatial light modulators (SLM) through a back projection setup. This system has the advantage of having very high...
Energy Technology Data Exchange (ETDEWEB)
Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de [Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg (Germany); Kibies, Patrick; Frach, Roland; Kast, Stefan M., E-mail: stefan.kast@tu-dortmund.de [Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund (Germany); Imoto, Sho, E-mail: sho.imoto@theochem.rub.de; Marx, Dominik [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany); Suladze, Saba; Winter, Roland [Physikalische Chemie I, Technische Universität Dortmund, 44227 Dortmund (Germany)
2016-04-14
Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.
Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M
2016-04-14
Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures--while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.
International Nuclear Information System (INIS)
Hölzl, Christoph; Horinek, Dominik; Kibies, Patrick; Frach, Roland; Kast, Stefan M.; Imoto, Sho; Marx, Dominik; Suladze, Saba; Winter, Roland
2016-01-01
Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.
Protocol for classical molecular dynamics simulations of nano-junctions in solution
Gkionis, Konstantinos; Rungger, Ivan; Sanvito, Stefano; Schwingenschlö gl, Udo
2012-01-01
Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite goldelectrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite goldsurfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the goldelectrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile.
Protocol for classical molecular dynamics simulations of nano-junctions in solution
Gkionis, Konstantinos
2012-10-19
Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite goldelectrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite goldsurfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the goldelectrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile.
National Research Council Canada - National Science Library
Bunte, Steven
2000-01-01
To investigate the mechanical and other condensed phase properties of energetic materials using atomistic simulation techniques, the COMPASS force field has been expanded to include high-energy nitro functional groups...
LASNEX simulations of the classical and laser-driven Rayleigh-Taylor instability
International Nuclear Information System (INIS)
Mikaelian, K.O.
1990-01-01
We present the results of two-dimensional LASNEX simulations of the classical and laser-driven Rayleigh-Taylor instability. Our growth rates and eigenmodes for classical two- and three-fluid problems agree closely with the exact analytic expressions. We illustrate in several examples how perturbations feed through from one interface to another. For targets driven by a 1/4-μm laser at I=2x10 14 W/cm 2 our growth rates are 40--80 % of the classical case rates for wavelengths between 5 and 100 μm. We find that radiation transport has a stabilizing effect on the Rayleigh-Taylor instability, particularly at high intensities. A brief comparison with a laser-driven experiment is also presented
Czech Academy of Sciences Publication Activity Database
Havrila, Marek; Zgarbová, M.; Jurečka, P.; Banáš, P.; Krepl, Miroslav; Otyepka, M.; Šponer, Jiří
2015-01-01
Roč. 119, č. 49 (2015), s. 15176-15190 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DIMERIZATION INITIATION SITE * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015
Yin, Jian; Fenley, Andrew T.; Henriksen, Niel M.; Gilson, Michael K.
2015-01-01
Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by non-optimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery. PMID:26181208
Oxygen transport properties estimation by classical trajectory–direct simulation Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Bruno, Domenico, E-mail: domenico.bruno@cnr.it [Istituto di Metodologie Inorganiche e dei Plasmi, Consiglio Nazionale delle Ricerche– Via G. Amendola 122, 70125 Bari (Italy); Frezzotti, Aldo, E-mail: aldo.frezzotti@polimi.it; Ghiroldi, Gian Pietro, E-mail: gpghiro@gmail.com [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano–Via La Masa 34, 20156 Milano (Italy)
2015-05-15
Coupling direct simulation Monte Carlo (DSMC) simulations with classical trajectory calculations is a powerful tool to improve predictive capabilities of computational dilute gas dynamics. The considerable increase in computational effort outlined in early applications of the method can be compensated by running simulations on massively parallel computers. In particular, Graphics Processing Unit acceleration has been found quite effective in reducing computing time of classical trajectory (CT)-DSMC simulations. The aim of the present work is to study dilute molecular oxygen flows by modeling binary collisions, in the rigid rotor approximation, through an accurate Potential Energy Surface (PES), obtained by molecular beams scattering. The PES accuracy is assessed by calculating molecular oxygen transport properties by different equilibrium and non-equilibrium CT-DSMC based simulations that provide close values of the transport properties. Comparisons with available experimental data are presented and discussed in the temperature range 300–900 K, where vibrational degrees of freedom are expected to play a limited (but not always negligible) role.
Martini Force Field Parameters for Glycolipids
Czech Academy of Sciences Publication Activity Database
Lopéz, C. A.; Sovová, Žofie; van Eerden, F. J.; de Vries, H.; Marrink, S.
2013-01-01
Roč. 9, č. 3 (2013), s. 1694-1708 ISSN 1549-9618 Institutional support: RVO:67179843 Keywords : molecular-dynamics simulations * coarse-grained model * phase-behavior * lipid-bilayer * ganglioside GM1 * domain formation * head groups * membrane * Monogalactosyldiacylglycerol * X-RAY Subject RIV: BO - Biophysics Impact factor: 5.310, year: 2013
Classical trajectory Monte Carlo simulations of particle confinement using dual levitated coils
Directory of Open Access Journals (Sweden)
R. A. Lane
2014-07-01
Full Text Available The particle confinement properties of plasma confinement systems that employ dual levitated magnetic coils are investigated using classical trajectory Monte Carlo simulations. Two model systems are examined. In one, two identical current-carrying loops are coaxial and separated axially. In the second, two concentric and coplanar loops have different radii and carry equal currents. In both systems, a magnetic null circle is present between the current loops. Simulations are carried out for seven current loop separations for each system and at numerous values of magnetic field strength. Particle confinement is investigated at three locations between the loops at different distances from the magnetic null circle. Each simulated particle that did not escape the system exhibited one of four modes of confinement. Reduced results are given for both systems as the lowest magnetic field strength that exhibits complete confinement of all simulated particles for a particular loop separation.
Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.
Vanommeslaeghe, K; MacKerell, A D
2012-12-21
Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ .
Tavakoli, Armin; Cabello, Adán
2018-03-01
We consider an ideal experiment in which unlimited nonprojective quantum measurements are sequentially performed on a system that is initially entangled with a distant one. At each step of the sequence, the measurements are randomly chosen between two. However, regardless of which measurement is chosen or which outcome is obtained, the quantum state of the pair always remains entangled. We show that the classical simulation of the reduced state of the distant system requires not only unlimited rounds of communication, but also that the distant system has infinite memory. Otherwise, a thermodynamical argument predicts heating at a distance. Our proposal can be used for experimentally ruling out nonlocal finite-memory classical models of quantum theory.
Mapping the force field of a hydrogen-bonded assembly
Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.
2014-05-01
Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.
2015-01-01
The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect
International Nuclear Information System (INIS)
Verkhovtsev, A.; Korol, A.V.; Solovyov, A.V.
2017-01-01
We present the results of classical molecular dynamics simulations of collision-induced fusion and fragmentation of C 60 fullerenes, performed by means of the MBN Explorer software package. The simulations provide information on structural differences of the fused compound depending on kinematics of the collision process. The analysis of fragmentation dynamics at different initial conditions shows that the size distributions of produced molecular fragments are peaked for dimers, which is in agreement with a well-established mechanism of C 60 fragmentation via preferential C 2 emission. Atomic trajectories of the colliding particles are analyzed and different fragmentation patterns are observed and discussed. On the basis of the performed simulations, characteristic time of C 2 emission is estimated as a function of collision energy. The results are compared with experimental time-of-flight distributions of molecular fragments and with earlier theoretical studies. Considering the widely explored case study of C 60 -C 60 collisions, we demonstrate broad capabilities of the MBN Explorer software, which can be utilized for studying collisions of a broad variety of nano-scale and bio-molecular systems by means of classical molecular dynamics. (authors)
How well do force fields capture the strength of salt bridges in proteins?
Directory of Open Access Journals (Sweden)
Mustapha Carab Ahmed
2018-06-01
Full Text Available Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1 to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.
Symmetrical Windowing for Quantum States in Quasi-Classical Trajectory Simulations
Cotton, Stephen Joshua
An approach has been developed for extracting approximate quantum state-to-state information from classical trajectory simulations which "quantizes" symmetrically both the initial and final classical actions associated with the degrees of freedom of interest using quantum number bins (or "window functions") which are significantly narrower than unit-width. This approach thus imposes a more stringent quantization condition on classical trajectory simulations than has been traditionally employed, while doing so in a manner that is time-symmetric and microscopically reversible. To demonstrate this "symmetric quasi-classical" (SQC) approach for a simple real system, collinear H + H2 reactive scattering calculations were performed [S.J. Cotton and W.H. Miller, J. Phys. Chem. A 117, 7190 (2013)] with SQC-quantization applied to the H 2 vibrational degree of freedom (DOF). It was seen that the use of window functions of approximately 1/2-unit width led to calculated reaction probabilities in very good agreement with quantum mechanical results over the threshold energy region, representing a significant improvement over what is obtained using the traditional quasi-classical procedure. The SQC approach was then applied [S.J. Cotton and W.H. Miller, J. Chem. Phys. 139, 234112 (2013)] to the much more interesting and challenging problem of incorporating non-adiabatic effects into what would otherwise be standard classical trajectory simulations. To do this, the classical Meyer-Miller (MM) Hamiltonian was used to model the electronic DOFs, with SQC-quantization applied to the classical "electronic" actions of the MM model---representing the occupations of the electronic states---in order to extract the electronic state population dynamics. It was demonstrated that if one ties the zero-point energy (ZPE) of the electronic DOFs to the SQC windowing function's width parameter this very simple SQC/MM approach is capable of quantitatively reproducing quantum mechanical results for
Zero-point energy conservation in classical trajectory simulations: Application to H2CO
Lee, Kin Long Kelvin; Quinn, Mitchell S.; Kolmann, Stephen J.; Kable, Scott H.; Jordan, Meredith J. T.
2018-05-01
A new approach for preventing zero-point energy (ZPE) violation in quasi-classical trajectory (QCT) simulations is presented and applied to H2CO "roaming" reactions. Zero-point energy may be problematic in roaming reactions because they occur at or near bond dissociation thresholds and these channels may be incorrectly open or closed depending on if, or how, ZPE has been treated. Here we run QCT simulations on a "ZPE-corrected" potential energy surface defined as the sum of the molecular potential energy surface (PES) and the global harmonic ZPE surface. Five different harmonic ZPE estimates are examined with four, on average, giving values within 4 kJ/mol—chemical accuracy—for H2CO. The local harmonic ZPE, at arbitrary molecular configurations, is subsequently defined in terms of "projected" Cartesian coordinates and a global ZPE "surface" is constructed using Shepard interpolation. This, combined with a second-order modified Shepard interpolated PES, V, allows us to construct a proof-of-concept ZPE-corrected PES for H2CO, Veff, at no additional computational cost to the PES itself. Both V and Veff are used to model product state distributions from the H + HCO → H2 + CO abstraction reaction, which are shown to reproduce the literature roaming product state distributions. Our ZPE-corrected PES allows all trajectories to be analysed, whereas, in previous simulations, a significant proportion was discarded because of ZPE violation. We find ZPE has little effect on product rotational distributions, validating previous QCT simulations. Running trajectories on V, however, shifts the product kinetic energy release to higher energy than on Veff and classical simulations of kinetic energy release should therefore be viewed with caution.
Simulations of collisions between N-body classical systems in interaction
International Nuclear Information System (INIS)
Morisseau, Francois
2006-05-01
The Classical N-body Dynamics (CNBD) is dedicated to the simulation of collisions between classical systems. The 2-body interaction used here has the properties of the Van der Waals potential and depends on just a few parameters. This work has two main goals. First, some theoretical approaches assume that the dynamical stage of the collisions plays an important role. Moreover, colliding nuclei are supposed to present a 1. order liquid-gas phase transition. Several signals have been introduced to show this transition. We have searched for two of them: the bimodality of the mass asymmetry and negative heat capacity. We have found them and we give an explanation of their presence in our calculations. Second, we have improved the interaction by adding a Coulomb like potential and by taking into account the stronger proton-neutron interaction in nuclei. Then we have figured out the relations that exist between the parameters of the 2-body interaction and the properties of the systems. These studies allow us to fit the properties of the classical systems to those of the nuclei. In this manuscript the first results of this fit are shown. (author)
Simplified TiO2 force fields for studies of its interaction with biomolecules
Luan, Binquan; Huynh, Tien; Zhou, Ruhong
2015-06-01
Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.
Ice and water droplets on graphite: A comparison of quantum and classical simulations
International Nuclear Information System (INIS)
Ramírez, Rafael; Singh, Jayant K.; Müller-Plathe, Florian; Böhm, Michael C.
2014-01-01
Ice and water droplets on graphite have been studied by quantum path integral and classical molecular dynamics simulations. The point-charge q-TIP4P/F potential was used to model the interaction between flexible water molecules, while the water-graphite interaction was described by a Lennard-Jones potential previously used to reproduce the macroscopic contact angle of water droplets on graphite. Several energetic and structural properties of water droplets with sizes between 10 2 and 10 3 molecules were analyzed in a temperature interval of 50–350 K. The vibrational density of states of crystalline and amorphous ice drops was correlated to the one of ice Ih to assess the influence of the droplet interface and molecular disorder on the vibrational properties. The average distance of covalent OH bonds is found 0.01 Å larger in the quantum limit than in the classical one. The OO distances are elongated by 0.03 Å in the quantum simulations at 50 K. Bond distance fluctuations are large as a consequence of the zero-point vibrations. The analysis of the H-bond network shows that the liquid droplet is more structured in the classical limit than in the quantum case. The average kinetic and potential energy of the ice and water droplets on graphite has been compared with the values of ice Ih and liquid water as a function of temperature. The droplet kinetic energy shows a temperature dependence similar to the one of liquid water, without apparent discontinuity at temperatures where the droplet is solid. However, the droplet potential energy becomes significantly larger than the one of ice or water at the same temperature. In the quantum limit, the ice droplet is more expanded than in a classical description. Liquid droplets display identical density profiles and liquid-vapor interfaces in the quantum and classical limits. The value of the contact angle is not influenced by quantum effects. Contact angles of droplets decrease as the size of the water droplet increases
Barone, Vincenzo; Cacelli, Ivo; De Mitri, Nicola; Licari, Daniele; Monti, Susanna; Prampolini, Giacomo
2013-03-21
The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.
Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer
Directory of Open Access Journals (Sweden)
Casuyac Miqueas
2016-01-01
Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.
Classical-trajectory simulation of accelerating neutral atoms with polarized intense laser pulses
Xia, Q. Z.; Fu, L. B.; Liu, J.
2013-03-01
In the present paper, we perform the classical trajectory Monte Carlo simulation of the complex dynamics of accelerating neutral atoms with linearly or circularly polarized intense laser pulses. Our simulations involve the ion motion as well as the tunneling ionization and the scattering dynamics of valence electron in the combined Coulomb and electromagnetic fields, for both helium (He) and magnesium (Mg). We show that for He atoms, only linearly polarized lasers can effectively accelerate the atoms, while for Mg atoms, we find that both linearly and circularly polarized lasers can successively accelerate the atoms. The underlying mechanism is discussed and the subcycle dynamics of accelerating trajectories is investigated. We have compared our theoretical results with a recent experiment [Eichmann Nature (London)NATUAS0028-083610.1038/nature08481 461, 1261 (2009)].
Energy Technology Data Exchange (ETDEWEB)
Costandy, Joseph; Michalis, Vasileios K.; Economou, Ioannis G., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu [Chemical Engineering Program, Texas A& M University at Qatar, P.O. Box 23874, Doha (Qatar); Tsimpanogiannis, Ioannis N., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu [Chemical Engineering Program, Texas A& M University at Qatar, P.O. Box 23874, Doha (Qatar); Environmental Research Laboratory, National Center for Scientific Research NCSR “Demokritos,” 15310 Aghia Paraskevi, Attikis (Greece); Stubos, Athanassios K. [Environmental Research Laboratory, National Center for Scientific Research NCSR “Demokritos,” 15310 Aghia Paraskevi, Attikis (Greece)
2016-03-28
We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies.
Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties
DEFF Research Database (Denmark)
Voroshylova, I. V.; Chaban, V. V.
2014-01-01
Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis......(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cationanion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove...... and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia LopesPadua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids....
DEFF Research Database (Denmark)
Josephsen, Jens
2005-01-01
Laboratory exercises, investigations, and experiments are invariably included in university chemistry teaching. The learning of empirical facts, chemical procedures and methods in chemistry depends heavily on the experience, which may be obtained from such teaching activities [1]. Experimental work...... in teaching is, however, both expensive and time consuming, and should therefor effectively benefit from the allotted student time, money, and staff time. If the instructions are too ambitious regarding what the students can manage to do and are overloaded with information [2,3] it may result in the students...... (and in university programmes it often isn’t), but rather to give them experience with chemicals and methods, a computer-based laboratory simulation may function as a cheap and fast extension of student lab time. Virtual investigations seem to be a promising kind of tool [6,7,8] for several reasons...
AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms.
Wu, Xiaojing; Clavaguera, Carine; Lagardère, Louis; Piquemal, Jean-Philip; de la Lande, Aurélien
2018-04-16
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H 2 O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.
Ojwang, J.G.O.; Chaudhuri, S.; Duin, van A.C.T.; Chabal, Y.J.; Veyan, J.-F.; Santen, van R.A.; Kramer, G.J.; Goddard III, W.A.
2010-01-01
We have used reactive force field (ReaxFF) to investigate the mechanism of interaction of alanes on Al(111) surface. Our simulations show that, on the Al(111) surface, alanes oligomerize into larger alanes. In addition, from our simulations, adsorption of atomic hydrogen on Al(111) surface leads to
Classical molecular dynamics simulation of weakly-bound projectile heavy-ion reactions
Directory of Open Access Journals (Sweden)
Morker Mitul R.
2015-01-01
Full Text Available A 3-body classical molecular dynamics approach for heavy-ion reactions involving weakly bound projectiles is developed. In this approach a weakly bound projectile is constructed as a two-body cluster of the constituent tightly bound nuclei in a configuration corresponding to the observed breakup energy. This 3-body system with their individual nucleon configuration in their ground state is dynamically evolved for given initial conditions using the three-stage classical molecular dynamics approach (3S-CMD. Various levels of rigidbody constraints on the projectile constituents and the target are considered at appropriate stages. This 3-dimensional approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but internal excitations and breakup probabilities at distances close to the barrier also. Dynamical simulations of 6Li+209Bi show all the possible reaction mechanism like complete fusion, incomplete fusion, scattering and breakup scattering. Complete fusion cross sections of 6Li+209Bi and 7Li+209Bi reactions are calculated in this approach with systematic relaxations of the rigid-body constraints on one or more constituent nuclei.
Czech Academy of Sciences Publication Activity Database
Vlček, L.; Uhlík, F.; Moučka, F.; Nezbeda, Ivo; Chialvo, L.
2015-01-01
Roč. 119, č. 3 (2015), s. 488-500 ISSN 1089-5639 Institutional support: RVO:67985858 Keywords : monte-carlo simulations * molecular-dynamic simulations * classical drude oscillators Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.883, year: 2015
Srivastava, Deepak; Saini, Subhash (Technical Monitor)
1998-01-01
The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.
Turesson, Martin; Szparaga, Ryan; Ma, Ke; Woodward, Clifford E; Forsman, Jan
2014-05-14
A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF₄⁻, respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented.
Martini Coarse-Grained Force Field : Extension to DNA
Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J.
We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the
Martini Coarse-Grained Force Field : Extension to Carbohydrates
Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.
2009-01-01
We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The
Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel
2018-06-01
We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.
International Nuclear Information System (INIS)
Crystal, T.L.; Kuhn, S.; Birdsall, C.K.
1984-01-01
The classical Pierce diode is a simple 1-d system of two shorted metal plates, a cold beam of electrons injected from one side and a neutralizing background of rigid ions. While the plasma medium is technically stable, the finiteness of the Pierce system allows stable and unstable operation. It is usefully studied as an archetypical bounded plasma system, related e.g., to Q-machines, particle accelerators, thermionic converters. New particle simulations of the Pierce diode have successfully recovered many novel linear phenomena including the dominant linear eigenmodes (seen in the internal electrostatic fields), and the dominant and subdominant eigenfrequencies, (seen both in the internal electrostatics and in the external circuit current, J/sub ext/(t)). These simulation results conform very well to detailed predictions of a new linear analysis. The final (nonlinear) state recovered can show critical dependence on initial (linear perturbation) conditions, and can be made steady-state (d.c.) or periodic-oscillatory by simply changing the initial conditions by a factor of 10/sup -4/ or less. A third class of final state is also possible which has oscillations which seem to be nonperiodic
Investigation of Numerical Dissipation in Classical and Implicit Large Eddy Simulations
Directory of Open Access Journals (Sweden)
Moutassem El Rafei
2017-12-01
Full Text Available The quantitative measure of dissipative properties of different numerical schemes is crucial to computational methods in the field of aerospace applications. Therefore, the objective of the present study is to examine the resolving power of Monotonic Upwind Scheme for Conservation Laws (MUSCL scheme with three different slope limiters: one second-order and two third-order used within the framework of Implicit Large Eddy Simulations (ILES. The performance of the dynamic Smagorinsky subgrid-scale model used in the classical Large Eddy Simulation (LES approach is examined. The assessment of these schemes is of significant importance to understand the numerical dissipation that could affect the accuracy of the numerical solution. A modified equation analysis has been employed to the convective term of the fully-compressible Navier–Stokes equations to formulate an analytical expression of truncation error for the second-order upwind scheme. The contribution of second-order partial derivatives in the expression of truncation error showed that the effect of this numerical error could not be neglected compared to the total kinetic energy dissipation rate. Transitions from laminar to turbulent flow are visualized considering the inviscid Taylor–Green Vortex (TGV test-case. The evolution in time of volumetrically-averaged kinetic energy and kinetic energy dissipation rate have been monitored for all numerical schemes and all grid levels. The dissipation mechanism has been compared to Direct Numerical Simulation (DNS data found in the literature at different Reynolds numbers. We found that the resolving power and the symmetry breaking property are enhanced with finer grid resolutions. The production of vorticity has been observed in terms of enstrophy and effective viscosity. The instantaneous kinetic energy spectrum has been computed using a three-dimensional Fast Fourier Transform (FFT. All combinations of numerical methods produce a k − 4 spectrum
Modeling Enzymatic Transition States by Force Field Methods
DEFF Research Database (Denmark)
Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank
2009-01-01
The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...... of the TS geometry on the flexibility of the system has been probed by fixing layers of atoms around the active site and using increasingly larger nonbonded cutoffs. The variability over the 20 structures is found to decrease as the system is made more flexible. Relative energies have been calculated...... by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part...
Xu, Dong; Zhang, Yang
2012-07-01
Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.
Mercadante, Davide; Milles, Sigrid; Fuertes, Gustavo; Svergun, Dmitri I; Lemke, Edward A; Gräter, Frauke
2015-06-25
Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.
Enhanced Particle Swarm Optimization Algorithm: Efficient Training of ReaxFF Reactive Force Fields.
Furman, David; Carmeli, Benny; Zeiri, Yehuda; Kosloff, Ronnie
2018-05-04
Particle swarm optimization is a powerful metaheuristic population-based global optimization algorithm. However, when applied to non-separable objective functions its performance on multimodal landscapes is significantly degraded. Here we show that a significant improvement in the search quality and efficiency on multimodal functions can be achieved by enhancing the basic rotation-invariant particle swarm optimization algorithm with isotropic Gaussian mutation operators. The new algorithm demonstrates a superior performance across several nonlinear, multimodal benchmark functions compared to the rotation-invariant Particle Swam Optimization (PSO) algorithm and the well-established simulated annealing and sequential one-parameter parabolic interpolation methods. A search for the optimal set of parameters for the dispersion interaction model in ReaxFF-lg reactive force field is carried out with respect to accurate DFT-TS calculations. The resulting optimized force field accurately describes the equations of state of several high-energy molecular crystals where such interactions are of crucial importance. The improved algorithm also presents a better performance compared to a Genetic Algorithm optimization method in the optimization of a ReaxFF-lg correction model parameters. The computational framework is implemented in a standalone C++ code that allows a straightforward development of ReaxFF reactive force fields.
Systematic Parameterization of Lignin for the CHARMM Force Field
Energy Technology Data Exchange (ETDEWEB)
Vermaas, Joshua; Petridis, Loukas; Beckham, Gregg; Crowley, Michael
2017-07-06
Plant cell walls have three primary components, cellulose, hemicellulose, and lignin, the latter of which is a recalcitrant, aromatic heteropolymer that provides structure to plants, water and nutrient transport through plant tissues, and a highly effective defense against pathogens. Overcoming the recalcitrance of lignin is key to effective biomass deconstruction, which would in turn enable the use of biomass as a feedstock for industrial processes. Our understanding of lignin structure in the plant cell wall is hampered by the limitations of the available lignin forcefields, which currently only account for a single linkage between lignins and lack explicit parameterization for emerging lignin structures both from natural variants and engineered lignin structures. Since polymerization of lignin occurs via radical intermediates, multiple C-O and C-C linkages have been isolated , and the current force field only represents a small subset of lignin the diverse lignin structures found in plants. In order to take into account the wide range of lignin polymerization chemistries, monomers and dimer combinations of C-, H-, G-, and S-lignins as well as with hydroxycinnamic acid linkages were subjected to extensive quantum mechanical calculations to establish target data from which to build a complete molecular mechanics force field tuned specifically for diverse lignins. This was carried out in a GPU-accelerated global optimization process, whereby all molecules were parameterized simultaneously using the same internal parameter set. By parameterizing lignin specifically, we are able to more accurately represent the interactions and conformations of lignin monomers and dimers relative to a general force field. This new force field will enables computational researchers to study the effects of different linkages on the structure of lignin, as well as construct more accurate plant cell wall models based on observed statistical distributions of lignin that differ between
International Nuclear Information System (INIS)
Gelman, David; Schwartz, Steven D.
2010-01-01
The recently developed quantum-classical method has been applied to the study of dissipative dynamics in multidimensional systems. The method is designed to treat many-body systems consisting of a low dimensional quantum part coupled to a classical bath. Assuming the approximate zeroth order evolution rule, the corrections to the quantum propagator are defined in terms of the total Hamiltonian and the zeroth order propagator. Then the corrections are taken to the classical limit by introducing the frozen Gaussian approximation for the bath degrees of freedom. The evolution of the primary part is governed by the corrected propagator yielding the exact quantum dynamics. The method has been tested on two model systems coupled to a harmonic bath: (i) an anharmonic (Morse) oscillator and (ii) a double-well potential. The simulations have been performed at zero temperature. The results have been compared to the exact quantum simulations using the surrogate Hamiltonian approach.
International Nuclear Information System (INIS)
Owolabi, Kolade M.
2016-01-01
The aim of this paper is to examine pattern formation in the sub— and super-diffusive scenarios and compare it with that of classical or standard diffusive processes in two-component fractional reaction-diffusion systems that modeled a predator-prey dynamics. The focus of the work concentrates on the use of two separate mathematical techniques, we formulate a Fourier spectral discretization method as an efficient alternative technique to solve fractional reaction-diffusion problems in higher-dimensional space, and later advance the resulting systems of ODEs in time with the adaptive exponential time-differencing solver. Obviously, the fractional Fourier approach is able to achieve spectral convergence up to machine precision regardless of the fractional order α, owing to the fact that our approach is able to give full diagonal representation of the fractional operator. The complexity of the dynamics in this system is theoretically discussed and graphically displayed with some examples and numerical simulations in one, two and three dimensions.
Directory of Open Access Journals (Sweden)
Pietra Paola
2012-04-01
Full Text Available We propose a hybrid classical-quantum model to study the motion of electrons in ultra-scaled confined nanostructures. The transport of charged particles, considered as one dimensional, is described by a quantum effective mass model in the active zone coupled directly to a drift-diffusion problem in the rest of the device. We explain how this hybrid model takes into account the peculiarities due to the strong confinement and we present numerical simulations for a simplified carbon nanotube. Nous proposons un modèle hybride classique-quantique pour décrire le mouvement des électrons dans des nanostructures très fortement confinées. Le transport des particules, consideré unidimensionel, est décrit par un modèle quantique avec masse effective dans la zone active couplé à un problème de dérive-diffusion dans le reste du domaine. Nous expliquons comment ce modèle hybride prend en compte les spécificités de ce très fort confinement et nous présentons des résultats numériques pour un nanotube de carbone simplifié.
DEFF Research Database (Denmark)
Monti, Susanna; Corozzi, Alessandro; Fristrup, Peter
2013-01-01
In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously rep...
Energy Technology Data Exchange (ETDEWEB)
Lynch, Vickie E.; Borreguero, Jose M. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Bhowmik, Debsindhu [Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Ganesh, Panchapakesan; Sumpter, Bobby G. [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Proffen, Thomas E. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Goswami, Monojoy, E-mail: goswamim@ornl.gov [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States)
2017-07-01
Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.
Secondary Structure of Rat and Human Amylin across Force Fields.
Directory of Open Access Journals (Sweden)
Kyle Quynn Hoffmann
Full Text Available The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient
Mangen, M.J.J.; Nielen, M.; Burrell, A.M.
2003-01-01
The effects of additional measures adopted during a classical swine fever (CSF) epidemic to reduce piglet supply, namely, an insemination ban, abortion of sows and killing of young piglets, are studied using a stochastic, spatial, dynamic epidemiological simulation model of the pig sector in the
Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra
2016-07-28
The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.
Improvement of a force field to model the edges of clay particles
International Nuclear Information System (INIS)
Pouvreau, Maxime
2016-01-01
The CLAYFF force field is widely used to model the interfaces of clay minerals - and related layered materials - with an aqueous phase. In the simulations, clay particles are typically represented by semi-infinite layers, i.e. only surfaces parallel to the layer plane (basal surfaces) are considered. This simplification is acceptable to a certain extent, but clay layers are really nano sized and terminated by lateral surfaces or edges. These surfaces can not only adsorb solvated species but are also subject to proton transfers, and all physico-chemical processes related to the aqueous phase acidity predominantly occur at the edges. By adding to the CLAYFF force field a Metal-O-H angle bending term whose parameters are correctly adjusted, the simulations of edge interfaces become possible.The parameters of Al-O-H and Mg-O-H terms were obtained from DFT calculations on bulk, basal surface and edge structural models of gibbsite Al(OH) 3 and brucite Mg(OH) 2 , whose layers can be considered as the backbones of clay minerals and related materials. In addition, the Si-O-H term was parametrized from an edge model of kaolinite Al 2 Si 2 O 5 (OH) 4 . Molecular dynamics simulations based on DFT and on CLAYFF with and without Metal-O-H term were performed. The modified force field clearly improves the description of hydroxylated surfaces: the orientation and the vibrational dynamics of the hydroxyl groups, the hydrogen bonding, and the coordination of metal atoms belonging to the edge are all closer to reality [fr
Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel
2018-04-05
Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.
Hydrodynamic Simulations of Classical Novae: Accretion onto CO White Dwarfs as SN Ia Progenitors
Starrfield, Sumner; Bose, Maitrayee; Iliadis, Christian; Hix, William R.; José, Jordi; Hernanz, Margarita
2017-06-01
We have continued our studies of accretion onto white dwarfs by following the evolution of thermonuclear runaways on Carbon Oxygen (CO) white dwarfs. We have varied the mass of the white dwarf and the composition of the accreted material but chosen to keep the mass accretion rate at 2 x 10^{-10} solar masses per year to obtain the largest amount of accreted material possible with rates near to those observed. We assume either 25% core material or 50% core material has been mixed into the accreting material prior to the explosion. We use our 1D, lagrangian, hydrodynamic code: NOVA. We will report on the results of these simulations and compare the ejecta abundances to those measured in pre-solar grains that are thought to arise from classical nova explosions. These results will also be compared to recent results with SHIVA (Jose and Hernanz). We find that in all cases and for all white dwarf masses that less mass is ejected than accreted and, therefore, the white dwarf is growing in mass as a result of the accretion and resulting explosion.This work was supported in part by NASA under the Astrophysics Theory Program grant 14-ATP14-0007 and the U.S. DOE under Contract No. DE-FG02- 97ER41041. SS acknowledges partial support from NASA, NSF, and HST grants to ASU and WRH is supported by the U.S. Department of Energy, Office of Nuclear Physics. The results reported herein benefitted from collaborations and/or information exchange within NASA’s Nexus for Exoplanet System Science (NExSS) research coordination network sponsored by NASA’s Science Mission Directorate.
Quantum mechanical force field for water with explicit electronic polarization.
Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali
2013-08-07
A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across
On the use of quartic force fields in variational calculations
Fortenberry, Ryan C.; Huang, Xinchuan; Yachmenev, Andrey; Thiel, Walter; Lee, Timothy J.
2013-06-01
Quartic force fields (QFFs) have been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this letter we discuss how the simple-internal or bond-length bond-angle (BLBA) coordinates can be transformed into Morse-cosine (-sine) coordinates which produce potential energy surfaces from QFFs that possess proper limiting behavior and can describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system to 5 cm-1 or better compared to experiment. We investigate parameter scaling in the Morse coordinate, symmetry considerations, and examples of transformed QFFs making use of the MULTIMODE, TROVE, and VTET variational vibrational methods.
Valence force fields and the lattice dynamics of beryllium oxide
International Nuclear Information System (INIS)
Ramani, R.; Mani, K.K.; Singh, R.P.
1976-01-01
The lattice dynamics of beryllium oxide have been studied using a rigid-ion model, with short-range forces represented by a valence force field. Various existing calculations on group-IV elements using such a field have been examined as a prelude to transference of force constants from diamond to beryllium oxide. The effects of ionicity on the force constants have been included in the form of scale factors. It is shown that no satisfactory fit to the long-wavelength data on BeO can be found with transferred force constants. However, adequate least-squares fits can be found both with four- and six-parameter valence force fields, the discrepancy with experiment being large only for one optical mode at the Brillouin-zone center. Dispersion curves along Δ and Σ are presented and are in fair agreement with experiment, deviations arising essentially from the quality of the fit to the long-wavelength data. The bond-bending interactions are found to play a significant role and arguments have been presented to show that the inclusion of further angle-angle interactions would yield a very satisfactory picture of the dynamics
Force-field compensation in a manual tracking task.
Directory of Open Access Journals (Sweden)
Valentina Squeri
2010-06-01
Full Text Available This study addresses force/movement control in a dynamic "hybrid" task: the master sub-task is continuous manual tracking of a target moving along an eight-shaped Lissajous figure, with the tracking error as the primary performance index; the slave sub-task is compensation of a disturbing curl viscous field, compatibly with the primary performance index. The two sub-tasks are correlated because the lateral force the subject must exert on the eight-shape must be proportional to the longitudinal movement speed in order to perform a good tracking. The results confirm that visuo-manual tracking is characterized by an intermittent control mechanism, in agreement with previous work; the novel finding is that the overall control patterns are not altered by the presence of a large deviating force field, if compared with the undisturbed condition. It is also found that the control of interaction-forces is achieved by a combination of arm stiffness properties and direct force control, as suggested by the systematic lateral deviation of the trajectories from the nominal path and the comparison between perturbed trials and catch trials. The coordination of the two sub-tasks is quickly learnt after the activation of the deviating force field and is achieved by a combination of force and the stiffness components (about 80% vs. 20%, which is a function of the implicit accuracy of the tracking task.
The Quantum Space Phase Transitions for Particles and Force Fields
Directory of Open Access Journals (Sweden)
Chung D.-Y.
2006-07-01
Full Text Available We introduce a phenomenological formalism in which the space structure is treated in terms of attachment space and detachment space. Attachment space attaches to an object, while detachment space detaches from the object. The combination of these spaces results in three quantum space phases: binary partition space, miscible space and binary lattice space. Binary lattice space consists of repetitive units of alternative attachment space and detachment space. In miscible space, attachment space is miscible to detachment space, and there is no separation between attachment space and detachment spaces. In binary partition space, detachment space and attachment space are in two separat continuous regions. The transition from wavefunction to the collapse of wavefuction under interference becomes the quantum space phase transition from binary lattice space to miscible space. At extremely conditions, the gauge boson force field undergoes a quantum space phase transition to a "hedge boson force field", consisting of a "vacuum" core surrounded by a hedge boson shell, like a bubble with boundary.
Probing the Importance of Charge Flux in Force Field Modeling.
Sedghamiz, Elaheh; Nagy, Balazs; Jensen, Frank
2017-08-08
We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.
García-Vela, A.
2000-05-01
A definition of a quantum-type phase-space distribution is proposed in order to represent the initial state of the system in a classical dynamics simulation. The central idea is to define an initial quantum phase-space state of the system as the direct product of the coordinate and momentum representations of the quantum initial state. The phase-space distribution is then obtained as the square modulus of this phase-space state. The resulting phase-space distribution closely resembles the quantum nature of the system initial state. The initial conditions are sampled with the distribution, using a grid technique in phase space. With this type of sampling the distribution of initial conditions reproduces more faithfully the shape of the original phase-space distribution. The method is applied to generate initial conditions describing the three-dimensional state of the Ar-HCl cluster prepared by ultraviolet excitation. The photodissociation dynamics is simulated by classical trajectories, and the results are compared with those of a wave packet calculation. The classical and quantum descriptions are found in good agreement for those dynamical events less subject to quantum effects. The classical result fails to reproduce the quantum mechanical one for the more strongly quantum features of the dynamics. The properties and applicability of the phase-space distribution and the sampling technique proposed are discussed.
International Nuclear Information System (INIS)
Carbonniere, Philippe; Begue, Didier; Dargelos, Alain; Pouchan, Claude
2004-01-01
In this work we present an attractive least-squares fitting procedure which allows for the calculation of a quartic force field by jointly using energy, gradient, and Hessian data, obtained from electronic wave function calculations on a suitably chosen grid of points. We use the experimental design to select the grid points: a 'simplex-sum' of Box and Behnken grid was chosen for its efficiency and accuracy. We illustrate the numerical implementations of the method by using the energy and gradient data for H 2 O and H 2 CO. The B3LYP/cc-pVTZ quartic force field performed from 11 and 44 simplex-sum configurations shows excellent agreement in comparison to the classical 44 and 168 energy calculations
A new united atom force field for adsorption of alkenes in zeolites
Liu, B.; Smit, B.; Rey, F.; Valencia, S.; Calero, S.
2008-01-01
A new united atom force field was developed that accurately describes the adsorption properties of linear alkenes in zeolites. The force field was specifically designed for use in the inhomogeneous system and therefore a truncated and shifted potential was used. With the determined force field, we
Force fields for silicas and aluminophosphates based on ab initio calculations
Beest, van B.W.H.; Kramer, G.J.; Santen, van R.A.
1990-01-01
Authors address the problem of finding interat. force fields for silicas from ab initio calcns. on small clusters. The force field cannot be detd. from cluster data alone; incorporation of bulk-system information into the force field remains essential. Bearing this in mind, authors derive a force
Rigorous force field optimization principles based on statistical distance minimization
Energy Technology Data Exchange (ETDEWEB)
Vlcek, Lukas, E-mail: vlcekl1@ornl.gov [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States); Joint Institute for Computational Sciences, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6173 (United States); Chialvo, Ariel A. [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States)
2015-10-14
We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.
A Multiposture Locomotor Training Device with Force-Field Control
Directory of Open Access Journals (Sweden)
Jianfeng Sui
2014-11-01
Full Text Available This paper introduces a multiposture locomotor training device (MPLTD with a closed-loop control scheme based on joint angle feedback, which is able to overcome various difficulties resulting from mechanical vibration and the weight of trainer to achieve higher accuracy trajectory. By introducing the force-field control scheme used in the closed-loop control, the device can obtain the active-constrained mode including the passive one. The MPLTD is mainly composed of three systems: posture adjusting and weight support system, lower limb exoskeleton system, and control system, of which the lower limb exoskeleton system mainly includes the indifferent equilibrium mechanism with two degrees of freedom (DOF and the driving torque is calculated by the Lagrangian function. In addition, a series of experiments, the weight support and the trajectory accuracy experiment, demonstrate a good performance of mechanical structure and the closed-loop control.
Álvarez-Rúa, Carmen; Borge, Javier
2016-01-01
Thermodynamic processes are complex phenomena that can be understood as a set of successive stages. When treating processes, classical thermodynamics (and most particularly, the Gibbsian formulation, predominantly used in chemistry) only pays attention to initial and final states. However, reintroducing the notion of process is absolutely…
Zhou, Shiqi; Lamperski, Stanisław; Sokołowska, Marta
2017-07-01
We have performed extensive Monte-Carlo simulations and classical density functional theory (DFT) calculations of the electrical double layer (EDL) near a cylindrical electrode in a primitive model (PM) modified by incorporating interionic dispersion interactions. It is concluded that (i) in general, an unsophisticated use of the mean field (MF) approximation for the interionic dispersion interactions does not distinctly worsen the classical DFT performance, even if the salt ions considered are highly asymmetrical in size (3:1) and charge (5:1), the bulk molar concentration considered is high up to a total bulk ion packing fraction of 0.314, and the surface charge density of up to 0.5 C m-2. (ii) More specifically, considering the possible noises in the simulation, the local volume charge density profiles are the most accurately predicted by the classical DFT in all situations, and the co- and counter-ion singlet distributions are also rather accurately predicted; whereas the mean electrostatic potential profile is relatively less accurately predicted due to an integral amplification of minor inaccuracy of the singlet distributions. (iii) It is found that the layered structure of the co-ion distribution is abnormally possible only if the surface charge density is high enough (for example 0.5 C m-2) moreover, the co-ion valence abnormally influences the peak height of the first counter-ion layer, which decreases with the former. (iv) Even if both the simulation and DFT indicate an insignificant contribution of the interionic dispersion interaction to the above three ‘local’ quantities, it is clearly shown by the classical DFT that the interionic dispersion interaction does significantly influence a ‘global’ quantity like the cylinder surface-aqueous electrolyte interfacial tension, and this may imply the role of the interionic dispersion interaction in explaining the specific Hofmeister effects. We elucidate all of the above observations based on the
Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field
DEFF Research Database (Denmark)
Davis, Ryan S.; Sunil Kumar, P. B.; Sperotto, Maria Maddalena
2013-01-01
The phase behavior of the coarse-grained MARTINI model for three-component lipid bilayers composed of dipalmytoyl-phosphatidylcholine (DPPC), cholesterol (Chol), and an unsaturated phosphatidylcholine (PC) was systematically investigated by molecular dynamics simulations. The aim of this study...... is to understand which types of unsaturated PC induce the formation of thermodynamically stable coexisting phases when added to mixtures of DPPC and Chol and to unravel the mechanisms that drive phase separation in such three-component mixtures. Our simulations indicate that the currently used MARTINI force field...... PCs, such as dilinoleyl-phosphatidylcholine (DUPC) and diarachidonoyl-phosphatidylcholine (DAPC). Through systematic tweaking of the interactions between the hydrophobic groups of the PC molecules, we show that the appearance of phase separation in three-component lipid bilayers, as modeled through...
Stochastic simulations of conditional states of partially observed systems, quantum and classical
International Nuclear Information System (INIS)
Gambetta, Jay; Wiseman, H M
2005-01-01
In a partially observed quantum or classical system the information that we cannot access results in our description of the system becoming mixed, even if we have perfect initial knowledge. That is, if the system is quantum the conditional state will be given by a state matrix ρ r (t), and if classical, the conditional state will be given by a probability distribution P r (x,t), where r is the result of the measurement. Thus to determine the evolution of this conditional state, under continuous-in-time monitoring, requires a numerically expensive calculation. In this paper we demonstrate a numerical technique based on linear measurement theory that allows us to determine the conditional state using only pure states. That is, our technique reduces the problem size by a factor of N, the number of basis states for the system. Furthermore we show that our method can be applied to joint classical and quantum systems such as arise in modelling realistic (finite bandwidth, noisy) measurement
Energy Technology Data Exchange (ETDEWEB)
Tran, Thanh Thuy; Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr; Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)
2016-05-28
Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ{sub 16−22} and Aβ{sub 37−42} of the full length Aβ{sub 1−42} Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ{sub 16−22} dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ{sub 16−22} and the dimer and trimer of Aβ{sub 37−42}. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ{sub 16−22} decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ{sub 37−42} decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.
The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.
Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr
2010-07-28
Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.
Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D
2015-10-08
Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.
Efficient nonparametric n -body force fields from machine learning
Glielmo, Aldo; Zeni, Claudio; De Vita, Alessandro
2018-05-01
We provide a definition and explicit expressions for n -body Gaussian process (GP) kernels, which can learn any interatomic interaction occurring in a physical system, up to n -body contributions, for any value of n . The series is complete, as it can be shown that the "universal approximator" squared exponential kernel can be written as a sum of n -body kernels. These recipes enable the choice of optimally efficient force models for each target system, as confirmed by extensive testing on various materials. We furthermore describe how the n -body kernels can be "mapped" on equivalent representations that provide database-size-independent predictions and are thus crucially more efficient. We explicitly carry out this mapping procedure for the first nontrivial (three-body) kernel of the series, and we show that this reproduces the GP-predicted forces with meV /Å accuracy while being orders of magnitude faster. These results pave the way to using novel force models (here named "M-FFs") that are computationally as fast as their corresponding standard parametrized n -body force fields, while retaining the nonparametric character, the ease of training and validation, and the accuracy of the best recently proposed machine-learning potentials.
International Acquisitons in Multinacionals: Under a Force Field
Directory of Open Access Journals (Sweden)
Américo da Costa Ramos Filho
2010-12-01
Full Text Available The purpose of this essay is to debate the performance of multinational companies concerning the management alternatives of their foreign unities, especially the ones derived from acquisitions, with consequences on the interaction between the headquarters and its subsidiaries or colligates and the managerial learning and knowledge associated to this process. First the problematic of internationalized companies by foreign direct investments – FDI’s, mainly by acquisitions and strategic alliances, is discussed. The intensity of the assimilation and interchange of values and practices within organizations in interacting process is stressed, including a set of typologies derived from the existing related literature. After this, a more specific approach about intra and interorganization aspects of the multinationals is performed, related to strategies, competences and roles of headquarters and subsidiaries, as well as their impact on the knowledge flux and its derived learning modes, evolving a established typologies set. The next step is to discuss two visions about the opposition between the universal and the particular in international management, with global and contextual aspects: a convergence-divergence opposition, like a force field, impacting on the knowledge transfer. Finally, some concluding comments are made, emphasizing, for the purpose of contribution, another type of multinationals typology relating the convergence-divergence duality to the organizational and national levels, as well the positioning of the companies in the resulted matrix.
Impossibility of Classically Simulating One-Clean-Qubit Model with Multiplicative Error
Fujii, Keisuke; Kobayashi, Hirotada; Morimae, Tomoyuki; Nishimura, Harumichi; Tamate, Shuhei; Tani, Seiichiro
2018-05-01
The one-clean-qubit model (or the deterministic quantum computation with one quantum bit model) is a restricted model of quantum computing where all but a single input qubits are maximally mixed. It is known that the probability distribution of measurement results on three output qubits of the one-clean-qubit model cannot be classically efficiently sampled within a constant multiplicative error unless the polynomial-time hierarchy collapses to the third level [T. Morimae, K. Fujii, and J. F. Fitzsimons, Phys. Rev. Lett. 112, 130502 (2014), 10.1103/PhysRevLett.112.130502]. It was open whether we can keep the no-go result while reducing the number of output qubits from three to one. Here, we solve the open problem affirmatively. We also show that the third-level collapse of the polynomial-time hierarchy can be strengthened to the second-level one. The strengthening of the collapse level from the third to the second also holds for other subuniversal models such as the instantaneous quantum polynomial model [M. Bremner, R. Jozsa, and D. J. Shepherd, Proc. R. Soc. A 467, 459 (2011), 10.1098/rspa.2010.0301] and the boson sampling model [S. Aaronson and A. Arkhipov, STOC 2011, p. 333]. We additionally study the classical simulatability of the one-clean-qubit model with further restrictions on the circuit depth or the gate types.
Quantum dynamics simulation of a small quantum system embedded in a classical environment
International Nuclear Information System (INIS)
Berendsen, H.J.C.; Mavri, J.; Mavri, J.
1996-01-01
The authors wish to consider quantum-dynamical processes that are not restricted to motion on a ground state Born-Oppenheimer surface, but may involve transitions between states. The authors interest is in such processes occurring in a complex environment that modulates the quantum process and interacts with it. In a system containing thousands degrees of freedom, the essential quantum behaviour is generally restricted to a small subsystem containing only a few degrees of freedom, while the environment can be treated classically. The challenge is threefold: 1) to treat the quantum subsystem correctly in a quantum-dynamical sense, 2) to treat the environment correctly in a classical dynamical sense, 3) to couple both systems in such a way that errors in the average or long-term behaviour are minimized. After an exposition of the theory, an insight into quantum-dynamical behaviour by using pictorial analogue, valid for a simple two-level system is given. Then, the authors give a short survey of applications related to collision processes involving quantum levels of one particle, and to proton transfer processes along hydrogen bonds in complex environments. Finally, they conclude with some general remarks on the validity of their approach. (N.T.)
International Nuclear Information System (INIS)
Miller, W.H.; Hase, W.L.; Darling, C.L.
1989-01-01
A simple model is proposed for correcting problems with zero point energy in classical trajectory simulations of dynamical processes in polyatomic molecules. The ''problems'' referred to are that classical mechanics allows the vibrational energy in a mode to decrease below its quantum zero point value, and since the total energy is conserved classically this can allow too much energy to pool in other modes. The proposed model introduces hard sphere-like terms in action--angle variables that prevent the vibrational energy in any mode from falling below its zero point value. The algorithm which results is quite simple in terms of the cartesian normal modes of the system: if the energy in a mode k, say, decreases below its zero point value at time t, then at this time the momentum P k for that mode has its sign changed, and the trajectory continues. This is essentially a time reversal for mode k (only exclamation point), and it conserves the total energy of the system. One can think of the model as supplying impulsive ''quantum kicks'' to a mode whose energy attempts to fall below its zero point value, a kind of ''Planck demon'' analogous to a Brownian-like random force. The model is illustrated by application to a model of CH overtone relaxation
Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David
2012-01-10
The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats
A quantum-classical simulation of the nuclear dynamics in NO 2 and ...
Indian Academy of Sciences (India)
Administrator
We perform the nuclear dynamics simulation to calculate the broad band as well as better resolved (a) ... The CIs significantly affect the molecular dynamics and henceforth ...... cluster with accessible 64 GB RAM and 1.65 GHz clock speed.
Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;
2002-01-01
A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.
Quantum–classical simulations of the electronic stopping force and charge on slow heavy channelling ions in metals
International Nuclear Information System (INIS)
Race, C P; Mason, D R; Foo, M H F; Foulkes, W M C; Sutton, A P; Horsfield, A P
2013-01-01
By simulating the passage of heavy ions along open channels in a model crystalline metal using semi-classical Ehrenfest dynamics we directly investigate the nature of non-adiabatic electronic effects. Our time-dependent tight-binding approach incorporates both an explicit quantum mechanical electronic system and an explicit representation of a set of classical ions. The coupled evolution of the ions and electrons allows us to explore phenomena that lie beyond the approximations made in classical molecular dynamics simulations and in theories of electronic stopping. We report a velocity-dependent charge-localization phenomenon not predicted by previous theoretical treatments of channelling. This charge localization can be attributed to the excitation of electrons into defect states highly localized on the channelling ion. These modes of excitation only become active when the frequency at which the channelling ion moves from interstitial point to equivalent interstitial point matches the frequency corresponding to excitations from the Fermi level into the localized states. Examining the stopping force exerted on the channelling ion by the electronic system, we find broad agreement with theories of slow ion stopping (a stopping force proportional to velocity) for a low velocity channelling ion (up to about 0.5 nm fs −1 from our calculations), and a reduction in stopping power attributable to the charge localization effect at higher velocities. By exploiting the simplicity of our electronic structure model we are able to illuminate the physics behind the excitation processes that we observe and present an intuitive picture of electronic stopping from a real-space, chemical perspective. (paper)
Pavlova, Anna; Parks, Jerry M; Gumbart, James C
2018-02-13
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co 3+ , Co 2+ , and Co 1+ , and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.
Bachmann, Stephan J; Lin, Zhixiong; Stafforst, Thorsten; van Gunsteren, Wilfred F; Dolenc, Jožica
2014-01-14
The technique of one-step perturbation to explore the relation between particular force-field parameters on the one hand and particular properties of a biomolecular system on the other hand from one or a few molecular dynamics simulations is applied to investigate the dependence of the free enthalpy of dimer formation and of crystal dissolution of a self-complementary fragment (H-CGTACG-NH2) of peptide nucleic acid, PNA, a mimic of DNA. The simulations show that PNA dimer formation in aqueous solution is favored by a decrease in the base charges with respect to values of the GROMOS 45A4 force field, while it is disfavored by a decrease in the backbone charges. In contrast, crystal dissolution of the PNA dimer is favored by a decrease in base charges, while a variation of backbone charges has a minor effect on this free enthalpy change. These opposite effects in a crystalline versus aqueous solution environment can be understood from the different water contents for these systems and have consequences for biomolecular force-field development.
Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe
2013-10-08
We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.
The influence of catch trials on the consolidation of motor memory in force field adaptation tasks
Directory of Open Access Journals (Sweden)
Anne eFocke
2013-07-01
Full Text Available In computational neuroscience it is generally accepted that human motor memory contains neural representations of the physics of the musculoskeletal system and the objects in the environment. These representations are called internal models. Force field studies, in which subjects have to adapt to dynamic perturbations induced by a robotic manipulandum, are an established tool to analyze the characteristics of such internal models. The aim of the current study was to investigate whether catch trials during force field learning could influence the consolidation of motor memory in more complex tasks. Thereby, the force field was more than double the force field of previous studies (35 Ns/m. Moreover, the arm of the subjects was not supported. A total of forty-six subjects participated in this study and performed center-out movements at a robotic manipulandum in two different force fields. Two control groups learned force field A on day 1 and were retested in the same force field on day 3 (AA. Two test groups additionally learned an interfering force field B (=-A on day 2 (ABA. The difference between the two test and control groups, respectively, was the absence (0% or presence (19% of catch trials, in which the force field was turned off suddenly. The results showed consolidation of force field A on day 3 for both control groups. Test groups showed no consolidation of force field A (19% catch trials and even poorer performance on day 3 (0% catch trials. In conclusion, it can be stated that catch trials seem to have a positive effect on the performance on day 3 but do not trigger a consolidation process as shown in previous studies that used a lower force field viscosity with supported arm. These findings indicate that the results of previous studies in which less complex tasks were analyzed, cannot be fully transferred to more complex tasks. Moreover, the effects of catch trials in these situations are insufficiently understood and further research
International Nuclear Information System (INIS)
Neimark, Alexander V; Ravikovitch, Peter I; Vishnyakov, Aleksey
2003-01-01
With the example of the capillary condensation of Lennard-Jones fluid in nanopores ranging from 1 to 10 nm, we show that the non-local density functional theory (NLDFT) with properly chosen parameters of intermolecular interactions bridges the scale gap from molecular simulations to macroscopic thermodynamics. On the one hand, NLDFT correctly approximates the results of Monte Carlo simulations (shift of vapour-liquid equilibrium, spinodals, density profiles, adsorption isotherms) for pores wider than about 2 nm. On the other hand, NLDFT smoothly merges (above 7-10 nm) with the Derjaguin-Broekhoff-de Boer equations which represent augmented Laplace-Kelvin equations of capillary condensation and desorption
Classic articles and workbook: EPRI monographs on simulation of electric power production
International Nuclear Information System (INIS)
Stremel, J.P.
1991-12-01
This monograph republishes several articles including a seminal one on probabilistic production costing for electric power generation. That article is given in the original French along with a English translation. Another article, written by R. Booth, gives a popular explanation of the theory, and a workbook by B. Manhire is included that carries through a simple example step by step. The classical analysis of non-probabilistic generator dispatch by L.K. Kirchmayer is republished along with an introductory essay by J.P. Stremel that puts in perspective the monograph material. The article in French was written by H. Baleriaux, E. Jamoulle, and Fr. Linard de Guertechin and first published in Brussels in 1967. It derived a method for calculating the expected value of production costs by modifying a load duration curve through the use of probability factors that account for unplanned random generator outages. Although the paper showed how pump storage plants could be included and how linear programming could be applied, the convolution technique used in the probabilistic calculations is the part most widely applied. The tutorial paper by Booth was written in a light style, and its lucidity helped popularize the method. The workbook by Manhire also shows how the calculation can be shortened significantly using cumulants to approximate the load duration curve
Matter waves from localized sources in homogeneous force fields
Kramer, Tobias
2010-01-01
We derive a scattering theory in constant potentials based on the energy-dependent Green function. This approach enables us to formulate modern experiments in terms of Green function. One application discussed is the photodetachment of electrons in external electromagnetic fields. In this case an intricate currentdensity distributions exists, that can be explained in terms of interfering classical trajectories. We also derive analytically the two-dimensional Green function in perpendicular el...
International Nuclear Information System (INIS)
Visbal, Jorge H. Wilches; Costa, Alessandro M.
2016-01-01
Percentage depth dose of electron beams represents an important item of data in radiation therapy treatment since it describes the dosimetric properties of these. Using an accurate transport theory, or the Monte Carlo method, has been shown obvious differences between the dose distribution of electron beams of a clinical accelerator in a water simulator object and the dose distribution of monoenergetic electrons of nominal energy of the clinical accelerator in water. In radiotherapy, the electron spectra should be considered to improve the accuracy of dose calculation since the shape of PDP curve depends of way how radiation particles deposit their energy in patient/phantom, that is, the spectrum. Exist three principal approaches to obtain electron energy spectra from central PDP: Monte Carlo Method, Direct Measurement and Inverse Reconstruction. In this work it will be presented the Simulated Annealing method as a practical, reliable and simple approach of inverse reconstruction as being an optimal alternative to other options. (author)
International Nuclear Information System (INIS)
Schoen, M.
1995-01-01
In this article the Taylor-expansion method is introduced by which Monte Carlo (MC) simulations in the canonical ensemble can be speeded up significantly, Substantial gains in computational speed of 20-40% over conventional implementations of the MC technique are obtained over a wide range of densities in homogeneous bulk phases. The basic philosophy behind the Taylor-expansion method is a division of the neighborhood of each atom (or molecule) into three different spatial zones. Interactions between atoms belonging to each zone are treated at different levels of computational sophistication. For example, only interactions between atoms belonging to the primary zone immediately surrounding an atom are treated explicitly before and after displacement. The change in the configurational energy contribution from secondary-zone interactions is obtained from the first-order term of a Taylor expansion of the configurational energy in terms of the displacement vector d. Interactions with atoms in the tertiary zone adjacent to the secondary zone are neglected throughout. The Taylor-expansion method is not restricted to the canonical ensemble but may be employed to enhance computational efficiency of MC simulations in other ensembles as well. This is demonstrated for grand canonical ensemble MC simulations of an inhomogeneous fluid which can be performed essentially on a modern personal computer
Energy Technology Data Exchange (ETDEWEB)
Morisseau, Francois [Laboratoire de Physique Corpusculaire de CAEN, ENSICAEN, Universite de Caen Basse-Normandie, UFR des Sciences, 6 bd Marechal Juin, 14050 Caen Cedex (France)
2006-05-15
The Classical N-body Dynamics (CNBD) is dedicated to the simulation of collisions between classical systems. The 2-body interaction used here has the properties of the Van der Waals potential and depends on just a few parameters. This work has two main goals. First, some theoretical approaches assume that the dynamical stage of the collisions plays an important role. Moreover, colliding nuclei are supposed to present a 1. order liquid-gas phase transition. Several signals have been introduced to show this transition. We have searched for two of them: the bimodality of the mass asymmetry and negative heat capacity. We have found them and we give an explanation of their presence in our calculations. Second, we have improved the interaction by adding a Coulomb like potential and by taking into account the stronger proton-neutron interaction in nuclei. Then we have figured out the relations that exist between the parameters of the 2-body interaction and the properties of the systems. These studies allow us to fit the properties of the classical systems to those of the nuclei. In this manuscript the first results of this fit are shown. (author)
Centering Ability of ProTaper Next and WaveOne Classic in J-Shape Simulated Root Canals.
Troiano, Giuseppe; Dioguardi, Mario; Cocco, Armando; Giuliani, Michele; Fabiani, Cristiano; D'Alessandro, Alfonso; Ciavarella, Domenico; Lo Muzio, Lorenzo
Introduction . The aim of this study was to evaluate and compare the shaping and centering ability of ProTaper Next (PTN; Dentsply Maillefer, Ballaigues, Switzerland) and WaveOne Classic systems (Dentsply Maillefer) in simulated root canals. Methods . Forty J-shaped canals in resin blocks were assigned to two groups ( n = 20 for each group). Photographic method was used to record pre- and postinstrumentation images. After superimposition, centering and shaping ability were recorded at 9 different levels from the apex using the software Autocad 2013 (Autodesk Inc., San Rafael, USA). Results . Shaping procedures with ProTaper Next resulted in a lower amount of resin removed at each reference point level. In addition, the pattern of centering ability improved after the use of ProTaper Next in 8 of 9 measurement points. Conclusions . Within the limitations of this study, shaping procedures with ProTaper Next instruments demonstrated a lower amount of resin removed and a better centering ability than WaveOne Classic system.
LEPS potential for H3 from force field data
International Nuclear Information System (INIS)
Varandas, A.J.C.
1979-01-01
A new potential energy surface for H 3 of the London--Eyring--Polanyi--Sato type has been obtained which reproduces the best available estimates for the geometry, classical barrier height, and quadratic force constants of the D/sub infinityh/ saddle point. Other attributes of the surface, e.g., minimum energy profile for the exchange process, spherically averaged potential V 0 , and leading anisotropic potential V 2 , are also shown to be in good agreement with the best available estimates. The simplicity of its functional form further commends it for future dynamical studies
Energy Technology Data Exchange (ETDEWEB)
Yang Zhenyu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080(China); Zhao Yapu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080 (China)]. E-mail: yzhao@lnm.imech.ac.cn
2006-05-15
The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by 'GAMESS', and the rest atoms are treated as MM part calculated by 'TINKER'. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.
Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S
2018-04-01
Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.
International Nuclear Information System (INIS)
Nishiyama, Yoshikazu; Kato, Tsuyoshi; Ohtsuki, Yukiyoshi; Fujimura, Yuichi
2004-01-01
A linearized optimal control method in combination with mixed quantum/classical molecular dynamics simulation is used for numerically investigating the possibility of controlling photodissociation wave packets of I 2 - in water. Optimal pulses are designed using an ensemble of photodissociation samples, aiming at the creation of localized dissociation wave packets. Numerical results clearly show the effectiveness of the control although the control achievement is reduced with an increase in the internuclear distance associated with a target region. We introduce effective optimal pulses that are designed using a statistically averaged effective dissociation potential, and show that they semiquantitatively reproduce the control achievements calculated by using optimal pulses. The control mechanisms are interpreted from the time- and frequency-resolved spectra of the effective optimal pulses
Energy Technology Data Exchange (ETDEWEB)
Kawazoe, Yoshiyuki (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Maruyama, Yutaka (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Rafii-Tabar, H. (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Ikeda, Makoto (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Kamiyama, Hiroshi (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Ohno, Kaoru (Inst. for Materials Research, Tohoku Univ., Sendai (Japan))
1993-04-19
The recent scanning tunnelling microscopy (STM) observations by Hashizume et al. concerning C[sub 60] buckeyballs deposited on an Si(100) surface revealed self-aligned c(4 x 4) and c(4 x 3) structures. Specific stripes on the buckeyballs in the STM images are also reported and this result proves that the buckeyballs on the Si surface are standing still, showing them to be pseudoatoms. A mixed-basis, all-electron calculation with the Car-Parinnello formalism has been introduced and performed to obtain a detailed understanding of the electronic states and dynamics of a single buckeyball. Based on the knowledge concerning a single buckeyball, a band structure calculation using the same formalism has been carried out and the experimental results have been explained clearly. A classical molecular dynamics simulation has also been performed to obtain the dynamics of the buckeyball motion on the Si surface. (orig.)
The ELBA force field for coarse-grain modeling of lipid membranes.
Directory of Open Access Journals (Sweden)
Mario Orsi
Full Text Available A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r = 1. Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC and dioleoylphosphatidylethanolamine (DOPE in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids; this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.
2016-01-01
We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642
Some recent progress in classical general relativity
Finster, Felix; Smoller, Joel; Yau, Shing-Tung
2000-06-01
In this short survey paper, we shall discuss certain recent results in classical gravity. Our main attention will be restricted to two topics in which we have been involved; the positive mass conjecture and its extensions to the case with horizons, including the Penrose conjecture (Part I), and the interaction of gravity with other force fields and quantum-mechanical particles (Part II).
Zhou, Shiqi; Lamperski, Stanisław; Zydorczak, Maria
2014-08-14
Monte Carlo (MC) simulation and classical density functional theory (DFT) results are reported for the structural and electrostatic properties of a planar electric double layer containing ions having highly asymmetric diameters or valencies under extreme concentration condition. In the applied DFT, for the excess free energy contribution due to the hard sphere repulsion, a recently elaborated extended form of the fundamental measure functional is used, and coupling of Coulombic and short range hard-sphere repulsion is described by a traditional second-order functional perturbation expansion approximation. Comparison between the MC and DFT results indicates that validity interval of the traditional DFT approximation expands to high ion valences running up to 3 and size asymmetry high up to diameter ratio of 4 whether the high valence ions or the large size ion are co- or counter-ions; and to a high bulk electrolyte concentration being close to the upper limit of the electrolyte mole concentration the MC simulation can deal with well. The DFT accuracy dependence on the ion parameters can be self-consistently explained using arguments of liquid state theory, and new EDL phenomena such as overscreening effect due to monovalent counter-ions, extreme layering effect of counter-ions, and appearance of a depletion layer with almost no counter- and co-ions are observed.
Romano, S.
1992-01-01
The present paper considers a classical system, consisting of n-component unit vectors (n=2 or 3), associated with a one-dimensional lattice \\{uk||k∈openZ\\}, and interacting via a translationally invariant pair potential of the long-range, ferromagnetic and anisotropic form W=Wjk=-ɛ||j-k||-2(auj,nuk,n +b tsumλuk,λ denotes the Cartesian components of the unit vectors. According to the available rigorous results, the system disorders at all finite temperatures when a=b, or n=3, a=0, and possesses an ordering transition at finite temperature when b=0. Approximate arguments and simulation results suggest that the isotropic models (a=b) produce a transition to a low-temperature phase with infinite susceptibility and power-law decay of the correlation function. If this is true, the available correlation inequalities entail that it also happens in the anisotropic but O(2)-invariant case n=3, b=0. We report here Monte Carlo calculations for this latter potential model; simulation results were found to be consistent with this conjecture, and to suggest that T*c=0.65+/-0.01.
Combination Rules for Morse-Based van der Waals Force Fields.
Yang, Li; Sun, Lei; Deng, Wei-Qiao
2018-02-15
In traditional force fields (FFs), van der Waals interactions have been usually described by the Lennard-Jones potentials. Conventional combination rules for the parameters of van der Waals (VDW) cross-termed interactions were developed for the Lennard-Jones based FFs. Here, we report that the Morse potentials were a better function to describe VDW interactions calculated by highly precise quantum mechanics methods. A new set of combination rules was developed for Morse-based FFs, in which VDW interactions were described by Morse potentials. The new set of combination rules has been verified by comparing the second virial coefficients of 11 noble gas mixtures. For all of the mixed binaries considered in this work, the combination rules work very well and are superior to all three other existing sets of combination rules reported in the literature. We further used the Morse-based FF by using the combination rules to simulate the adsorption isotherms of CH 4 at 298 K in four covalent-organic frameworks (COFs). The overall agreement is great, which supports the further applications of this new set of combination rules in more realistic simulation systems.
Ligandbook: an online repository for small and drug-like molecule force field parameters.
Domanski, Jan; Beckstein, Oliver; Iorga, Bogdan I
2017-06-01
Ligandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Ligandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit. oliver.beckstein@asu.edu or bogdan.iorga@cnrs.fr ; contact@ligandbook.org . Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.
Energy Technology Data Exchange (ETDEWEB)
Zou, Chenyu; van Duin, Adri C.T.; Sorescu, Dan C.
2012-06-01
We have developed a ReaxFF reactive force field to describe hydrogen adsorption and dissociation on iron and iron carbide surfaces relevant for simulation of Fischer–Tropsch (FT) synthesis on iron catalysts. This force field enables large system (>>1000 atoms) simulations of hydrogen related reactions with iron. The ReaxFF force field parameters are trained against a substantial amount of structural and energetic data including the equations of state and heats of formation of iron and iron carbide related materials, as well as hydrogen interaction with iron surfaces and different phases of bulk iron. We have validated the accuracy and applicability of ReaxFF force field by carrying out molecular dynamics simulations of hydrogen adsorption, dissociation and recombination on iron and iron carbide surfaces. The barriers and reaction energies for molecular dissociation on these two types of surfaces have been compared and the effect of subsurface carbon on hydrogen interaction with iron surface is evaluated. We found that existence of carbon atoms at subsurface iron sites tends to increase the hydrogen dissociation energy barrier on the surface, and also makes the corresponding hydrogen dissociative state relatively more stable compared to that on bare iron. These properties of iron carbide will affect the dissociation rate of H{sub 2} and will retain more surface hydride species, thus influencing the dynamics of the FT synthesis process.
Hierarchical atom type definitions and extensible all-atom force fields.
Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai
2016-03-15
The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
Comparison of three empirical force fields for phonon calculations in CdSe quantum dots
Energy Technology Data Exchange (ETDEWEB)
Kelley, Anne Myers [Chemistry and Chemical Biology, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States)
2016-06-07
Three empirical interatomic force fields are parametrized using structural, elastic, and phonon dispersion data for bulk CdSe and their predictions are then compared for the structures and phonons of CdSe quantum dots having average diameters of ~2.8 and ~5.2 nm (~410 and ~2630 atoms, respectively). The three force fields include one that contains only two-body interactions (Lennard-Jones plus Coulomb), a Tersoff-type force field that contains both two-body and three-body interactions but no Coulombic terms, and a Stillinger-Weber type force field that contains Coulombic interactions plus two-body and three-body terms. While all three force fields predict nearly identical peak frequencies for the strongly Raman-active “longitudinal optical” phonon in the quantum dots, the predictions for the width of the Raman peak, the peak frequency and width of the infrared absorption peak, and the degree of disorder in the structure are very different. The three force fields also give very different predictions for the variation in phonon frequency with radial position (core versus surface). The Stillinger-Weber plus Coulomb type force field gives the best overall agreement with available experimental data.
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.
Best, Robert B; Hummer, Gerhard
2009-07-02
Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.
International Nuclear Information System (INIS)
Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.
2016-01-01
An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%
Zeman, Johannes; Uhlig, Frank; Smiatek, Jens; Holm, Christian
2017-12-01
We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.
Critical Assessment of Current Force Fields. Short Peptide Test Case
Czech Academy of Sciences Publication Activity Database
Vymětal, Jiří; Vondrášek, Jiří
2013-01-01
Roč. 9, č. 1 (2013), s. 441-451 ISSN 1549-9618 R&D Projects: GA MŠk(CZ) LH11020 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : Helix-coil transition * protein-folding simulations * amino-acids * side-chain * alanine dipeptide Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013
Rapid changes in corticospinal excitability during force field adaptation of human walking
DEFF Research Database (Denmark)
Barthélemy, Dorothy; Alain, S; Grey, Michael James
2012-01-01
measured changes in motor-evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) in the tibialis anterior (TA) muscle before, during, and after subjects adapted to a force field applied to the ankle joint during treadmill walking. When the force field assisted dorsiflexion during...... the swing phase of the step cycle, subjects adapted by decreasing TA EMG activity. In contrast, when the force field resisted dorsiflexion, they increased TA EMG activity. After the force field was removed, normal EMG activity gradually returned over the next 5 min of walking. TA MEPs elicited in the early...... be explained by changes in background TA EMG activity. These effects seemed specific to walking, as similar changes in TA MEP were not seen when seated subjects were tested during static dorsiflexion. These observations suggest that the corticospinal tract contributes to the adaptation of walking...
Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David
2018-04-10
Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.
Force-Field Prediction of Materials Properties in Metal-Organic Frameworks
2016-01-01
In this work, MOF bulk properties are evaluated and compared using several force fields on several well-studied MOFs, including IRMOF-1 (MOF-5), IRMOF-10, HKUST-1, and UiO-66. It is found that, surprisingly, UFF and DREIDING provide good values for the bulk modulus and linear thermal expansion coefficients for these materials, excluding those that they are not parametrized for. Force fields developed specifically for MOFs including UFF4MOF, BTW-FF, and the DWES force field are also found to provide accurate values for these materials’ properties. While we find that each force field offers a moderately good picture of these properties, noticeable deviations can be observed when looking at properties sensitive to framework vibrational modes. This observation is more pronounced upon the introduction of framework charges. PMID:28008758
Radosinski, Lukasz; Labus, Karolina
2017-10-05
Polyvinyl alcohol (PVA) is a material with a variety of applications in separation, biotechnology, and biomedicine. Using combined Monte Carlo and molecular dynamics techniques, we present an extensive comparative study of second- and third-generation force fields Universal, COMPASS, COMPASS II, PCFF, and the newly developed INTERFACE, as applied to this system. In particular, we show that an INTERFACE force field provides a possibility of composing a reliable atomistic model to reproduce density change of PVA matrix in a narrow temperature range (298-348 K) and calculate a thermal expansion coefficient with reasonable accuracy. Thus, the INTERFACE force field may be used to predict mechanical properties of the PVA system, being a scaffold for hydrogels, with much greater accuracy than latter approaches. Graphical abstract Molecular Dynamics and Monte Carlo studies indicate that it is possible to predict properties of the PVA in narrow temperature range by using the INTERFACE force field.
Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David
2018-04-01
Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.
Louarn, K.; Claveau, Y.; Hapiuk, D.; Fontaine, C.; Arnoult, A.; Taliercio, T.; Licitra, C.; Piquemal, F.; Bounouh, A.; Cavassilas, N.; Almuneau, G.
2017-09-01
The aim of this study is to investigate the impact of multiband corrections on the current density in GaAs tunnel junctions (TJs) calculated with a refined yet simple semi-classical interband tunneling model (SCITM). The non-parabolicity of the considered bands and the spin-orbit effects are considered by using a recently revisited SCITM available in the literature. The model is confronted to experimental results from a series of molecular beam epitaxy grown GaAs TJs and to numerical results obtained with a full quantum model based on the non-equilibrium Green’s function formalism and a 6-band k.p Hamiltonian. We emphasize the importance of considering the non-parabolicity of the conduction band by two different measurements of the energy-dependent electron effective mass in N-doped GaAs. We also propose an innovative method to compute the non-uniform electric field in the TJ for the SCITM simulations, which is of prime importance for a successful operation of the model. We demonstrate that, when considering the multiband corrections and this new computation of the non-uniform electric field, the SCITM succeeds in predicting the electrical characteristics of GaAs TJs, and are also in agreement with the quantum model. Besides the fundamental study of the tunneling phenomenon in TJs, the main benefit of this SCITM is that it can be easily embedded into drift-diffusion software, which are the most widely-used simulation tools for electronic and opto-electronic devices such as multi-junction solar cells, tunnel field-effect transistors, or vertical-cavity surface-emitting lasers.
Directory of Open Access Journals (Sweden)
Pasquale Pisani
Full Text Available Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS. The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms
International Nuclear Information System (INIS)
Bauer, David S G; Mavropoulos, Phivos; Bluegel, Stefan; Lounis, Samir
2011-01-01
We analyse the spontaneous magnetization reversal of supported monatomic chains of finite length due to thermal fluctuations via atomistic spin-dynamics simulations. Our approach is based on the integration of the Landau-Lifshitz equation of motion of a classical spin Hamiltonian in the presence of stochastic forces. The associated magnetization lifetime is found to obey an Arrhenius law with an activation barrier equal to the domain wall energy in the chain. For chains longer than one domain wall width, the reversal is initiated by nucleation of a reversed magnetization domain primarily at the chain edge followed by a subsequent propagation of the domain wall to the other edge in a random-walk fashion. This results in a linear dependence of the lifetime on the chain length, if the magnetization correlation length is not exceeded. We studied chains of uniaxial and triaxial anisotropy and found that a triaxial anisotropy leads to a reduction of the magnetization lifetime due to a higher reversal attempt rate, even though the activation barrier is not changed.
International Nuclear Information System (INIS)
Ghosh, P.S.; Arya, A.; Dey, G.K.; Somayajulu, P.S.
2015-01-01
This paper calculates lattice thermal expansion (LTE) and thermal conductivity (TC) of Th 1-x Ce x O 2 (x=0.0, 0.0625 and 0.125) MOX using classical molecular dynamic simulations. The potential parameters of Coulomb-Buckingham function for Th-O, Ce-O and O-O were determined by fitting experimentally available LTE data for pure ThO 2 and CeO 2 . The calculated linear thermal expansion coefficients in the temperature range 300-1500K for ThO 2 , CeO 2 , Th 93.75 Ce 6.25 O 2 and Th 87.5 Ce 12.5 O 2 are 10.61, 13.08, 10.78 and 10.93x10 -6 K -1 , respectively. The MD calculated LTE values of ThO 2 and (Th,Ce)O 2 MOX are slightly higher than the experimentally determined values. The MD calculated TC values of ThO 2 and (Th,Ce)O 2 MOX in the high temperature range (600 to 1200 K) our results accords very well with the experimental measurements and at the low temperature range (300-500 K) our results are slightly different from some experimental results as the difference comes from our presumption that the dominant mechanism for phonon scattering is the Umklapp process. (author)
Determination of a silane intermolecular force field potential model from an ab initio calculation
International Nuclear Information System (INIS)
Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng
2010-01-01
Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.
Combining experimental and simulation data of molecular processes via augmented Markov models.
Olsson, Simon; Wu, Hao; Paul, Fabian; Clementi, Cecilia; Noé, Frank
2017-08-01
Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.
Recent advances toward a general purpose linear-scaling quantum force field.
Giese, Timothy J; Huang, Ming; Chen, Haoyuan; York, Darrin M
2014-09-16
Conspectus There is need in the molecular simulation community to develop new quantum mechanical (QM) methods that can be routinely applied to the simulation of large molecular systems in complex, heterogeneous condensed phase environments. Although conventional methods, such as the hybrid quantum mechanical/molecular mechanical (QM/MM) method, are adequate for many problems, there remain other applications that demand a fully quantum mechanical approach. QM methods are generally required in applications that involve changes in electronic structure, such as when chemical bond formation or cleavage occurs, when molecules respond to one another through polarization or charge transfer, or when matter interacts with electromagnetic fields. A full QM treatment, rather than QM/MM, is necessary when these features present themselves over a wide spatial range that, in some cases, may span the entire system. Specific examples include the study of catalytic events that involve delocalized changes in chemical bonds, charge transfer, or extensive polarization of the macromolecular environment; drug discovery applications, where the wide range of nonstandard residues and protonation states are challenging to model with purely empirical MM force fields; and the interpretation of spectroscopic observables. Unfortunately, the enormous computational cost of conventional QM methods limit their practical application to small systems. Linear-scaling electronic structure methods (LSQMs) make possible the calculation of large systems but are still too computationally intensive to be applied with the degree of configurational sampling often required to make meaningful comparison with experiment. In this work, we present advances in the development of a quantum mechanical force field (QMFF) suitable for application to biological macromolecules and condensed phase simulations. QMFFs leverage the benefits provided by the LSQM and QM/MM approaches to produce a fully QM method that is able to
International Nuclear Information System (INIS)
Costella, J.P.; McKellar, B.H.J.; Rawlinson, A.A.
1997-03-01
We review how antiparticles may be introduced in classical relativistic mechanics, and emphasize that many of their paradoxical properties can be more transparently understood in the classical than in the quantum domain. (authors)
Directory of Open Access Journals (Sweden)
Collings Matthew D
2002-11-01
Full Text Available Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of metals in such brines increases the solubility of minerals and plays a fundamental role in the genesis of hydrothermal ore deposits. There is experimental evidence that the molecular nature of the NaCl–water system changes over the pressure–temperature range of the Earth's crust. A transition of concentrated NaCl–H2O brines to a "hydrous molten salt" at high P and T has been argued to stabilize an aqueous fluid phase in the deep crust. In this work, we have done molecular dynamic simulations using classical potentials to determine the nature of concentrated (0.5–16 m NaCl–water mixtures under ambient (25°C, 1 bar, hydrothermal (325°C, 1 kbar and deep crustal (625°C, 15 kbar conditions. We used the well-established SPCE model for water together with the Smith and Dang Lennard-Jones potentials for the ions (J. Chem. Phys., 1994, 100, 3757. With increasing temperature at 1 kbar, the dielectric constant of water decreases to give extensive ion-association and the formation of polyatomic (NanClmn-m clusters in addition to simple NaCl ion pairs. Large polyatomic (NanClmn-m clusters resemble what would be expected in a hydrous NaCl melt in which water and NaCl were completely miscible. Although ion association decreases with pressure, temperatures of 625°C are not enough to overcome pressures of 15 kbar; consequently, there is still enhanced Na–Cl association in brines under deep crustal conditions.
Klvana, Martin; Pavlova, Martina; Koudelakova, Tana; Chaloupkova, Radka; Dvorak, Pavel; Prokop, Zbynek; Stsiapanava, Alena; Kuty, Michal; Kuta-Smatanova, Ivana; Dohnalek, Jan; Kulhanek, Petr; Wade, Rebecca C; Damborsky, Jiri
2009-10-09
Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein X-ray crystallography, were constructed and biochemically characterized. The mutants showed distinct catalytic efficiencies with the halogenated substrate 1,2,3-trichloropropane. Release pathways for the two dehalogenation products, 2,3-dichloropropane-1-ol and the chloride ion, and exchange pathways for water molecules, were studied using classical and random acceleration molecular dynamics simulations. Five different pathways, denoted p1, p2a, p2b, p2c, and p3, were identified. The individual pathways showed differing selectivity for the products: the chloride ion releases solely through p1, whereas the alcohol releases through all five pathways. Water molecules play a crucial role for release of both products by breakage of their hydrogen-bonding interactions with the active-site residues and shielding the charged chloride ion during its passage through a hydrophobic tunnel. Exchange of the chloride ions, the alcohol product, and the waters between the buried active site and the bulk solvent can be realized by three different mechanisms: (i) passage through a permanent tunnel, (ii) passage through a transient tunnel, and (iii) migration through a protein matrix. We demonstrate that the accessibility of the pathways and the mechanisms of ligand exchange were modified by mutations. Insertion of bulky aromatic residues in the tunnel corresponding to pathway p1 leads to reduced accessibility to the ligands and a change in mechanism of opening from permanent to transient. We propose that engineering the accessibility of tunnels and the mechanisms of ligand exchange is a powerful strategy for modification of the functional properties of enzymes with buried active sites.
Energy Technology Data Exchange (ETDEWEB)
Wang Zunjing; Deserno, Markus, E-mail: zwang@cmu.ed, E-mail: deserno@andrew.cmu.ed [Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213 (United States)
2010-09-15
We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.
International Nuclear Information System (INIS)
Wang Zunjing; Deserno, Markus
2010-01-01
We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.
Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep
2014-10-16
Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of
Pezzotti, Simone; Serva, Alessandra; Gaigeot, Marie-Pierre
2018-05-01
Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ˜90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.
Heinen, Jurn; Burtch, Nicholas C; Walton, Krista S; Fonseca Guerra, Célia; Dubbeldam, David
2016-12-12
For the design of adsorptive-separation units, knowledge is required of the multicomponent adsorption behavior. Ideal adsorbed solution theory (IAST) breaks down for olefin adsorption in open-metal site (OMS) materials due to non-ideal donor-acceptor interactions. Using a density-function-theory-based energy decomposition scheme, we develop a physically justifiable classical force field that incorporates the missing orbital interactions using an appropriate functional form. Our first-principles derived force field shows greatly improved quantitative agreement with the inflection points, initial uptake, saturation capacity, and enthalpies of adsorption obtained from our in-house adsorption experiments. While IAST fails to make accurate predictions, our improved force field model is able to correctly predict the multicomponent behavior. Our approach is also transferable to other OMS structures, allowing the accurate study of their separation performances for olefins/paraffins and further mixtures involving complex donor-acceptor interactions. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Energy Technology Data Exchange (ETDEWEB)
Williams, Robert W. [Department of Biomedical Informatics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20815 (United States)], E-mail: bob@bob.usuhs.mil; Schluecker, Sebastian [Institute of Physical Chemistry, University of Wuerzburg, Wuerzburg (Germany); Hudson, Bruce S. [Department of Chemistry, Syracuse University, Syracuse, NY (United States)
2008-01-22
A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K L-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline L-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the L-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes.
International Nuclear Information System (INIS)
Williams, Robert W.; Schluecker, Sebastian; Hudson, Bruce S.
2008-01-01
A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K L-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline L-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the L-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes
ANLIZE: a molecular mechanics force field visualization tool and its application to 18-crown-6.
Stolworthy, L D; Shirts, R B
1997-03-01
We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.
Modeling the sorption dynamics of NaH using a reactive force field
International Nuclear Information System (INIS)
Ojwang, J. G. O.; Santen, Rutger van; Kramer, Gert Jan; Duin, Adri C. T. van; Goddard, William A. III
2008-01-01
We have parametrized a reactive force field for NaH, ReaxFF NaH , against a training set of ab initio derived data. To ascertain that ReaxFF NaH is properly parametrized, a comparison between ab initio heats of formation of small representative NaH clusters with ReaxFF NaH was done. The results and trend of ReaxFF NaH are found to be consistent with ab initio values. Further validation includes comparing the equations of state of condensed phases of Na and NaH as calculated from ab initio and ReaxFF NaH . There is a good match between the two results, showing that ReaxFF NaH is correctly parametrized by the ab initio training set. ReaxFF NaH has been used to study the dynamics of hydrogen desorption in NaH particles. We find that ReaxFF NaH properly describes the surface molecular hydrogen charge transfer during the abstraction process. Results on heat of desorption versus cluster size shows that there is a strong dependence on the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. To gain more insight into the structural transformations of NaH during thermal decomposition, we performed a heating run in a molecular dynamics simulation. These runs exhibit a series of drops in potential energy, associated with cluster fragmentation and desorption of molecular hydrogen. This is consistent with experimental evidence that NaH dissociates at its melting point into smaller fragments
A bidirectional brain-machine interface algorithm that approximates arbitrary force-fields.
Directory of Open Access Journals (Sweden)
Alessandro Vato
Full Text Available We examine bidirectional brain-machine interfaces that control external devices in a closed loop by decoding motor cortical activity to command the device and by encoding the state of the device by delivering electrical stimuli to sensory areas. Although it is possible to design this artificial sensory-motor interaction while maintaining two independent channels of communication, here we propose a rule that closes the loop between flows of sensory and motor information in a way that approximates a desired dynamical policy expressed as a field of forces acting upon the controlled external device. We previously developed a first implementation of this approach based on linear decoding of neural activity recorded from the motor cortex into a set of forces (a force field applied to a point mass, and on encoding of position of the point mass into patterns of electrical stimuli delivered to somatosensory areas. However, this previous algorithm had the limitation that it only worked in situations when the position-to-force map to be implemented is invertible. Here we overcome this limitation by developing a new non-linear form of the bidirectional interface that can approximate a virtually unlimited family of continuous fields. The new algorithm bases both the encoding of position information and the decoding of motor cortical activity on an explicit map between spike trains and the state space of the device computed with Multi-Dimensional-Scaling. We present a detailed computational analysis of the performance of the interface and a validation of its robustness by using synthetic neural responses in a simulated sensory-motor loop.
Tommasino, Paolo; Campolo, Domenico
2017-02-03
In this work, we address human-like motor planning in redundant manipulators. Specifically, we want to capture postural synergies such as Donders' law, experimentally observed in humans during kinematically redundant tasks, and infer a minimal set of parameters to implement similar postural synergies in a kinematic model. For the model itself, although the focus of this paper is to solve redundancy by implementing postural strategies derived from experimental data, we also want to ensure that such postural control strategies do not interfere with other possible forms of motion control (in the task-space), i.e. solving the posture/movement problem. The redundancy problem is framed as a constrained optimization problem, traditionally solved via the method of Lagrange multipliers. The posture/movement problem can be tackled via the separation principle which, derived from experimental evidence, posits that the brain processes static torques (i.e. posture-dependent, such as gravitational torques) separately from dynamic torques (i.e. velocity-dependent). The separation principle has traditionally been applied at a joint torque level. Our main contribution is to apply the separation principle to Lagrange multipliers, which act as task-space force fields, leading to a task-space separation principle. In this way, we can separate postural control (implementing Donders' law) from various types of tasks-space movement planners. As an example, the proposed framework is applied to the (redundant) task of pointing with the human wrist. Nonlinear inverse optimization (NIO) is used to fit the model parameters and to capture motor strategies displayed by six human subjects during pointing tasks. The novelty of our NIO approach is that (i) the fitted motor strategy, rather than raw data, is used to filter and down-sample human behaviours; (ii) our framework is used to efficiently simulate model behaviour iteratively, until it converges towards the experimental human strategies.
Macdonald, R. L.; Grover, M. S.; Schwartzentruber, T. E.; Panesi, M.
2018-02-01
This work presents the analysis of non-equilibrium energy transfer and dissociation of nitrogen molecules (N2(g+1Σ) ) using two different approaches: the direct molecular simulation (DMS) method and the coarse-grain quasi-classical trajectory (CG-QCT) method. The two methods are used to study thermochemical relaxation in a zero-dimensional isochoric and isothermal reactor in which the nitrogen molecules are heated to several thousand degrees Kelvin, forcing the system into strong non-equilibrium. The analysis considers thermochemical relaxation for temperatures ranging from 10 000 to 25 000 K. Both methods make use of the same potential energy surface for the N2(g+1Σ ) -N2(g+1Σ ) system taken from the NASA Ames quantum chemistry database. Within the CG-QCT method, the rovibrational energy levels of the electronic ground state of the nitrogen molecule are lumped into a reduced number of bins. Two different grouping strategies are used: the more conventional vibrational-based grouping, widely used in the literature, and energy-based grouping. The analysis of both the internal state populations and concentration profiles show excellent agreement between the energy-based grouping and the DMS solutions. During the energy transfer process, discrepancies arise between the energy-based grouping and DMS solution due to the increased importance of mode separation for low energy states. By contrast, the vibrational grouping, traditionally considered state-of-the-art, captures well the behavior of the energy relaxation but fails to consistently predict the dissociation process. The deficiency of the vibrational grouping model is due to the assumption of strict mode separation and equilibrium of rotational energy states. These assumptions result in errors predicting the energy contribution to dissociation from the rotational and vibrational modes, with rotational energy actually contributing 30%-40% of the energy required to dissociate a molecule. This work confirms the
International Nuclear Information System (INIS)
Azadegan, B.; Wagner, W.
2015-01-01
We present a Mathematica package for simulation of spectral-angular distributions and energy spectra of planar channeling radiation of relativistic electrons and positrons channeled along major crystallographic planes of a diamond-structure or tungsten single crystal. The program is based on the classical theory of channeling radiation which has been successfully applied to study planar channeling of light charged particles at energies higher than 100 MeV. Continuous potentials for different planes of diamond, Si, Ge and W single crystals are calculated using the Doyle–Turner approximation to the atomic scattering factor and taking thermal vibrations of the crystal atoms into account. Numerical methods are applied to solve the classical one-dimensional equation of motion. The code is designed to calculate the trajectories, velocities and accelerations of electrons (positrons) channeled by the planar continuous potential. In the framework of classical electrodynamics, these data allow realistic simulations of spectral-angular distributions and energy spectra of planar channeling radiation. Since the generated output is quantitative, the results of calculation may be useful, e.g., for setup configuration and crystal alignment in channeling experiments, for the study of the dependence of channeling radiation on the input parameters of particle beams with respect to the crystal orientation, but also for the simulation of positron production by means of pair creation what is mandatory for the design of efficient positron sources necessary in high-energy and collider physics. Although the classical theory of channeling is well established for long time, there is no adequate library program for simulation of channeling radiation up to now, which is commonly available, sufficiently simple and effective to employ and, therefore, of benefit as for special investigations as for a quick overview of basic features of this type of radiation
Energy Technology Data Exchange (ETDEWEB)
Soares, T. A. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Daura, X. [Universitat Autonoma de Barcelona, InstitucioCatalana de Recerca i Estudis Avancats and Institut de Biotecnologia i Biomedicina (Spain); Oostenbrink, C. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Smith, L. J. [University of Oxford, Oxford Centre for Molecular Sciences, Central Chemistry Laboratory (United Kingdom); Gunsteren, W. F. van [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland)], E-mail: wfvgn@igc.phys.chem.ethz.ch
2004-12-15
The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, {sup 3}J{sub NH{alpha}} and {sup 3}J{sub {alpha}}{sub {beta}} coupling constants, and {sup 1}5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone {sup 3}J{sub HN{alpha}}-coupling constants and {sup 1}H- {sup 1}5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain {sup 3}J{sub {alpha}}{sub {beta}}-coupling constants and {sup 1}H- {sup 1}5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the
International Nuclear Information System (INIS)
Soares, T. A.; Daura, X.; Oostenbrink, C.; Smith, L. J.; Gunsteren, W. F. van
2004-01-01
The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, 3 J NHα and 3 J αβ coupling constants, and 1 5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone 3 J HNα -coupling constants and 1 H- 1 5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain 3 J αβ -coupling constants and 1 H- 1 5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result
International Nuclear Information System (INIS)
Gellert, M; Beltrame, P; Egbers, C
2005-01-01
Spherical Rayleigh-Benard convection under the influence of an artificial central force field produced by the so-called dielectrophoretic effect is studied as a simplified model of the flow in the outer earth core. The fluid motion there is most probably driving the earth's dynamo and the energy source for the earth's magnetic field. Studying convective flows in earth-like geometry could lead to a deeper understanding of the basics of these processes. This research is a preparatory study for the experiments on the International Space Station (ISS). A bifurcation-theoretical approach shows the existence of heteroclinic cycles between spherical modes (l, l + 1) for the non-rotating system. This behavior depends strong on the radius ratio of the spheres and will be hard to detect in the experiment. For slow rotations interactions of the azimuthal modes (m, m + 1) found in numerical simulations for supercritical states are supposed to be experimentally observable
Shan, Tzu-Ray; van Duin, Adri C T; Thompson, Aidan P
2014-02-27
We have developed a new ReaxFF reactive force field parametrization for ammonium nitrate. Starting with an existing nitramine/TATB ReaxFF parametrization, we optimized it to reproduce electronic structure calculations for dissociation barriers, heats of formation, and crystal structure properties of ammonium nitrate phases. We have used it to predict the isothermal pressure-volume curve and the unreacted principal Hugoniot states. The predicted isothermal pressure-volume curve for phase IV solid ammonium nitrate agreed with electronic structure calculations and experimental data within 10% error for the considered range of compression. The predicted unreacted principal Hugoniot states were approximately 17% stiffer than experimental measurements. We then simulated thermal decomposition during heating to 2500 K. Thermal decomposition pathways agreed with experimental findings.
Study of deformation of droplet in external force field by using liquid-gas model of lattice-gas
International Nuclear Information System (INIS)
Ebihara, Ken-ichi; Watanabe, Tadashi
2000-10-01
The deformation of the droplet by the external force which is assumed to be gravity is studied by using the liquid-gas model of lattice-gas. Two types of liquid-gas models, one is the minimal model and the other is the maximal model, which are distinguished from each other by the added long-range interactions are used for the simulation of the droplet deformation. The difference of the droplet deformation between the maximal model and the minimal model was observed. While the droplet of the minimal model elongates in the direction of the external force, the droplet of the maximal model elongates in the perpendicular direction to the external force. Therefore the droplet deformation in the external force field of the maximal model is more similar to the droplet deformation which is observed in experiments than that of the minimal model. (author)
Accurate van der Waals force field for gas adsorption in porous materials.
Sun, Lei; Yang, Li; Zhang, Ya-Dong; Shi, Qi; Lu, Rui-Feng; Deng, Wei-Qiao
2017-09-05
An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements. This force field can be applied to the prediction of the gas density (H 2 , CO 2 , C 2 H 4 , CH 4 , N 2 , O 2 ) and adsorption performance inside porous materials, such as covalent organic frameworks (COFs), zeolites and metal organic frameworks (MOFs), consisting of H, B, N, C, O, S, Si, Al, Zn, Mg, Ni, and Co. This work provides a solid basis for studying gas adsorption in porous materials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Adaptation of multi-joint balance coordination to whole body force fields
Engelhart, Denise; Schouten, Alfred Christiaan; Pasma, Jantsje; Aarts, Ronald G.K.M.; Pasma, J.; Meskers, Carel; Maier, Andrea; van der Kooij, Herman
2014-01-01
Background and aim: The ankles and the hips play an important role in standing balance. Multi-joint coordination adapts with task, the magnitude and type of disturbance [1]. Arm studies show that postural responses are highly dependent on externally applied force fields [2]. Our aim is to study how
Force-field dependence of the conformational properties of ,-dimethoxypolyethylene glycol
Winger, Moritz; de Vries, Alex H.; van Gunsteren, Wilfred F.
2009-01-01
A molecular dynamics (MD) study of ,-dimethoxypolyethylene glycol has been carried out under various conditions with respect to solvent composition, ionic strength, chain length, force field and temperature. A previous MD study on a 15-mer of polyethyleneglycol (PEG) suggested a helical equilibrium
An Energy Conservative Ray-Tracing Method With a Time Interpolation of the Force Field
Energy Technology Data Exchange (ETDEWEB)
Yao, Jin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-02-10
A new algorithm that constructs a continuous force field interpolated in time is proposed for resolving existing difficulties in numerical methods for ray-tracing. This new method has improved accuracy, but with the same degree of algebraic complexity compared to Kaisers method.
Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam
2014-12-23
To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.
Núñez-Rojas, Edgar; Aguilar-Pineda, Jorge Alberto; Pérez de la Luz, Alexander; de Jesús González, Edith Nadir; Alejandre, José
2018-02-08
The transferable potential for a phase equilibria force field in its united-atom version, TraPPE_UA, is evaluated for 41 polar liquids that include alcohols, thiols, ethers, sulfides, aldehydes, ketones, and esters to determine its ability to reproduce experimental properties that were not included in the parametrization procedure. The intermolecular force field parameters for pure components were fit to reproduce experimental boiling temperature, vapor-liquid coexisting densities, and critical point (temperature, density, and pressure) using Monte Carlo simulations in different ensembles. The properties calculated in this work are liquid density, heat of vaporization, dielectric constant, surface tension, volumetric expansion coefficient, and isothermal compressibility. Molecular dynamics simulations were performed in the gas and liquid phases, and also at the liquid-vapor interface. We found that relative error between calculated and experimental data is 1.2% for density, 6% for heat of vaporization, and 6.2% for surface tension, in good agreement with the experimental data. The dielectric constant is systematically underestimated, and the relative error is 37%. Evaluating the performance of the force field to reproduce the volumetric expansion coefficient and isothermal compressibility requires more experimental data.
Energy Technology Data Exchange (ETDEWEB)
Minoshima, Yusuke; Seki, Yusuke [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Takayanagi, Toshiyuki, E-mail: tako@mail.saitama-u.ac.jp [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Shiga, Motoyuki [Center for Computational Science and E-Systems, Japan Atomic Energy Agency, 148-4, Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba 277-0871 (Japan)
2016-06-15
Highlights: • Dynamics of excess electron attachment to guanine–cytosine base pair. • Ring-polymer and classical molecular dynamics simulations are performed. • Temperature and isotope substitution effects are investigated. - Abstract: The dynamical process of electron attachment to a guanine–cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.
International Nuclear Information System (INIS)
Minoshima, Yusuke; Seki, Yusuke; Takayanagi, Toshiyuki; Shiga, Motoyuki
2016-01-01
Highlights: • Dynamics of excess electron attachment to guanine–cytosine base pair. • Ring-polymer and classical molecular dynamics simulations are performed. • Temperature and isotope substitution effects are investigated. - Abstract: The dynamical process of electron attachment to a guanine–cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.
International Nuclear Information System (INIS)
Breza, J. jr.; Necas, V.; Daoeilek, P.
2005-01-01
The classical nuclear fuel UO 2 is well known for VVER reactors. Nevertheless, in the near future it will be possible to replace this fuel by novel, advanced kinds of fuel, for instance MOX, inert matrices fuel, etc., that will allow to increase the level of burn-up and minimize the amount of hazardous waste. The code Transuranus [2], designed at ITU Karlsruhe, is intended for thermal and mechanical analyses of fuel elements in nuclear reactors. We have utilized the code Transuranus to simulate the neutron-physical properties of the classical UO 2 fuel and of MOX fuel during the burn-up to a level of 40 MWd/kgHM. We compare obtained results of uranium and plutonium nuclides concentrations, their changes during burn-up, with results obtained by code HELIOS [3], which is well-validated code for this kind of applications. We performed calculations of fission gasses concentrations, namely xenon and krypton. (author)
Pai, Sung Jin; Yeo, Byung Chul; Han, Sang Soo
2016-01-21
Liquid CBN (carbon-boron-nitrogen) hydrogen-storage materials such as 3-methyl-1,2-BN-cyclopentane have the advantage of being easily accessible for use in current liquid-fuel infrastructure. To develop practical liquid CBN hydrogen-storage materials, it is of great importance to understand the reaction pathways of hydrogenation/dehydrogenation in the liquid phase, which are difficult to discover by experimental methods. Herein, we developed a reactive force field (ReaxFFCBN) from quantum mechanical (QM) calculations based on density functional theory for the storage of hydrogen in BN-substituted cyclic hydrocarbon materials. The developed ReaxFFCBN provides similar dehydrogenation pathways and energetics to those predicted by QM calculations. Moreover, molecular dynamics (MD) simulations with the developed ReaxFFCBN can predict the stability and dehydrogenation behavior of various liquid CBN hydrogen-storage materials. Our simulations reveal that a unimolecular dehydrogenation mechanism is preferred in liquid CBN hydrogen-storage materials. However, as the temperature in the simulation increases, the contribution of a bimolecular dehydrogenation mechanism also increases. Moreover, our ReaxFF MD simulations show that in terms of thermal stability and dehydrogenation kinetics, liquid CBN materials with a hexagonal structure are more suitable materials than those with a pentagonal structure. We expect that the developed ReaxFFCBN could be a useful protocol in developing novel liquid CBN hydrogen-storage materials.
Benacquista, Matthew J
2018-01-01
This textbook provides an introduction to classical mechanics at a level intermediate between the typical undergraduate and advanced graduate level. This text describes the background and tools for use in the fields of modern physics, such as quantum mechanics, astrophysics, particle physics, and relativity. Students who have had basic undergraduate classical mechanics or who have a good understanding of the mathematical methods of physics will benefit from this book.
Dependence of A-RNA simulations on the choice of the force field and salt strength
Czech Academy of Sciences Publication Activity Database
Beššeová, Ivana; Otyepka, Michal; Réblová, Kamila; Šponer, Jiří
2009-01-01
Roč. 11, č. 45 (2009), s. 10701-10711 ISSN 1463-9076 R&D Projects: GA MŠk(CZ) LC06030; GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GD203/09/H046 Grant - others:GA MŠk(CZ) LC512; GA ČR(CZ) GA203/09/1476 Program:LC; GA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : force fileds * RNA * A-form Subject RIV: BO - Biophysics Impact factor: 4.116, year: 2009
Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations
Czech Academy of Sciences Publication Activity Database
Fadrná, E.; Špačková, Naďa; Štefl, R.; Koča, J.; Cheatham III, T. E.; Šponer, Jiří
2004-01-01
Roč. 87, č. 1 (2004), s. 227-242 ISSN 0006-3495 R&D Projects: GA MŠk LN00A016 Grant - others:Wellcome Trust(GB) GR067507MF Institutional research plan: CEZ:AV0Z5004920 Keywords : quanine quadruplex * four-thymidine loop * locally enhanced sampling Subject RIV: BO - Biophysics Impact factor: 4.585, year: 2004
Kim, Seonah; Orendt, Anita M; Ferraro, Marta B; Facelli, Julio C
2009-10-01
This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.
Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF
2014-01-01
We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157
A molecular mechanics (MM3(96)) force field for metal-amide complexes
International Nuclear Information System (INIS)
Hay, B.P.; Clement, O.; Sandrone, G.; Dixon, D.A.
1998-01-01
A molecular mechanics (MM3(96)) force field is reported for modeling metal complexes of amides in which the amide is coordinated through oxygen. This model uses a points-on-a-sphere approach which involves the parameterization of the Msingle bondO stretch, the Msingle bondO double-bond C bend, and the Msingle bondO double-bond Csingle bondX (X = C, H, N) torsion interactions. Relationships between force field parameters and metal ion properties (charge, ionic radius, and electronegativity) are presented that allow the application of this model to a wide range of metal ions. The model satisfactorily reproduces the structures of over fifty amide complexes with the alkaline earths, transition metals, lanthanides, and actinides
Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations.
Govers, H A J; Krop, H B; Parsons, J R; Tambach, T; Kubicki, J D
2002-03-01
Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.
Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case
DEFF Research Database (Denmark)
Rossi, G.; Monticelli, L.; Puisto, S. R.
2011-01-01
We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets...... of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced....
Relativistic equation of the orbit of a particle in a arbitrary central force field
International Nuclear Information System (INIS)
Aaron, Francisc D.
2005-01-01
The equation of the orbit of a relativistic particle moving in an arbitrary central force field is derived. Straightforward generalizations of well-known first and second order differential equations are given. It is pointed out that the relativistic equation of the orbit has the same form as in the non-relativistic case, the only changes consisting in the appearance of additional terms proportional to 1/c 2 in both potential and total energies. (author)
Iselin, F Christoph
1996-01-01
Exchange of data and algorithms among accelerator physics programs is difficult because of unnecessary differences in input formats and internal data structures. To alleviate these problems a C++ class library called CLASSIC (Clas Library for Accelerator System Simulation and Control) is being developed with the goal to provide standard building blocks for computer programs used in accelerator lattice structures in computer memory using a standard input language, a graphical user interface, or a programmed algorithm. It also provides simulation algorithms. These can easily be replaced by modules which communicate with the control system of the accelerator. Exchange of both data and algorithm between different programs using the CLASSIC library should present no difficulty.
Classical-quantum correspondence in electron-positron pair creation
International Nuclear Information System (INIS)
Chott, N. I.; Su, Q.; Grobe, R.
2007-01-01
We examine the creation of electron-positron pairs in a very strong force field. Using numerical solutions to quantum field theory we calculate the spatial and momentum probability distributions for the created particles. A comparison with classical mechanical phase space calculations suggests that despite the fully relativistic and quantum mechanical nature of the matter creation process, most aspects can be reproduced accurately in terms of classical mechanics
Pietropolli Charmet, Andrea; Cornaton, Yann
2018-05-01
This work presents an investigation of the theoretical predictions yielded by anharmonic force fields having the cubic and quartic force constants are computed analytically by means of density functional theory (DFT) using the recursive scheme developed by M. Ringholm et al. (J. Comput. Chem. 35 (2014) 622). Different functionals (namely B3LYP, PBE, PBE0 and PW86x) and basis sets were used for calculating the anharmonic vibrational spectra of two halomethanes. The benchmark analysis carried out demonstrates the reliability and overall good performances offered by hybrid approaches, where the harmonic data obtained at the coupled cluster with single and double excitations level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T), are combined with the fully analytic higher order force constants yielded by DFT functionals. These methods lead to reliable and computationally affordable calculations of anharmonic vibrational spectra with an accuracy comparable to that yielded by hybrid force fields having the anharmonic force fields computed at second order Møller-Plesset perturbation theory (MP2) level of theory using numerical differentiation but without the corresponding potential issues related to computational costs and numerical errors.
Mourot, Laurent; Fabre, Nicolas; Andersson, Erik; Willis, Sarah J; Hébert-Losier, Kim; Holmberg, Hans-Christer
2014-08-01
The aim of this study was to assess potential changes in the performance and cardiorespiratory responses of elite cross-country skiers following transition from the classic (CL) to the skating (SK) technique during a simulated skiathlon. Eight elite male skiers performed two 6 km (2 × 3 km) roller-skiing time trials on a treadmill at racing speed: one starting with the classic and switching to the skating technique (CL1-SK2) and another employing the skating technique throughout (SK1-SK2), with continuous monitoring of gas exchanges, heart rates, and kinematics (video). The overall performance times in the CL1-SK2 (21:12 ± 1:24) and SK1-SK2 (20:48 ± 2:00) trials were similar, and during the second section of each performance times and overall cardiopulmonary responses were also comparable. However, in comparison with SK1-SK2, the CL1-SK2 trial involved significantly higher increases in minute ventilation (V̇E, 89.8 ± 26.8 vs. 106.8 ± 17.6 L·min(-1)) and oxygen uptake (V̇O2; 3.1 ± 0.8 vs 3.5 ± 0.5 L·min(-1)) 2 min after the transition as well as longer time constants for V̇E, V̇O2, and heart rate during the first 3 min after the transition. This higher cardiopulmonary exertion was associated with ∼3% faster cycle rates. In conclusion, overall performance during the 2 time trials did not differ. The similar performance times during the second sections were achieved with comparable mean cardiopulmonary responses. However, the observation that during the initial 3-min post-transition following classic skiing cardiopulmonary responses and cycle rates were slightly higher supports the conclusion that an initial section of classic skiing exerts an impact on performance during a subsequent section of skate skiing.
An object oriented Python interface for atomistic simulations
Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.
2016-01-01
Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.
The scaled-charge additive force field for amino acid based ionic liquids
DEFF Research Database (Denmark)
Fileti, E. E.; Chaban, V. V.
2014-01-01
Ionic liquids (ILs) constitute an emerging research field. New ILs involve more and more organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their evolutional connection to proteins. We report a new non-polarizable force field (FF) for the eight AAILs...... comprising 1-ethyl-3-methylimidazolium cation and amino acid anions. The anions were obtained via deprotonation of carboxyl group. Specific cation-anion non-covalent interactions were taken into account by computing electrostatic potential for ion pairs. The van der Waals interactions were adopted from...
Verbaro, Daniel; Ghosh, Indrajit; Nau, Werner M; Schweitzer-Stenner, Reinhard
2010-12-30
Structural preferences in the unfolded state of peptides determined by molecular dynamics still contradict experimental data. A remedy in this regard has been suggested by MD simulations with an optimized Amber force field ff03* ( Best, R. Hummer, G. J. Phys. Chem. B 2009 , 113 , 9004 - 9015 ). The simulations yielded a statistical coil distribution for alanine which is at variance with recent experimental results. To check the validity of this distribution, we investigated the peptide H-A(5)W-OH, which with the exception of the additional terminal tryptophan is analogous to the peptide used to optimize the force fields ff03*. Electronic circular dichroism, vibrational circular dichroism, and infrared spectroscopy as well as J-coupling constants obtained from NMR experiments were used to derive the peptide's conformational ensemble. Additionally, Förster resonance energy transfer between the terminal chromophores of the fluorescently labeled peptide analogue H-Dbo-A(5)W-OH was used to determine its average length, from which the end-to-end distance of the unlabeled peptide was estimated. Qualitatively, the experimental (3)J(H(N),C(α)), VCD, and ECD indicated a preference of alanine for polyproline II-like conformations. The experimental (3)J(H(N),C(α)) for A(5)W closely resembles the constants obtained for A(5). In order to quantitatively relate the conformational distribution of A(5) obtained with the optimized AMBER ff03* force field to experimental data, the former was used to derive a distribution function which expressed the conformational ensemble as a mixture of polyproline II, β-strand, helical, and turn conformations. This model was found to satisfactorily reproduce all experimental J-coupling constants. We employed the model to calculate the amide I' profiles of the IR and vibrational circular dichroism spectrum of A(5)W, as well as the distance between the two terminal peptide carbonyls. This led to an underestimated negative VCD couplet and an
Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash
2003-01-01
Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.
Energy Technology Data Exchange (ETDEWEB)
Tran, H., E-mail: ha.tran@lisa.u-pec.fr [Laboratoire Interuniversitaire des Systèmes Atmosphériques, UMR CNRS 7583, Université Paris Est Créteil, Université Paris Diderot, Institut Pierre-Simon Laplace, 94010 Créteil Cedex (France); Domenech, J.-L. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, (IEM-CSIC), Serrano 123, 28006 Madrid (Spain)
2014-08-14
Spectral shapes of isolated lines of HCl perturbed by Ar are investigated for the first time using classical molecular dynamics simulations (CMDS). Using reliable intermolecular potentials taken from the literature, these CMDS provide the time evolution of the auto-correlation function of the dipole moment, whose Fourier-Laplace transform leads to the absorption spectrum. In order to test these calculations, room temperature spectra of various lines in the fundamental band of HCl diluted in Ar are measured, in a large pressure range, with a difference-frequency laser spectrometer. Comparisons between measured and calculated spectra show that the CMDS are able to predict the large Dicke narrowing effect on the shape of HCl lines and to satisfactorily reproduce the shapes of HCl spectra at different pressures and for various rotational quantum numbers.
Directory of Open Access Journals (Sweden)
Alexandru Capatina
2017-09-01
Full Text Available This article presents an original conceptual framework for the strategic management of intellectual capital assets in software development companies. The framework is based on Lewin's Force Field Analysis. The framework makes it possible to assess software company managers’ opinions regarding the way driving and restraining forces affect the pillars of intellectual capital. The capacity to adapt to change is vital for companies in knowledge-intensive industries. Accordingly, this study examined a sample of 74 Romanian software development companies. The aim was to help companies benefit from managing the driving and restraining forces acting upon the pillars of intellectual capital (human, structural, and relational. The effects of the driving forces, quantified by PathMaker software's Force Field Tool, were observed to be greater than the restraining forces for each pillar of intellectual capital. This paper contributes by showing the explanatory power of this framework. The framework thus offers a tool that helps managers drive change in their organizations through effective intellectual capital management. Furthermore, this article describes how to encourage the implementation of changes that create value for software development companies.
Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.
Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David
2015-07-14
In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http
CERN. Geneva; Franklin, M
2001-01-01
These will be a set of lectures on classic particle physics experiments, with emphasis on how the emasurements are made. I will discuss experiments made to measure the electric charge distribution of particles, to measure the symmetries of the weak decays, to measure the magnetic moment of the muon. As well as experiments performed which discovered new particles or resonances, like the tAU2and the J/Psi. The coverage will be general and should be understandable to someone knowing little particle physics.
Capturing the H 2 –Metal Interaction in Mg-MOF-74 Using Classical Polarization
Pham, Tony; Forrest, Katherine A.; McLaughlin, Keith; Eckert, Juergen; Space, Brian
2014-01-01
© 2014 American Chemical Society. Grand canonical Monte Carlo (GCMC) simulations of H2 sorption were performed in Mg-MOF-74, a metal-organic framework (MOF) that displays very high H2 sorption affinity. Experimental H2 sorption isotherms and isosteric heats of adsorption (Qst) values were reproduced using a general purpose materials sorption potential that includes many-body polarization interactions. In contrast, using two models that include only charge-quadrupole interactions failed to reproduce such experimental measurements even though they are the type normally employed in such classical force field calculations. Utilizing the present explicit polarizable model in GCMC simulation resulted in a Mg2+-H2 distance of 2.60 Å, which is close to a previously reported value that was obtained using electronic structure methods and comparable to similar experimental measurements. The induced dipole distribution obtained from simulation assisted in the characterization of two previously identified sorption sites in the MOF: the Mg2+ ions and the oxido group of the linkers. The calculated two-dimensional quantum rotational levels for a H2 molecule sorbed onto the Mg2+ ion were in good agreement with experimental inelastic neutron scattering (INS) data. Although the H2-metal interaction in MOFs may be thought of as a quantum mechanical effect, this study demonstrates how the interaction between the sorbate molecules and the open-metal sites in a particular highly sorbing MOF can be captured using classical simulation techniques that involve a polarizable potential.
Capturing the H 2 –Metal Interaction in Mg-MOF-74 Using Classical Polarization
Pham, Tony
2014-10-02
© 2014 American Chemical Society. Grand canonical Monte Carlo (GCMC) simulations of H2 sorption were performed in Mg-MOF-74, a metal-organic framework (MOF) that displays very high H2 sorption affinity. Experimental H2 sorption isotherms and isosteric heats of adsorption (Qst) values were reproduced using a general purpose materials sorption potential that includes many-body polarization interactions. In contrast, using two models that include only charge-quadrupole interactions failed to reproduce such experimental measurements even though they are the type normally employed in such classical force field calculations. Utilizing the present explicit polarizable model in GCMC simulation resulted in a Mg2+-H2 distance of 2.60 Å, which is close to a previously reported value that was obtained using electronic structure methods and comparable to similar experimental measurements. The induced dipole distribution obtained from simulation assisted in the characterization of two previously identified sorption sites in the MOF: the Mg2+ ions and the oxido group of the linkers. The calculated two-dimensional quantum rotational levels for a H2 molecule sorbed onto the Mg2+ ion were in good agreement with experimental inelastic neutron scattering (INS) data. Although the H2-metal interaction in MOFs may be thought of as a quantum mechanical effect, this study demonstrates how the interaction between the sorbate molecules and the open-metal sites in a particular highly sorbing MOF can be captured using classical simulation techniques that involve a polarizable potential.
Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.
Saito, Minoru; Okazaki, Isao
2009-12-01
The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. (c) 2009 Wiley Periodicals, Inc.
Directory of Open Access Journals (Sweden)
Xiaolei Wang
2013-12-01
Full Text Available We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All three platinum agents could respectively combine with the monomeric Atox1 protein and the dimeric Atox1 protein to form a stable binary and ternary complex due to the covalent interaction of the platinum center with the Atox1 protein. The results suggested that the extra interaction from the oxaliplatin ligand–Atox1 protein interface increases its affinity only for the OxaliPt + Atox1 model. The binding of the oxaliplatin agent to the Atox1 protein might cause larger deformation of the protein than those of the cisplatin and transplatin agents due to the larger size of the oxaliplatin ligand. However, the extra interactions to facilitate the stabilities of the ternary CisPt + 2Atox1 and OxaliPt + 2Atox1 models come from the α1 helices and α2-β4 loops of the Atox1 protein–Atox1 protein interface due to the cis conformation of the platinum agents. The combinations of two Atox1 proteins in an asymmetric way in the three ternary models were analyzed. These investigations might provide detailed information for understanding the interaction mechanism of the platinum agents binding to the Atox1 protein in the cytoplasm.
Bounceur, Nabila; Crucifix, Michel
2010-05-01
analysis (NLPCA) taking on account the non linear dependences between data. The choice on the one hand of the values of the orbital parameters and on the other hand the number of simulations has been chosen using an optimal experimental plan. This method allow us to maximise the information about the model considering the variation of its parameters in a minimum experiences. A great number of these simulations have been done already and the next step will be to apply all the reduction methods. These methodologies have been applied on two simple models. First, the Lorenz attractor, a simple model which takes into account the main characteristics of the complex dynamics of the climate system. Second, a model of the terrestrial insolation determined by the three orbital parameters varying in time, has been analysed using PCA and EOF reduction methods. In this case, five dominant modes have been found to be sufficient. These first results justify the use of the several methods and prove their efficiency in the case of these simple models and encourage us to apply them to the outputs already computed with LoveClim.
International Nuclear Information System (INIS)
Recami, E.
1984-01-01
A review of tachyons, with particular attention to their classical theory, is presented. The extension of Special Relativity to tachyons in two dimensional is first presented, an elegant model-theory which allows a better understanding also of ordinary physics. Then, the results are extended to the four-dimensional case (particular on tachyon mechanics) that can be derived without assuming the existence of Super-luminal reference-frames. Localizability and the unexpected apparent shape of tachyonic objects are discussed, and it is shown (on the basis of tachyon kinematics) how to solve the common causal paradoxes. In connection with General Relativity, particularly the problem of the apparent superluminal expansions in astrophysics is reviewed. The problem (still open) of the extension of relativitic theories to tachyons in four dimensions is tackled, and the electromagnetic theory of tachyons, a topic that can be relevant also for the experimental side, is reviewed. (Author) [pt
Directory of Open Access Journals (Sweden)
Jiang Hualiang
2010-11-01
Full Text Available Abstract Background Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA, we have developed a conformational generation method called Cyndi in the previous study. In this work, in addition to Tripos force field in the previous version, Cyndi was updated by incorporation of MMFF94 force field to assess the conformational energy more rationally. With two force fields against a larger dataset of 742 bioactive conformations of small ligands extracted from PDB, a comparative analysis was performed between pure force field based method (FFBM and multiple empirical criteria based method (MECBM hybrided with different force fields. Results Our analysis reveals that incorporating multiple empirical rules can significantly improve the accuracy of conformational generation. MECBM, which takes both empirical and force field criteria as the objective functions, can reproduce about 54% (within 1Å RMSD of the bioactive conformations in the 742-molecule testset, much higher than that of pure force field method (FFBM, about 37%. On the other hand, MECBM achieved a more complete and efficient sampling of the conformational space because the average size of unique conformations ensemble per molecule is about 6 times larger than that of FFBM, while the time scale for conformational generation is nearly the same as FFBM. Furthermore, as a complementary comparison study between the methods with and without empirical biases, we also tested the performance of the three conformational generation methods in MacroModel in combination with different force fields. Compared with the methods in MacroModel, MECBM is more competitive in retrieving the bioactive conformations in light of accuracy but has much lower computational cost. Conclusions By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational
International Nuclear Information System (INIS)
Iselin, F. Christoph
1997-01-01
Exchange of data and algorithms among accelerator physics programs is difficult because of unnecessary differences in input formats and internal data structures. To alleviate these problems a C++ class library called CLASSIC (Class Library for Accelerator System Simulation and Control) is being developed with the goal to provide standard building blocks for computer programs used in accelerator design. It includes modules for building accelerator lattice structures in computer memory using a standard input language, a graphical user interface, or a programmed algorithm. It also provides simulation algorithms. These can easily be replaced by modules which communicate with the control system of the accelerator. Exchange of both data and algorithm between different programs using the CLASSIC library should present no difficulty
Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations
DEFF Research Database (Denmark)
Hemmingsen, Lars Bo Stegeager; Madsen, D.E.; Esbensen, A.L.
2004-01-01
of the (gg, gt and tg) rotamers of methyl alpha-D-glucopyranoside and methyl alpha-D-galactopyranoside are (0.13, 0.00, 0.15) and (0.64, 0.00, 0.77) kcal/mol. respectively. The results of the quantum mechanical calculations are compared with the results of calculations using the 20 second...... for monosaccharide carbohydrate benchmark systems. Selected results are: (i) The interaction energy of the alpha-D-alucopyranose-H2O heterodimer is estimated to be 4.9 kcal/mol, using a composite method including terms at highly correlated (CCSD(T)) level. Most molecular mechanics force fields are in error...
Research on desulfurisation of fine coal under compounding the physics force field
Energy Technology Data Exchange (ETDEWEB)
Tao, Y.; Fu, D.; Tao, D.; Liu, J.; Zhao, Y. [China University of Mining and Technology, Xuzhou (China)
2005-08-15
Desulphurization experiment carried on under compounding the physics force field was described for -0.5 mm fine particle of high sulphur coal. The experiment factorial plan of desulphurization on centrifugal gravity Falcon separator was designed and its results were analyzed by using Design-Expert 6.0 software. The 2-reactor interaction relation model between comprehensive desulphurization efficiency of pyrite sulphur and different operation variable was drawn, i.e. 2 FI model, and the 2-factor interaction on pyrite desulphurization efficiency of the operation factors differently was analyzed. The interaction on pyrite desulphurization efficiency of feed rate and feed concentration is significant. The optimization test condition for desulphurization was proposed by Design-Expert 6.0, and comprehensive desulphurization efficiency of 86.90% can be achieved. 5 refs., 3 figs., 7 tabs.
Force field inside the void in complex plasmas under microgravity conditions
International Nuclear Information System (INIS)
Kretschmer, M.; Khrapak, S.A.; Zhdanov, S.K.; Thomas, H.M.; Morfill, G.E.; Fortov, V.E.; Lipaev, A.M.; Molotkov, V.I.; Ivanov, A.I.; Turin, M.V.
2005-01-01
Observations of complex plasmas under microgravity conditions onboard the International Space Station performed with the Plasma-Kristall experiment-Nefedov facility are reported. A weak instability of the boundary between the central void (region free of microparticles) and the microparticle cloud is observed at low gas pressures. The instability leads to periodic injections of a relatively small number of particles into the void region (by analogy this effect is called the 'trampoline effect'). The trajectories of injected particles are analyzed providing information on the force field inside the void. The experimental results are compared with theory which assumes that the most important forces inside the void are the electric and the ion drag forces. Good agreement is found clearly indicating that under conditions investigated the void formation is caused by the ion drag force
Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration
DEFF Research Database (Denmark)
Maciejewski, A.; Pasenkiewicz-Gierula, M.; Cramariuc, O.
2014-01-01
validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule....... In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Moller-Plesset perturbation theory (MP2), and (3...... one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM)....
Energy Technology Data Exchange (ETDEWEB)
Ganesh, Panchapakesan [ORNL; Kent, Paul R [ORNL; Mochalin, Vadym N [ORNL
2011-01-01
We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbon nanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core of the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbon nanostructure appears, with a shell-shell spacing of about {approx}3.4 {angstrom} for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large ({approx}29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.
Energy Technology Data Exchange (ETDEWEB)
Ganesh, P. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science; Kent, P. R. C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science; Mochalin, V. [Drexel Univ., Philadelphia, PA (United States). Dept. of Materials Science and Engineering
2011-10-01
We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbonnanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core of the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbonnanostructure appears, with a shell-shell spacing of about ~3.4 Å for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large (~29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.
Sun, Delin; Forsman, Jan; Woodward, Clifford E
2015-04-14
Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.
Horta, Bruno A C; Merz, Pascal T; Fuchs, Patrick F J; Dolenc, Jozica; Riniker, Sereina; Hünenberger, Philippe H
2016-08-09
This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of
Bayse, Craig A; Merz, Kenneth M
2014-08-05
Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.
International Nuclear Information System (INIS)
Karolewski, M.A.
2004-01-01
Classical dynamics simulations of sputtering have been carried out for 2 keV Cu projectiles incident on a Cu(1 0 0) crystallite target, in order to study the effects of projectile fluence on sputtering properties. Five projectiles are delivered into a 400 Ang 2 region of a Cu crystallite target at 5 ps intervals, giving a maximum fluence of 1.25 x 10 14 cm -2 in the primary impact zone. The altitudinal angle (φ) of the projectiles was 30 deg. (measured with respect to the surface), and the azimuthal (phi) direction of incidence was parallel to the surface atomic rows. The sputter yield is found not to depend sensitively on fluence. Over the fluence range investigated, the predicted standard deviation of the sputter yield is only 5% of the mean value of 11.7. Resputtered projectiles contribute less than 2% of the total sputter yield. With increasing fluence, the angular distribution of sputtered atoms tends to become less anisotropic. For example, the intensity modulations in the azimuthal angular distribution are reduced. This effect is due to the increasing contribution from atoms that are sputtered from defective structural environments. However, sputtered atom energy distributions and emission statistics show little dependence on fluence. The information depth of sputtered atoms increases rapidly with fluence, from 0.11 monolayers (ML) initially, to 1.2 ML after sputtering 0.25 ML from the primary impact zone
Molecular models and simulations of layered materials
International Nuclear Information System (INIS)
Kalinichev, Andrey G.; Cygan, Randall Timothy; Heinz, Hendrik; Greathouse, Jeffery A.
2008-01-01
The micro- to nano-sized nature of layered materials, particularly characteristic of naturally occurring clay minerals, limits our ability to fully interrogate their atomic dispositions and crystal structures. The low symmetry, multicomponent compositions, defects, and disorder phenomena of clays and related phases necessitate the use of molecular models and modern simulation methods. Computational chemistry tools based on classical force fields and quantum-chemical methods of electronic structure calculations provide a practical approach to evaluate structure and dynamics of the materials on an atomic scale. Combined with classical energy minimization, molecular dynamics, and Monte Carlo techniques, quantum methods provide accurate models of layered materials such as clay minerals, layered double hydroxides, and clay-polymer nanocomposites
Starrfield, Sumner; Bose, Maitrayee; Iliadis, Christian; Hix, William R.; Wagner, R. Mark; Woodward, Charles E.; Jose', Jordi; Hernanz, Margarita
2018-01-01
We have continued our studies of Classical Nova explosions by following the evolution of thermonuclear runaways (TNRs) on Carbon Oxygen white dwarfs (WDs). We have varied both the mass of the WD and the composition of the accreted material. We now rely on the results of multi-D studies of TNRs in WDs that accrete only Solar matter. They find that mixing with the core occurs after the TNR is well underway, reaching enrichment levels in agreement with observations of the ejecta abundances. We, therefore, accrete only Solar matter with NOVA (our 1-D, fully implicit, hydro code) until the TNR is initiated and then switch the accreted composition to a mixed composition: either 25% core and 75% Solar or 50% core and 50% Solar. Because the amount of accreted material is inversely proportional to the initial 12C abundance, by accreting Solar matter the amount of material taking part in the outburst is larger than if we had used mixed material from the beginning. We follow the TNR through the peak and tabulate the amount of ejected gases, their velocities and abundances. We also predict the amount of 7Li and 7Be produced and ejected by the explosion and compare our predictions to the observations in a companion poster describing the LBT measurements of 7Li in V5668 Sgr. We also compare our abundance predictions to those measured in pre-solar grains that may arise from Classical Nova explosions. Our predictions are also compared to results with SHIVA (Josè and Hernanz). Finally, many of these simulations eject significantly less mass than accreted and, therefore, the WD is growing in mass toward the Chandrasekhar Limit. This suggests that the single degenerate scenario is still a viable option for SN Ia progenitors. This work was supported in part by NASA under the Astrophysics Theory Program grant 14-ATP14-0007 and the U.S. DOE under Contract No. DE-FG02- 97ER41041. SS acknowledges partial support from NASA and HST grants to ASU and WRH is supported by the U.S. Department
Quantum Computing's Classical Problem, Classical Computing's Quantum Problem
Van Meter, Rodney
2013-01-01
Tasked with the challenge to build better and better computers, quantum computing and classical computing face the same conundrum: the success of classical computing systems. Small quantum computing systems have been demonstrated, and intermediate-scale systems are on the horizon, capable of calculating numeric results or simulating physical systems far beyond what humans can do by hand. However, to be commercially viable, they must surpass what our wildly successful, highly advanced classica...
Force fields of charged particles in micro-nanofluidic preconcentration systems
Gong, Lingyan; Ouyang, Wei; Li, Zirui; Han, Jongyoon
2017-12-01
Electrokinetic concentration devices based on the ion concentration polarization (ICP) phenomenon have drawn much attention due to their simple setup, high enrichment factor, and easy integration with many subsequent processes, such as separation, reaction, and extraction etc. Despite significant progress in the experimental research, fundamental understanding and detailed modeling of the preconcentration systems is still lacking. The mechanism of the electrokinetic trapping of charged particles is currently limited to the force balance analysis between the electric force and fluid drag force in an over-simplified one-dimensional (1D) model, which misses many signatures of the actual system. This letter studies the particle trapping phenomena that are not explainable in the 1D model through the calculation of the two-dimensional (2D) force fields. The trapping of charged particles is shown to significantly distort the electric field and fluid flow pattern, which in turn leads to the different trapping behaviors of particles of different sizes. The mechanisms behind the protrusions and instability of the focused band, which are important factors determining overall preconcentration efficiency, are revealed through analyzing the rotating fluxes of particles in the vicinity of the ion-selective membrane. The differences in the enrichment factors of differently sized particles are understood through the interplay between the electric force and convective fluid flow. These results provide insights into the electrokinetic concentration effect, which could facilitate the design and optimization of ICP-based preconcentration systems.
Comparison of force fields and calculation methods for vibration intervals of isotopic H+3 molecules
International Nuclear Information System (INIS)
Carney, G.D.; Adler-Golden, S.M.; Lesseski, D.C.
1986-01-01
This paper reports (a) improved values for low-lying vibration intervals of H + 3 , H 2 D + , D 2 H + , and D + 3 calculated using the variational method and Simons--Parr--Finlan representations of the Carney--Porter and Dykstra--Swope ab initio H + 3 potential energy surfaces, (b) quartic normal coordinate force fields for isotopic H + 3 molecules, (c) comparisons of variational and second-order perturbation theory, and (d) convergence properties of the Lai--Hagstrom internal coordinate vibrational Hamiltonian. Standard deviations between experimental and ab initio fundamental vibration intervals of H + 3 , H 2 D + , D 2 H + , and D + 3 for these potential surfaces are 6.9 (Carney--Porter) and 1.2 cm -1 (Dykstra--Swope). The standard deviations between perturbation theory and exact variational fundamentals are 5 and 10 cm -1 for the respective surfaces. The internal coordinate Hamiltonian is found to be less efficient than the previously employed ''t'' coordinate Hamiltonian for these molecules, except in the case of H 2 D +
Kutateladze, Andrei G; Mukhina, Olga A
2014-09-05
Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.
Energy Technology Data Exchange (ETDEWEB)
Ramakrishnan, Raghunathan [Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel (Switzerland); Rauhut, Guntram, E-mail: rauhut@theochem.uni-stuttgart.de [Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany)
2015-04-21
Semi-quartic force fields (QFF) rely on a Taylor-expansion of the multi-dimensional Born-Oppenheimer potential energy surface (PES) and are frequently used within the calculation of anharmonic vibrational frequencies based on 2nd order vibrational perturbation theory (VPT2). As such they are usually determined by differentiation of the electronic energy with respect to the nuclear coordinates. Alternatively, potential energy surfaces can be expanded in terms of multi-mode expansions, which typically do not require any derivative techniques. The computational effort to retrieve QFF from size-reduced multi-mode expansions has been studied and has been compared with standard Taylor-expansions. As multi-mode expansions allow for the convenient introduction of subtle approximations, these will be discussed in some detail. In addition, a preliminary study about the applicability of a generalized Duschinsky transformation to QFFs is provided. This transformation allows for the efficient evaluation of VPT2 frequencies of isotopologues from the PES of the parent compound and thus avoids the recalculation of PESs in different axes systems.
A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces.
Schneider, Julian; Ciacchi, Lucio Colombi
2011-02-08
The behavior of titanium implants in physiological environments is governed by the thin oxide layer that forms spontaneously on the metal surface and mediates the interactions with adsorbate molecules. In order to study the adsorption of biomolecules on titanium in a realistic fashion, we first build up a model of an oxidized Ti surface in contact with liquid water by means of extensive first-principles molecular dynamics simulations. Taking the obtained structure as reference, we then develop a classical potential to model the Ti/TiOx/water interface. This is based on the mapping with Coulomb and Lennard-Jones potentials of the adsorption energy landscape of single water and ammonia molecules on the rutile TiO2(110) surface. The interactions with arbitrary organic molecules are obtained via standard combination rules to established biomolecular force fields. The transferability of our potential to the case of organic molecules adsorbing on the oxidized Ti surface is checked by comparing the classical potential energy surfaces of representative systems to quantum mechanical results at the level of density functional theory. Moreover, we calculate the heat of immersion of the TiO2 rutile surface and the detachment force of a single tyrosine residue from steered molecular dynamics simulations, finding good agreement with experimental reference data in both cases. As a first application, we study the adsorption behavior of the Arg-Gly-Asp (RGD) peptide on the oxidized titanium surface, focusing particularly on the calculation of the free energy of desorption.
Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.
Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this
International Nuclear Information System (INIS)
Bankura, Arindam; Chandra, Amalendu
2015-01-01
The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water
Olson, Mark A
2018-01-22
Intrinsically disordered proteins are characterized by their large manifold of thermally accessible conformations and their related statistical weights, making them an interesting target of simulation studies. To assess the development of a computational framework for modeling this distinct class of proteins, this work examines temperature-based replica-exchange simulations to generate a conformational ensemble of a 28-residue peptide from the Ebola virus protein VP35. Starting from a prefolded helix-β-turn-helix topology observed in a crystallographic assembly, the simulation strategy tested is the recently refined CHARMM36m force field combined with a generalized Born solvent model. A comparison of two replica-exchange methods is provided, where one is a traditional approach with a fixed set of temperatures and the other is an adaptive scheme in which the thermal windows are allowed to move in temperature space. The assessment is further extended to include a comparison with equivalent CHARMM22 simulation data sets. The analysis finds CHARMM36m to shift the minimum in the potential of mean force (PMF) to a lower fractional helicity compared with CHARMM22, while the latter showed greater conformational plasticity along the helix-forming reaction coordinate. Among the simulation models, only the adaptive tempering method with CHARMM36m found an ensemble of conformational heterogeneity consisting of transitions between α-helix-β-hairpin folds and unstructured states that produced a PMF of fractional fold propensity in qualitative agreement with circular dichroism experiments reporting a disordered peptide.
An ionic force-field study of monomers, dimers and higher polymers in pentafluoride vapors
Energy Technology Data Exchange (ETDEWEB)
Cicek Onem, Z. [Department of Physics, Istanbul University, Istanbul (Turkey); Akdeniz, Z. [Department of Physics, Istanbul University, Istanbul (Turkey); Classe di Scienze, Scuola Normale Superiore, I-56126 Pisa (Italy)], E-mail: zakdeniz@istanbul.edu.tr; Tosi, M.P. [Classe di Scienze, Scuola Normale Superiore, I-56126 Pisa (Italy)], E-mail: tosim@sns.it
2008-08-01
Pentafluoride compounds such as NbF{sub 5} and TaF{sub 5} have been reported in the literature to admit various states of polymerization coexisting with monomers in their vapor phase, in relative concentrations that vary with temperature and pressure. We construct a microscopic interionic force-field model for the molecular monomer of these compounds (including VF{sub 5}, SbF{sub 5} and MoF{sub 5} in addition to NbF{sub 5} and TaF{sub 5}), the stable form of the monomer being in the shape of a D{sub 3h} trigonal bipyramid in all cases. The model emulates chemical bonds by allowing for electrical and short-range overlap polarizabilities of the fluorines, and is used to evaluate the structure and the stability of (MF{sub 5}){sub n} molecules with n running from 2 to 6. The dimer is formed by two distorted edge-sharing octahedral, while the trimer and the higher polymers can form rings of distorted corner-sharing octahedra. A chain-like configuration is also found for the trimer of NbF{sub 5}, which consists of a seven-fold coordinated Nb bonded to two distorted octahedra via edge sharing. Comparison of calculated vibrational frequencies and bond lengths with experimental data is made whenever possible. We find that there is a small net gain of energy in the formation of a dimer, while otherwise the static energy of the n-mer is very close to that of n separated monomers. High sensitivity of the state of molecular aggregation to the thermodynamic conditions of the vapor is clearly indicated by our calculations.
International Nuclear Information System (INIS)
Khrapak, S. A.; Kretschmer, M.; Zhdanov, S. K.; Thomas, H. M.; MOrfill, G. e.; Fortov, V. E.; Lipaev, A. M.; Molotkov, V. I.; Ivanov, A. I.; Turin, M. V.
2005-01-01
The PKE-Nefedov facility onboard the International Space Station (ISS),operational since March, 2'001, has enabled the study of complex (dusty) plasmas under microgravity conditions. A complex plasma is generated by introducing micron sized grains in a capacitively coupled rf discharge. The grains form a cloud inside the bulk of the discharge and can be easily visualized with the help of standard tools-laser illumination and video cameras. In most of the experiments under microgravity conditions the central region of the discharge is free of grains a so called void is formed. Due to recent theoretical advances, showing that the ion drag force can be more than a factor of ten larger than had traditionally been believed, void formation is now through to be a consequence of this (enhanced) interaction. The way this process works is the following: the ions drifting from the central region of a discharge to its walls and electrodes transfer their momentum to the grains pushing them out of the center. However, no direct experimental results on the origin of the void formation were reported so far. In this paper we report new results on the observation of a weak instability of the void-complex plasma interface observed at a relatively low gas pressure (p=12Pa). The instability leads to periodic injections of a relatively small number of particles into the void region (by analogy this effect is called trampoline effect), The trajectories of injected particles are analyzed providing information on the force field and potential energy distribution inside the void. For the relatively low neutral gas pressure used in the experiment a direct comparison with theory involving a model of the ion drag force in the collisionless regime is possible. Such a comparison yields good agreement, implying that we have observed the first experimental confirmation of the ion drag mechanism as being responsible for the void formation. (Author)
Energy Technology Data Exchange (ETDEWEB)
Khrapak, S. A.; Kretschmer, M.; Zhdanov, S. K.; Thomas, H. M.; MOrfill, G. e.; Fortov, V. E.; Lipaev, A. M.; Molotkov, V. I.; Ivanov, A. I.; Turin, M. V.
2005-07-01
The PKE-Nefedov facility onboard the International Space Station (ISS),operational since March, 2'001, has enabled the study of complex (dusty) plasmas under microgravity conditions. A complex plasma is generated by introducing micron sized grains in a capacitively coupled rf discharge. The grains form a cloud inside the bulk of the discharge and can be easily visualized with the help of standard tools-laser illumination and video cameras. In most of the experiments under microgravity conditions the central region of the discharge is free of grains a so called void is formed. Due to recent theoretical advances, showing that the ion drag force can be more than a factor of ten larger than had traditionally been believed, void formation is now through to be a consequence of this (enhanced) interaction. The way this process works is the following: the ions drifting from the central region of a discharge to its walls and electrodes transfer their momentum to the grains pushing them out of the center. However, no direct experimental results on the origin of the void formation were reported so far. In this paper we report new results on the observation of a weak instability of the void-complex plasma interface observed at a relatively low gas pressure (p=12Pa). The instability leads to periodic injections of a relatively small number of particles into the void region (by analogy this effect is called trampoline effect), The trajectories of injected particles are analyzed providing information on the force field and potential energy distribution inside the void. For the relatively low neutral gas pressure used in the experiment a direct comparison with theory involving a model of the ion drag force in the collisionless regime is possible. Such a comparison yields good agreement, implying that we have observed the first experimental confirmation of the ion drag mechanism as being responsible for the void formation. (Author)
Houldin, Adina; Chua, Romeo; Carpenter, Mark G; Lam, Tania
2012-08-01
Several studies have demonstrated that motor adaptations to a novel task environment can be transferred between limbs. Such interlimb transfer of motor commands is consistent with the notion of centrally driven strategies that can be generalized across different frames of reference. So far, studies of interlimb transfer of locomotor adaptations have yielded disparate results. Here we sought to determine whether locomotor adaptations in one (trained) leg show transfer to the other (test) leg during a unipedal walking task. We hypothesized that adaptation in the test leg to a velocity-dependent force field previously experienced by the trained leg will be faster, as revealed by faster recovery of kinematic errors and earlier onset of aftereffects. Twenty able-bodied adults walked unipedally in the Lokomat robotic gait orthosis, which applied velocity-dependent resistance to the legs. The amount of resistance was scaled to 10% of each individual's maximum voluntary contraction of the hip flexors. Electromyography and kinematics of the lower limb were recorded. All subjects were right-leg dominant and were tested for transfer of motor adaptations from the right leg to the left leg. Catch trials, consisting of unexpected removal of resistance, were presented after the first step with resistance and after a period of adaptation to test for aftereffects. We found no significant differences in the sizes of the aftereffects between the two legs, except for peak hip flexion during swing, or in the rate at which peak hip flexion adapted during steps against resistance between the two legs. Our results indicate that interlimb transfer of these types of locomotor adaptation is not a robust phenomenon. These findings add to our current understanding of motor adaptations and provide further evidence that generalization of adaptations may be dependent on the movement task.
Adaptive resolution simulation of salt solutions
International Nuclear Information System (INIS)
Bevc, Staš; Praprotnik, Matej; Junghans, Christoph; Kremer, Kurt
2013-01-01
We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the other. We employ standard extended simple point charge (SPC/E) and simple point charge (SPC) water models in combination with AMBER and GROMOS force fields for ion interactions in the atomistic domain. Electrostatics in our model are described by the generalized reaction field method. The effective interactions for water–water and water–ion interactions in the coarse-grained model are derived using structure-based coarse-graining approach while the Coulomb interactions between ions are appropriately screened. To ensure an even distribution of water molecules and ions across the simulation box we employ thermodynamic forces. We demonstrate that the equilibrium structural, e.g. radial distribution functions and density distributions of all the species, and dynamical properties are correctly reproduced by our adaptive resolution method. Our multiscale approach, which is general and can be used for any classical non-polarizable force-field and/or types of ions, will significantly speed up biomolecular simulation involving aqueous salt. (paper)
Sulimov, Alexey V; Kutov, Danil C; Katkova, Ekaterina V; Ilin, Ivan S; Sulimov, Vladimir B
2017-11-01
Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target protein and the disease is cured. Computer-aided molecular modeling can considerably increase effectiveness of new inhibitors development. Reliable predictions of the target protein inhibition by a small molecule, ligand, is defined by the accuracy of docking programs. Such programs position a ligand in the target protein and estimate the protein-ligand binding energy. Positioning accuracy of modern docking programs is satisfactory. However, the accuracy of binding energy calculations is too low to predict good inhibitors. For effective application of docking programs to new inhibitors development the accuracy of binding energy calculations should be higher than 1kcal/mol. Reasons of limited accuracy of modern docking programs are discussed. One of the most important aspects limiting this accuracy is imperfection of protein-ligand energy calculations. Results of supercomputer validation of several force fields and quantum-chemical methods for docking are presented. The validation was performed by quasi-docking as follows. First, the low energy minima spectra of 16 protein-ligand complexes were found by exhaustive minima search in the MMFF94 force field. Second, energies of the lowest 8192 minima are recalculated with CHARMM force field and PM6-D3H4X and PM7 quantum-chemical methods for each complex. The analysis of minima energies reveals the docking positioning accuracies of the PM7 and PM6-D3H4X quantum-chemical methods and the CHARMM force field are close to one another and they are better than the positioning accuracy of the MMFF94 force field. Copyright © 2017 Elsevier Inc. All rights reserved.
Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio
2015-02-10
Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.
Energy Technology Data Exchange (ETDEWEB)
Tian, Ye [Sanford-Burnham-Prebys Medical Discovery Institute (United States); Schwieters, Charles D. [National Institutes of Health, Center for Information Technology (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford-Burnham-Prebys Medical Discovery Institute (United States)
2017-01-15
Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision
DEFF Research Database (Denmark)
Boklund, Anette; Goldbach, Stine G.; Uttenthal, Åse
2008-01-01
of CSFV between the hypothetical wild-boar population and the domestic population. Furthermore, the economic impact is assessed taking the perspective of the Danish national budget and the Danish pig industry. We used InterSpreadPlus to model the differential classical swine fever (CSF) risk due to wild......Denmark has no free-range wild-boar population. However, Danish wildlife organizations have suggested that wild boar should be reintroduced into the wild to broaden national biodiversity. Danish pig farmers fear that this would lead to a higher risk of introduction of classical swine fever virus...
DEFF Research Database (Denmark)
Li, Xiaozhou; Neumann, Marcus A.; van de Streek, Jacco
2017-01-01
of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base...
Karczyńska, Agnieszka S; Mozolewska, Magdalena A; Krupa, Paweł; Giełdoń, Artur; Liwo, Adam; Czaplewski, Cezary
2018-03-01
A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction. © 2017 Wiley Periodicals, Inc.
International Nuclear Information System (INIS)
Huberman, T; Tennant, D A; Cowley, R A; Coldea, R; Frost, C D
2008-01-01
We report comprehensive inelastic neutron scattering measurements of the magnetic excitations in the 2D spin-5/2 Heisenberg antiferromagnet Rb 2 MnF 4 as a function of temperature from deep in the Néel ordered phase up to paramagnetic, 0.13 B T/4JS −1 for temperatures up to near the Curie–Weiss temperature, Θ CW . For wavevectors smaller than ξ −1 , relaxational dynamics occurs. The observed renormalization of spin wave energies, and evolution of excitation lineshapes, with increasing temperature are quantitatively compared with finite-temperature spin wave theory and computer simulations for classical spins. Random phase approximation calculations provide a good description of the low temperature renormalization of spin waves. In contrast, lifetime broadening calculated using the first Born approximation shows, at best, modest agreement around the zone boundary at low temperatures. Classical dynamics simulations using an appropriate quantum classical correspondence were found to provide a good description of the intermediate and high temperature regimes over all wavevector and energy scales, and the crossover from quantum to classical dynamics observed around Θ CW /S, where the spin S = 5/2. A characterization of the data over the whole wavevector/energy/temperature parameter space is given. In this, T 2 behaviour is found to dominate the wavevector and temperature dependence of the linewidths over a large parameter range, and no evidence of hydrodynamic behaviour or dynamical scaling behaviour found within the accuracy of the datasets. An efficient and easily implemented classical dynamics methodology is presented that provides a practical method for modelling other semiclassical quantum magnets
Indian Academy of Sciences (India)
Journal of Genetics, Vol. 85, No. 2, August 2006. 101. Page 2. J. Genet. classic. 102. Journal of Genetics, Vol. 85, No. 2, August 2006. Page 3. J. Genet. classic. Journal of Genetics, Vol. 85, No. 2, August 2006. 103. Page 4. J. Genet. classic. 104. Journal of Genetics, Vol. 85, No. 2, August 2006. Page 5. J. Genet. classic.
Indian Academy of Sciences (India)
Unknown
Journal of Genetics, Vol. 84, No. 1, April 2005. 37. Page 2. J. Genet. classic. Journal of Genetics, Vol. 84, No. 1, April 2005. 38. Page 3. J. Genet. classic. Journal of Genetics, Vol. 84, No. 1, April 2005. 39. Page 4. J. Genet. classic. Journal of Genetics, Vol. 84, No. 1, April 2005. 40. Page 5. J. Genet. classic. Journal of ...
Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective
Czech Academy of Sciences Publication Activity Database
Szabla, Rafal; Havrila, Marek; Kruse, Holger; Sponer, Jiri
2016-01-01
Roč. 120, č. 41 (2016), s. 10635-10648 ISSN 1520-6106 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * quantum-chemical computations Subject RIV: BO - Biophysics Impact factor: 3.177, year: 2016
Quantum formalism for classical statistics
Wetterich, C.
2018-06-01
In static classical statistical systems the problem of information transport from a boundary to the bulk finds a simple description in terms of wave functions or density matrices. While the transfer matrix formalism is a type of Heisenberg picture for this problem, we develop here the associated Schrödinger picture that keeps track of the local probabilistic information. The transport of the probabilistic information between neighboring hypersurfaces obeys a linear evolution equation, and therefore the superposition principle for the possible solutions. Operators are associated to local observables, with rules for the computation of expectation values similar to quantum mechanics. We discuss how non-commutativity naturally arises in this setting. Also other features characteristic of quantum mechanics, such as complex structure, change of basis or symmetry transformations, can be found in classical statistics once formulated in terms of wave functions or density matrices. We construct for every quantum system an equivalent classical statistical system, such that time in quantum mechanics corresponds to the location of hypersurfaces in the classical probabilistic ensemble. For suitable choices of local observables in the classical statistical system one can, in principle, compute all expectation values and correlations of observables in the quantum system from the local probabilistic information of the associated classical statistical system. Realizing a static memory material as a quantum simulator for a given quantum system is not a matter of principle, but rather of practical simplicity.
DEFF Research Database (Denmark)
Kaszuba, K.; Postila, P. A.; Cramariuc, O.
2013-01-01
studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular...... interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
Czech Academy of Sciences Publication Activity Database
Kührová, P.; Best, R.B.; Bottaro, S.; Bussi, G.; Sponer, Jiri; Otyepka, Michal; Banáš, Pavel
2016-01-01
Roč. 12, č. 9 (2016), s. 4534-4548 ISSN 1549-9618 R&D Projects: GA ČR GAP208/12/1878 Institutional support: RVO:68081707 Keywords : molecular- dynamics simulations * base-pairs * tertiary interactions * explicit-solvent Subject RIV: BO - Biophysics Impact factor: 5.245, year: 2016
Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simblations with Implicit Solvent
Arnarez, Clement; Uusitalo, Jaakko J.; Masman, Marcelo F.; Ingolfsson, Helgi I.; de Jong, Djurre H.; Melo, Manuel N.; Periole, Xavier; de Vries, Alex H.; Marrink, Siewert J.
Coarse-grained (CG) models allow simulation of larger systems for longer times by decreasing the number of degrees of freedom compared with all-atom models. Here we introduce an implicit-solvent version of the popular CG Martini model, nicknamed Dry Martini. To account for the omitted solvent
Assessing the Current State of Amber Force Field Modifications for DNA
Czech Academy of Sciences Publication Activity Database
Galindo-Murillo, R.; Robertson, J.; Zgarbová, M.; Šponer, Jiří; Otyepka, M.; Jurečka, P.; Cheatham III, T. E.
2016-01-01
Roč. 12, č. 8 (2016), s. 4114-4127 ISSN 1549-9618 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * particle mesh ewald * pair opening kinetics Subject RIV: BO - Biophysics Impact factor: 5.245, year: 2016
Ships in an Artificial Force Field : A Multi-agent System for Nautical Traffic and Safety
Xiao, F.
2014-01-01
The main objective of this research is developing a simulation tool that provides information of detailed ship behavior in a specific navigational environment, on both the ship traffic level and the individual ship level, for safety analysis, decision making, planning of ports and waterways, and
Reuter, Eva-Maria; Cunnington, Ross; Mattingley, Jason B; Riek, Stephan; Carroll, Timothy J
2016-11-01
There are well-documented differences in the way that people typically perform identical motor tasks with their dominant and the nondominant arms. According to Yadav and Sainburg's (Neuroscience 196: 153-167, 2011) hybrid-control model, this is because the two arms rely to different degrees on impedance control versus predictive control processes. Here, we assessed whether differences in limb control mechanisms influence the rate of feedforward compensation to a novel dynamic environment. Seventy-five healthy, right-handed participants, divided into four subsamples depending on the arm (left, right) and direction of the force field (ipsilateral, contralateral), reached to central targets in velocity-dependent curl force fields. We assessed the rate at which participants developed predictive compensation for the force field using intermittent error-clamp trials and assessed both kinematic errors and initial aiming angles in the field trials. Participants who were exposed to fields that pushed the limb toward ipsilateral space reduced kinematic errors more slowly, built up less predictive field compensation, and relied more on strategic reaiming than those exposed to contralateral fields. However, there were no significant differences in predictive field compensation or kinematic errors between limbs, suggesting that participants using either the left or the right arm could adapt equally well to novel dynamics. It therefore appears that the distinct preferences in control mechanisms typically observed for the dominant and nondominant arms reflect a default mode that is based on habitual functional requirements rather than an absolute limit in capacity to access the controller specialized for the opposite limb. Copyright © 2016 the American Physiological Society.
Batcho, C S; Gagné, M; Bouyer, L J; Roy, J S; Mercier, C
2016-11-19
When subjects learn a novel motor task, several sources of feedback (proprioceptive, visual or auditory) contribute to the performance. Over the past few years, several studies have investigated the role of visual feedback in motor learning, yet evidence remains conflicting. The aim of this study was therefore to investigate the role of online visual feedback (VFb) on the acquisition and retention stages of motor learning associated with training in a reaching task. Thirty healthy subjects made ballistic reaching movements with their dominant arm toward two targets, on 2 consecutive days using a robotized exoskeleton (KINARM). They were randomly assigned to a group with (VFb) or without (NoVFb) VFb of index position during movement. On day 1, the task was performed before (baseline) and during the application of a velocity-dependent resistive force field (adaptation). To assess retention, participants repeated the task with the force field on day 2. Motor learning was characterized by: (1) the final endpoint error (movement accuracy) and (2) the initial angle (iANG) of deviation (motor planning). Even though both groups showed motor adaptation, the NoVFb-group exhibited slower learning and higher final endpoint error than the VFb-group. In some condition, subjects trained without visual feedback used more curved initial trajectories to anticipate for the perturbation. This observation suggests that learning to reach targets in a velocity-dependent resistive force field is possible even when feedback is limited. However, the absence of VFb leads to different strategies that were only apparent when reaching toward the most challenging target. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.
Pukrittayakamee, A.; Malshe, M.; Hagan, M.; Raff, L. M.; Narulkar, R.; Bukkapatnum, S.; Komanduri, R.
2009-04-01
An improved neural network (NN) approach is presented for the simultaneous development of accurate potential-energy hypersurfaces and corresponding force fields that can be utilized to conduct ab initio molecular dynamics and Monte Carlo studies on gas-phase chemical reactions. The method is termed as combined function derivative approximation (CFDA). The novelty of the CFDA method lies in the fact that although the NN has only a single output neuron that represents potential energy, the network is trained in such a way that the derivatives of the NN output match the gradient of the potential-energy hypersurface. Accurate force fields can therefore be computed simply by differentiating the network. Both the computed energies and the gradients are then accurately interpolated using the NN. This approach is superior to having the gradients appear in the output layer of the NN because it greatly simplifies the required architecture of the network. The CFDA permits weighting of function fitting relative to gradient fitting. In every test that we have run on six different systems, CFDA training (without a validation set) has produced smaller out-of-sample testing error than early stopping (with a validation set) or Bayesian regularization (without a validation set). This indicates that CFDA training does a better job of preventing overfitting than the standard methods currently in use. The training data can be obtained using an empirical potential surface or any ab initio method. The accuracy and interpolation power of the method have been tested for the reaction dynamics of H+HBr using an analytical potential. The results show that the present NN training technique produces more accurate fits to both the potential-energy surface as well as the corresponding force fields than the previous methods. The fitting and interpolation accuracy is so high (rms error=1.2 cm-1) that trajectories computed on the NN potential exhibit point-by-point agreement with corresponding
Czech Academy of Sciences Publication Activity Database
Smith, W.R.; Jirsák, Jan; Nezbeda, Ivo; Qi, W.
2017-01-01
Roč. 147, č. 3 (2017), č. článku 034508. ISSN 0021-9606 R&D Projects: GA ČR GA15-19542S Grant - others:NSERC(CA) STPGP479466-15 Institutional support: RVO:67985858 Keywords : thermodynamic derivative properties * linear contraint solver * monte-carlo simulation Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 2.965, year: 2016
Indian Academy of Sciences (India)
Unknown
Journal of Genetics, Vol. 83, No. 3, December 2004. 235. Page 2. J. Genet. classic. Journal of Genetics, Vol. 83, No. 3, December 2004. 236. Page 3. J. Genet. classic. Journal of Genetics, Vol. 83, No. 3, December 2004. 237. Page 4. J. Genet. classic. Journal of Genetics, Vol. 83, No. 3, December 2004. 238. Page 5 ...
Optimizing photophoresis and asymmetric force fields for grading of Brownian particles.
Neild, Adrian; Ng, Tuck Wah; Woods, Timothy
2009-12-10
We discuss a scheme that incorporates restricted spatial input location, orthogonal sort, and movement direction features, with particle sorting achieved by using an asymmetric potential cycled on and off, while movement is accomplished by photophoresis. Careful investigation has uncovered the odds of sorting between certain pairs of particle sizes to be solely dependent on radii in each phase of the process. This means that the most effective overall sorting can be achieved by maximizing the number of phases. This optimized approach is demonstrated using numerical simulation to permit grading of a range of nanometer-scale particle sizes.
Hu, Xiao Liang; Ciaglia, Riccardo; Pietrucci, Fabio; Gallet, Grégoire A; Andreoni, Wanda
2014-06-19
We introduce a new ab initio derived reactive potential for the simulation of CdTe within density functional theory (DFT) and apply it to calculate both static and dynamical properties of a number of systems (bulk solid, defective structures, liquid, surfaces) at finite temperature. In particular, we also consider cases with low sulfur concentration (CdTe:S). The analysis of DFT and classical molecular dynamics (MD) simulations performed with the same protocol leads to stringent performance tests and to a detailed comparison of the two schemes. Metadynamics techniques are used to empower both Car-Parrinello and classical molecular dynamics for the simulation of activated processes. For the latter, we consider surface reconstruction and sulfur diffusion in the bulk. The same procedures are applied using previously proposed force fields for CdTe and CdTeS materials, thus allowing for a detailed comparison of the various schemes.
Directory of Open Access Journals (Sweden)
Raiker Witter
2015-01-01
Full Text Available Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT. Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.
DEFF Research Database (Denmark)
Lanzarotti, Esteban; Marcatili, Paolo; Nielsen, Morten
2018-01-01
Interactions of T cell receptors (TCR) to peptides in complex with MHC (p:MHC) are key features that mediate cellular immune responses. While MHC binding is required for a peptide to be presented to T cells, not all MHC binders are immunogenic. The interaction of a TCR to the p:MHC complex holds...... terms. Building a benchmark of TCR:p:MHC complexes where epitopes and non-epitopes are modelled using state-of-the-art molecular modelling tools, scoring p:MHC to a given TCR using force-fields, optimized in a cross-validation setup to evaluate TCR inter atomic interactions involved with each p:MHC, we...... and model the TCR:p:MHC complex structure. In summary, we conclude that it is possible to identify the TCR cognate target among different candidate peptides by using a force-field based model, and believe this works could lay the foundation for future work within prediction of TCR:p:MHC interactions....
Czech Academy of Sciences Publication Activity Database
Sellers, M.S.; Lísal, Martin; Brennan, J.K.
2016-01-01
Roč. 18, č. 11 (2016), s. 7841-7850 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA13-02938S Grant - others:ARL(US) W911NF-10-2-0039 Institutional support: RVO:67985858 Keywords : solid-liquid coexistence * atomistic simulation * dynamics simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.123, year: 2016
Lipid Configurations from Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek
2018-01-01
of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...
ReaxFF Reactive Force-Field Study of Molybdenum Disulfide (MoS2).
Ostadhossein, Alireza; Rahnamoun, Ali; Wang, Yuanxi; Zhao, Peng; Zhang, Sulin; Crespi, Vincent H; van Duin, Adri C T
2017-02-02
Two-dimensional layers of molybdenum disulfide, MoS 2 , have been recognized as promising materials for nanoelectronics due to their exceptional electronic and optical properties. Here we develop a new ReaxFF reactive potential that can accurately describe the thermodynamic and structural properties of MoS 2 sheets, guided by extensive density functional theory simulations. This potential is then applied to the formation energies of five different types of vacancies, various vacancy migration barriers, and the transition barrier between the semiconducting 2H and metallic 1T phases. The energetics of ripplocations, a recently observed defect in van der Waals layers, is examined, and the interplay between these defects and sulfur vacancies is studied. As strain engineering of MoS 2 sheets is an effective way to manipulate the sheets' electronic and optical properties, the new ReaxFF description can provide valuable insights into morphological changes that occur under various loading conditions and defect distributions, thus allowing one to tailor the electronic properties of these 2D crystals.
Classicality in quantum mechanics
International Nuclear Information System (INIS)
Dreyer, Olaf
2007-01-01
In this article we propose a solution to the measurement problem in quantum mechanics. We point out that the measurement problem can be traced to an a priori notion of classicality in the formulation of quantum mechanics. If this notion of classicality is dropped and instead classicality is defined in purely quantum mechanical terms the measurement problem can be avoided. We give such a definition of classicality. It identifies classicality as a property of large quantum system. We show how the probabilistic nature of quantum mechanics is a result of this notion of classicality. We also comment on what the implications of this view are for the search of a quantum theory of gravity
Classicality in quantum mechanics
Energy Technology Data Exchange (ETDEWEB)
Dreyer, Olaf [Theoretical Physics, Blackett Laboratory, Imperial College London, London, SW7 2AZ (United Kingdom)
2007-05-15
In this article we propose a solution to the measurement problem in quantum mechanics. We point out that the measurement problem can be traced to an a priori notion of classicality in the formulation of quantum mechanics. If this notion of classicality is dropped and instead classicality is defined in purely quantum mechanical terms the measurement problem can be avoided. We give such a definition of classicality. It identifies classicality as a property of large quantum system. We show how the probabilistic nature of quantum mechanics is a result of this notion of classicality. We also comment on what the implications of this view are for the search of a quantum theory of gravity.
Energy Technology Data Exchange (ETDEWEB)
Pincu, Madeleine [Univ. of California, Irvine, CA (United States); Gerber, Robert Benny [Univ. of California, Irvine, CA (United States). Dept. of Chemistry
2013-07-17
This work was undertaken with the main objective to investigate basic reactions that take place in relatively simple saccharides (mono-saccharides and cellobiose - the building block of cellulose) , in isolation and in cluster with few water molecules or with (gas-phase) clusters of few waters and ionic compounds (salt, isolated ions like H^{+} or OH^{-}). Within the context of this work, different potentials were investigated; among them, were the PM3 semi empirical potential, DFT/BLYP and a new hybrid potential constructed from MP2 for the harmonic part and from adjusted Hartree-Fock anharmonic interactions (VSCF-PT2). These potentials were evaluated by comparison with experimental data from published sources and from several collaborating groups. The findings show excellent agreement between experiments and predictions with the hybrid VSCF-PT2 potential and very good agreement with predictions obtained from dynamics with dispersion corrected DFT/BLYP potential. Investigation of hydration of cellobiose, was another topic of interest. Guided by a hydration motif demonstrated by our experimental collaborators (team of Prof J.P. Simons), we demonstrated large energetic and structural differences between the two species of cellobiose: cis and trans. The later, which is dominant in solid and liquid phases, is higher in energy in the gas-phase and compared to pure water, it does not disturb as much the network of H bonds. In contrast, the cis species exhibits asymmetric hydration in cluster with up to 25 waters, indicating that it has surfactant properties. Another highlight of this research effort was the successful first time spectrometric and spectroscopic study of a gas-phase protonated sugar derivative (alpha-D-Galactopyranoside) and its interpretation by Ab Initio molecular dynamics (AIMD) simulations. The findings demonstrate the formation of a motif in which a proton bridges between two Oxygen atoms (belonging to OH groups) at the sugar; The
Classical, Semi-classical and Quantum Noise
Poor, H; Scully, Marlan
2012-01-01
David Middleton was a towering figure of 20th Century engineering and science and one of the founders of statistical communication theory. During the second World War, the young David Middleton, working with Van Fleck, devised the notion of the matched filter, which is the most basic method used for detecting signals in noise. Over the intervening six decades, the contributions of Middleton have become classics. This collection of essays by leading scientists, engineers and colleagues of David are in his honor and reflect the wide influence that he has had on many fields. Also included is the introduction by Middleton to his forthcoming book, which gives a wonderful view of the field of communication, its history and his own views on the field that he developed over the past 60 years. Focusing on classical noise modeling and applications, Classical, Semi-Classical and Quantum Noise includes coverage of statistical communication theory, non-stationary noise, molecular footprints, noise suppression, Quantum e...
Georgieva, Miglena K.
2004-03-01
The structure of diazonium dicyanomethylide (diazodicyanomethane) +N 2-C(CN) 2-↔N 2C(CN) 2 has been studied on the basis of ab initio HF, MP2 and DFT BLYP force field calculations, as well as of literature IR spectra and X-ray diffraction structural data. The results have been compared with those obtained for a series of chemical relatives of the title compound, i.e. molecules, push-pull molecules, anions and zwitterions, containing α-dicyano or diazo fragments, and especially substituted ammonium dicyanomethylides and diazomethane +N 2-CH 2-↔N 2CH 2. It has been found on the basis of spectral, bond length, bond order and electric charge analyses that the diazonium (or carbanionic, left) canonical form is much more important for the title zwitterion, than the corresponding one for diazomethane. So, the title compound can be named (and considered as) both diazonium dicyanomethylide and dicyanodiazomethane.
Classical spins in superconductors
Energy Technology Data Exchange (ETDEWEB)
Shiba, H [Tokyo Univ.; Maki, K
1968-08-01
It is shown that there exists a localized excited state in the energy gap in a superconductor with a classical spin. At finite concentration localized excited states around classical spins form an impurity band. The process of growth of the impurity band and its effects on observable quantities are investigated.
Valley, Lois
1989-01-01
The SPS product, Classic-Ada, is a software tool that supports object-oriented Ada programming with powerful inheritance and dynamic binding. Object Oriented Design (OOD) is an easy, natural development paradigm, but it is not supported by Ada. Following the DOD Ada mandate, SPS developed Classic-Ada to provide a tool which supports OOD and implements code in Ada. It consists of a design language, a code generator and a toolset. As a design language, Classic-Ada supports the object-oriented principles of information hiding, data abstraction, dynamic binding, and inheritance. It also supports natural reuse and incremental development through inheritance, code factoring, and Ada, Classic-Ada, dynamic binding and static binding in the same program. Only nine new constructs were added to Ada to provide object-oriented design capabilities. The Classic-Ada code generator translates user application code into fully compliant, ready-to-run, standard Ada. The Classic-Ada toolset is fully supported by SPS and consists of an object generator, a builder, a dictionary manager, and a reporter. Demonstrations of Classic-Ada and the Classic-Ada Browser were given at the workshop.
Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.
Lev, Bogdan; Roux, Benoît; Noskov, Sergei Yu
2013-09-10
Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to offer a viable option for assessing the chemistry of ion solvation. Although MD and free energy simulations of ion solvation with classical force fields have proven their usefulness, a number of challenges still remain. One of them is the difficulty of force field benchmarking and validation against structural and thermodynamic data obtained for a condensed phase. Hybrid quantum mechanical/molecular mechanical (QM/MM) models combined with sampling algorithms have the potential to provide an accurate solvation model and to incorporate the effects from the surrounding, which is often missing in gas-phase ab initio computations. Herein, we report the results from QM/MM free energy simulations of Na(+)/K(+) and Cl(-)/Br(-) hydration where we simultaneously characterized the relative thermodynamics of ion solvation and changes in the solvation structure. The Flexible Inner Region Ensemble Separator (FIRES) method was used to impose a spatial separation between QM region and the outer sphere of solvent molecules treated with the CHARMM27 force field. FEP calculations based on QM/MM simulations utilizing the CHARMM/deMon2k interface were performed with different basis set combinations for K(+)/Na(+) and Cl(-)/Br(-) perturbations to establish the dependence of the computed free energies on the basis set level. The dependence of the computed relative free energies on the size of the QM and MM regions is discussed. The current methodology offers an accurate description of structural and thermodynamic aspects of the hydration of alkali and halide ions in neat solvents and can be used to obtain thermodynamic data on ion solvation in condensed phase along with underlying
Fermions from classical statistics
International Nuclear Information System (INIS)
Wetterich, C.
2010-01-01
We describe fermions in terms of a classical statistical ensemble. The states τ of this ensemble are characterized by a sequence of values one or zero or a corresponding set of two-level observables. Every classical probability distribution can be associated to a quantum state for fermions. If the time evolution of the classical probabilities p τ amounts to a rotation of the wave function q τ (t)=±√(p τ (t)), we infer the unitary time evolution of a quantum system of fermions according to a Schroedinger equation. We establish how such classical statistical ensembles can be mapped to Grassmann functional integrals. Quantum field theories for fermions arise for a suitable time evolution of classical probabilities for generalized Ising models.
From classical to quantum chaos
International Nuclear Information System (INIS)
Zaslavsky, G.M.
1991-01-01
The analysis is done for the quantum properties of systems that possess dynamical chaos in classical limit. Two main topics are considered: (i) the problem of quantum macroscopical description of the system and the Ehrenfest-Einstein problem of the validity of the classical approximation; and (ii) the problem of levels spacing distribution for the nonintegrable case. For the first topic the method of projecting on the coherent states base is considered and the ln 1/(h/2π) time for the quasiclassical approximation breaking is described. For the second topic the discussion of GOE and non-GOE distributions is done and estimations and simulations for the non-GOE case are reviewed. (author). 44 refs, 2 figs
Noel, Martin; Fortin, Karine; Bouyer, Laurent J
2009-06-03
Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; approximately 10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. When initially exposed to a mid-stance force field (FF 20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF 20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over approximately 50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF 50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF 50% catch strides were not simply due to a large ankle impedance. Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during
Directory of Open Access Journals (Sweden)
Bouyer Laurent J
2009-06-01
Full Text Available Abstract Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min, during (5 min and after (5 min exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion. To evaluate modifications in feedforward control, strides with no force field ('catch strides' were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%, subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99. Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%, plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive
Noel, Martin; Fortin, Karine; Bouyer, Laurent J
2009-01-01
Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle
Directory of Open Access Journals (Sweden)
S. Ghosh
Full Text Available Many Large Eddy Simulation (LES models use the classic Kessler parameterisation either as it is or in a modified form to model the process of cloud water autoconversion into precipitation. The Kessler scheme, being linear, is particularly useful and is computationally straightforward to implement. However, a major limitation with this scheme lies in its inability to predict different autoconversion rates for maritime and continental clouds. In contrast, the Berry formulation overcomes this difficulty, although it is cubic. Due to their different forms, it is difficult to match the two solutions to each other. In this paper we single out the processes of cloud conversion and accretion operating in a deep model cloud and neglect the advection terms for simplicity. This facilitates exact analytical integration and we are able to derive new expressions for the time of onset of precipitation using both the Kessler and Berry formulations. We then discuss the conditions when the two schemes are equivalent. Finally, we also critically examine the process of droplet evaporation within the framework of the classic Kessler scheme. We improve the existing parameterisation with an accurate estimation of the diffusional mass transport of water vapour. We then demonstrate the overall robustness of our calculations by comparing our results with the experimental observations of Beard and Pruppacher, and find excellent agreement.
Key words. Atmospheric composition and structure · Cloud physics and chemistry · Pollution · Meteorology and atmospheric dynamics · Precipitation
Directory of Open Access Journals (Sweden)
S. Ghosh
1998-05-01
Full Text Available Many Large Eddy Simulation (LES models use the classic Kessler parameterisation either as it is or in a modified form to model the process of cloud water autoconversion into precipitation. The Kessler scheme, being linear, is particularly useful and is computationally straightforward to implement. However, a major limitation with this scheme lies in its inability to predict different autoconversion rates for maritime and continental clouds. In contrast, the Berry formulation overcomes this difficulty, although it is cubic. Due to their different forms, it is difficult to match the two solutions to each other. In this paper we single out the processes of cloud conversion and accretion operating in a deep model cloud and neglect the advection terms for simplicity. This facilitates exact analytical integration and we are able to derive new expressions for the time of onset of precipitation using both the Kessler and Berry formulations. We then discuss the conditions when the two schemes are equivalent. Finally, we also critically examine the process of droplet evaporation within the framework of the classic Kessler scheme. We improve the existing parameterisation with an accurate estimation of the diffusional mass transport of water vapour. We then demonstrate the overall robustness of our calculations by comparing our results with the experimental observations of Beard and Pruppacher, and find excellent agreement.Key words. Atmospheric composition and structure · Cloud physics and chemistry · Pollution · Meteorology and atmospheric dynamics · Precipitation
2007-01-01
M51, whose name comes from being the 51st entry in Charles Messier's catalog, is considered to be one of the classic examples of a spiral galaxy. At a distance of about 30 million light-years from Earth, it is also one of the brightest spirals in the night sky. A composite image of M51, also known as the Whirlpool Galaxy, shows the majesty of its structure in a dramatic new way through several of NASA's orbiting observatories. X-ray data from NASA's Chandra X-ray Observatory reveals point-like sources (purple) that are black holes and neutron stars in binary star systems. Chandra also detects a diffuse glow of hot gas that permeates the space between the stars. Optical data from the Hubble Space Telescope (green) and infrared emission from the Spitzer Space Telescope (red) both highlight long lanes in the spiral arms that consist of stars and gas laced with dust. A view of M51 with the Galaxy Evolution Explorer telescope shows hot, young stars that produce lots of ultraviolet energy (blue). The textbook spiral structure is thought be the result of an interaction M51 is experiencing with its close galactic neighbor, NGC 5195, which is seen just above. Some simulations suggest M51's sharp spiral shape was partially caused when NGC 5195 passed through its main disk about 500 million years ago. This gravitational tug of war may also have triggered an increased level of star formation in M51. The companion galaxy's pull would be inducing extra starbirth by compressing gas, jump-starting the process by which stars form.
Driven topological systems in the classical limit
Duncan, Callum W.; Öhberg, Patrik; Valiente, Manuel
2017-03-01
Periodically driven quantum systems can exhibit topologically nontrivial behavior, even when their quasienergy bands have zero Chern numbers. Much work has been conducted on noninteracting quantum-mechanical models where this kind of behavior is present. However, the inclusion of interactions in out-of-equilibrium quantum systems can prove to be quite challenging. On the other hand, the classical counterpart of hard-core interactions can be simulated efficiently via constrained random walks. The noninteracting model, proposed by Rudner et al. [Phys. Rev. X 3, 031005 (2013), 10.1103/PhysRevX.3.031005], has a special point for which the system is equivalent to a classical random walk. We consider the classical counterpart of this model, which is exact at a special point even when hard-core interactions are present, and show how these quantitatively affect the edge currents in a strip geometry. We find that the interacting classical system is well described by a mean-field theory. Using this we simulate the dynamics of the classical system, which show that the interactions play the role of Markovian, or time-dependent disorder. By comparing the evolution of classical and quantum edge currents in small lattices, we find regimes where the classical limit considered gives good insight into the quantum problem.
Supersymmetric classical mechanics
International Nuclear Information System (INIS)
Biswas, S.N.; Soni, S.K.
1986-01-01
The purpose of the paper is to construct a supersymmetric Lagrangian within the framework of classical mechanics which would be regarded as a candidate for passage to supersymmetric quantum mechanics. 5 refs. (author)
Mathematical physics classical mechanics
Knauf, Andreas
2018-01-01
As a limit theory of quantum mechanics, classical dynamics comprises a large variety of phenomena, from computable (integrable) to chaotic (mixing) behavior. This book presents the KAM (Kolmogorov-Arnold-Moser) theory and asymptotic completeness in classical scattering. Including a wealth of fascinating examples in physics, it offers not only an excellent selection of basic topics, but also an introduction to a number of current areas of research in the field of classical mechanics. Thanks to the didactic structure and concise appendices, the presentation is self-contained and requires only knowledge of the basic courses in mathematics. The book addresses the needs of graduate and senior undergraduate students in mathematics and physics, and of researchers interested in approaching classical mechanics from a modern point of view.
Morgan, W James; Matthews, Devin A; Ringholm, Magnus; Agarwal, Jay; Gong, Justin Z; Ruud, Kenneth; Allen, Wesley D; Stanton, John F; Schaefer, Henry F
2018-03-13
Geometric energy derivatives which rely on core-corrected focal-point energies extrapolated to the complete basis set (CBS) limit of coupled cluster theory with iterative and noniterative quadruple excitations, CCSDTQ and CCSDT(Q), are used as elements of molecular gradients and, in the case of CCSDT(Q), expansion coefficients of an anharmonic force field. These gradients are used to determine the CCSDTQ/CBS and CCSDT(Q)/CBS equilibrium structure of the S 0 ground state of H 2 CO where excellent agreement is observed with previous work and experimentally derived results. A fourth-order expansion about this CCSDT(Q)/CBS reference geometry using the same level of theory produces an exceptional level of agreement to spectroscopically observed vibrational band origins with a MAE of 0.57 cm -1 . Second-order vibrational perturbation theory (VPT2) and variational discrete variable representation (DVR) results are contrasted and discussed. Vibration-rotation, anharmonicity, and centrifugal distortion constants from the VPT2 analysis are reported and compared to previous work. Additionally, an initial application of a sum-over-states fourth-order vibrational perturbation theory (VPT4) formalism is employed herein, utilizing quintic and sextic derivatives obtained with a recursive algorithmic approach for response theory.
DEFF Research Database (Denmark)
Christensen, Steen; Peters, Günther H.J.; Hansen, Flemming Yssing
2007-01-01
on isobaric–isothermal molecular dynamics (NPT-MD) simulations, using force field parameters published in the literature and fitted CHARMM force field parameters. Systems studied previously [S. Christensen, G.H. Peters, F.Y. Hansen, J.P. O’Connell, J. Abildskov, Molecular Simulation 33 (2007) 449...
Directory of Open Access Journals (Sweden)
Boyer François
2010-03-01
Full Text Available Abstract Background Patients-Reported Outcomes (PRO are increasingly used in clinical and epidemiological research. Two main types of analytical strategies can be found for these data: classical test theory (CTT based on the observed scores and models coming from Item Response Theory (IRT. However, whether IRT or CTT would be the most appropriate method to analyse PRO data remains unknown. The statistical properties of CTT and IRT, regarding power and corresponding effect sizes, were compared. Methods Two-group cross-sectional studies were simulated for the comparison of PRO data using IRT or CTT-based analysis. For IRT, different scenarios were investigated according to whether items or person parameters were assumed to be known, to a certain extent for item parameters, from good to poor precision, or unknown and therefore had to be estimated. The powers obtained with IRT or CTT were compared and parameters having the strongest impact on them were identified. Results When person parameters were assumed to be unknown and items parameters to be either known or not, the power achieved using IRT or CTT were similar and always lower than the expected power using the well-known sample size formula for normally distributed endpoints. The number of items had a substantial impact on power for both methods. Conclusion Without any missing data, IRT and CTT seem to provide comparable power. The classical sample size formula for CTT seems to be adequate under some conditions but is not appropriate for IRT. In IRT, it seems important to take account of the number of items to obtain an accurate formula.
Leib, Raz; Karniel, Amir; Nisky, Ilana
2015-05-01
During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. Copyright © 2015 the American Physiological Society.
Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3
International Nuclear Information System (INIS)
Schie, Marcel; Marchewka, Astrid; Waser, Rainer; Müller, Thomas; De Souza, Roger A
2012-01-01
A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO 3 ). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO 3 was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.
Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3.
Schie, Marcel; Marchewka, Astrid; Müller, Thomas; De Souza, Roger A; Waser, Rainer
2012-12-05
A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO(3)). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO(3) was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.
DEFF Research Database (Denmark)
Brincker, Benedikte
The last book Anthony D. Smith wrote before he died, and which will be published in Spring 2017, has the title Nation and Classical Music. Smith had for a long time been intrigued by the intimate relationship between the nation and classical music. At the most manifest level it involves...... them into their compositions thus challenging the romantic musical style searching for an authentic national musical expression. Against the backdrop of the extensive research carried out by Anthony Smith into the relationship between the nation and classical music, the present paper seeks to add...... cultural centers. In doing this, the paper seeks to unfold how composers channeled musical inspiration embedded in cultural environments that cut across national boundaries into national musical traditions thus catering to specific national audiences. The paper is written as a tribute to a great mentor...
Twisted classical Poincare algebras
International Nuclear Information System (INIS)
Lukierski, J.; Ruegg, H.; Tolstoy, V.N.; Nowicki, A.
1993-11-01
We consider the twisting of Hopf structure for classical enveloping algebra U(g), where g is the inhomogeneous rotations algebra, with explicite formulae given for D=4 Poincare algebra (g=P 4 ). The comultiplications of twisted U F (P 4 ) are obtained by conjugating primitive classical coproducts by F element of U(c)xU(c), where c denotes any Abelian subalgebra of P 4 , and the universal R-matrices for U F (P 4 ) are triangular. As an example we show that the quantum deformation of Poincare algebra recently proposed by Chaichian and Demiczev is a twisted classical Poincare algebra. The interpretation of twisted Poincare algebra as describing relativistic symmetries with clustered 2-particle states is proposed. (orig.)
Classical mechanics with Maxima
Timberlake, Todd Keene
2016-01-01
This book guides undergraduate students in the use of Maxima—a computer algebra system—in solving problems in classical mechanics. It functions well as a supplement to a typical classical mechanics textbook. When it comes to problems that are too difficult to solve by hand, computer algebra systems that can perform symbolic mathematical manipulations are a valuable tool. Maxima is particularly attractive in that it is open-source, multiple-platform software that students can download and install free of charge. Lessons learned and capabilities developed using Maxima are easily transferred to other, proprietary software.
Learning Classical Music Club
2010-01-01
There is a new CERN Club called “Learning Classical Music at CERN”. We are aiming to give classical music lessons for different instruments (see link) for students from 5 to 100 years old. We are now ready to start our activities in the CERN barracks. We are now in the enrollment phase and hope to start lessons very soon ! Club info can be found in the list of CERN Club: http://user.web.cern.ch/user/Communication/SocialLifeActivities/Clubs/Clubs.html Salvatore Buontempo Club President
International Nuclear Information System (INIS)
Starrfield, S.G.
1988-01-01
The classical nova outburst occurs on the white dwarf component in a close binary system. Nova systems are members of the general class of cataclysmic variables and other members of the class are the Dwarf Novae, AM Her variables, Intermediate Polars, Recurrent Novae, and some of the Symbiotic variables. Although multiwavelength observations have already provided important information about all of these systems, in this review I will concentrate on the outbursts of the classical and recurrent novae and refer to other members of the class only when necessary. 140 refs., 1 tab
Elementary classical hydrodynamics
Chirgwin, B H; Langford, W J; Maxwell, E A; Plumpton, C
1967-01-01
Elementary Classical Hydrodynamics deals with the fundamental principles of elementary classical hydrodynamics, with emphasis on the mechanics of inviscid fluids. Topics covered by this book include direct use of the equations of hydrodynamics, potential flows, two-dimensional fluid motion, waves in liquids, and compressible flows. Some general theorems such as Bernoulli's equation are also considered. This book is comprised of six chapters and begins by introducing the reader to the fundamental principles of fluid hydrodynamics, with emphasis on ways of studying the motion of a fluid. Basic c
Classic Problems of Probability
Gorroochurn, Prakash
2012-01-01
"A great book, one that I will certainly add to my personal library."—Paul J. Nahin, Professor Emeritus of Electrical Engineering, University of New Hampshire Classic Problems of Probability presents a lively account of the most intriguing aspects of statistics. The book features a large collection of more than thirty classic probability problems which have been carefully selected for their interesting history, the way they have shaped the field, and their counterintuitive nature. From Cardano's 1564 Games of Chance to Jacob Bernoulli's 1713 Golden Theorem to Parrondo's 1996 Perplexin
Fortenberry, Ryan
The Spitzer Space Telescope observation of spectra most likely attributable to diverse and abundant populations of polycyclic aromatic hydrocarbons (PAHs) in space has led to tremendous interest in these molecules as tracers of the physical conditions in different astrophysical regions. A major challenge in using PAHs as molecular tracers is the complexity of the spectral features in the 3-20 μm region. The large number and vibrational similarity of the putative PAHs responsible for these spectra necessitate determination for the most accurate basis spectra possible for comparison. It is essential that these spectra be established in order for the regions explored with the newest generation of observatories such as SOFIA and JWST to be understood. Current strategies to develop these spectra for individual PAHs involve either matrixisolation IR measurements or quantum chemical calculations of harmonic vibrational frequencies. These strategies have been employed to develop the successful PAH IR spectral database as a repository of basis functions used to fit astronomically observed spectra, but they are limited in important ways. Both techniques provide an adequate description of the molecules in their electronic, vibrational, and rotational ground state, but these conditions do not represent energetically hot regions for PAHs near strong radiation fields of stars and are not direct representations of the gas phase. Some non-negligible matrix effects are known in condensed-phase studies, and the inclusion of anharmonicity in quantum chemical calculations is essential to generate physically-relevant results especially for hot bands. While scaling factors in either case can be useful, they are agnostic to the system studied and are not robustly predictive. One strategy that has emerged to calculate the molecular vibrational structure uses vibrational perturbation theory along with a quartic force field (QFF) to account for higher-order derivatives of the potential
Can classical noise enhance quantum transmission?
International Nuclear Information System (INIS)
Wilde, Mark M
2009-01-01
A modified quantum teleportation protocol broadens the scope of the classical forbidden-interval theorems for stochastic resonance. The fidelity measures performance of quantum communication. The sender encodes the two classical bits for quantum teleportation as weak bipolar subthreshold signals and sends them over a noisy classical channel. Two forbidden-interval theorems provide a necessary and sufficient condition for the occurrence of the nonmonotone stochastic resonance effect in the fidelity of quantum teleportation. The condition is that the noise mean must fall outside a forbidden interval related to the detection threshold and signal value. An optimal amount of classical noise benefits quantum communication when the sender transmits weak signals, the receiver detects with a high threshold and the noise mean lies outside the forbidden interval. Theorems and simulations demonstrate that both finite-variance and infinite-variance noise benefit the fidelity of quantum teleportation.
Effect of tonic pain on motor acquisition and retention while learning to reach in a force field.
Lamothe, Mélanie; Roy, Jean-Sébastien; Bouffard, Jason; Gagné, Martin; Bouyer, Laurent J; Mercier, Catherine
2014-01-01
Most patients receiving intensive rehabilitation to improve their upper limb function experience pain. Despite this, the impact of pain on the ability to learn a specific motor task is still unknown. The aim of this study was to determine whether the presence of experimental tonic pain interferes with the acquisition and retention stages of motor learning associated with training in a reaching task. Twenty-nine healthy subjects were randomized to either a Control or Pain Group (receiving topical capsaicin cream on the upper arm during training on Day 1). On two consecutive days, subjects made ballistic movements towards two targets (NEAR/FAR) using a robotized exoskeleton. On Day 1, the task was performed without (baseline) and with a force field (adaptation). The adaptation task was repeated on Day 2. Task performance was assessed using index distance from the target at the end of the reaching movement. Motor planning was assessed using initial angle of deviation of index trajectory from a straight line to the target. Results show that tonic pain did not affect baseline reaching. Both groups improved task performance across time (pControl group for the FAR target (p = 0.030) during both acquisition and retention. Moreover, a Group x Time interaction (p = 0.028) was observed on initial angle of deviation, suggesting that subjects with Pain made larger adjustments in the feedforward component of the movement over time. Interestingly, behaviour of the Pain group was very stable from the end of Day 1 (with pain) to the beginning of Day 2 (pain-free), indicating that the differences observed could not solely be explained by the impact of pain on immediate performance. This suggests that if people learn to move differently in the presence of pain, they might maintain this altered strategy over time.
Effect of tonic pain on motor acquisition and retention while learning to reach in a force field.
Directory of Open Access Journals (Sweden)
Mélanie Lamothe
Full Text Available Most patients receiving intensive rehabilitation to improve their upper limb function experience pain. Despite this, the impact of pain on the ability to learn a specific motor task is still unknown. The aim of this study was to determine whether the presence of experimental tonic pain interferes with the acquisition and retention stages of motor learning associated with training in a reaching task. Twenty-nine healthy subjects were randomized to either a Control or Pain Group (receiving topical capsaicin cream on the upper arm during training on Day 1. On two consecutive days, subjects made ballistic movements towards two targets (NEAR/FAR using a robotized exoskeleton. On Day 1, the task was performed without (baseline and with a force field (adaptation. The adaptation task was repeated on Day 2. Task performance was assessed using index distance from the target at the end of the reaching movement. Motor planning was assessed using initial angle of deviation of index trajectory from a straight line to the target. Results show that tonic pain did not affect baseline reaching. Both groups improved task performance across time (p<0.001, but the Pain group showed a larger final error (under-compensation than the Control group for the FAR target (p = 0.030 during both acquisition and retention. Moreover, a Group x Time interaction (p = 0.028 was observed on initial angle of deviation, suggesting that subjects with Pain made larger adjustments in the feedforward component of the movement over time. Interestingly, behaviour of the Pain group was very stable from the end of Day 1 (with pain to the beginning of Day 2 (pain-free, indicating that the differences observed could not solely be explained by the impact of pain on immediate performance. This suggests that if people learn to move differently in the presence of pain, they might maintain this altered strategy over time.
Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan
2017-02-14
In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.
George, Judith W.
2009-01-01
The article identifies some key findings in pedagogical research over recent decades, placing them within a framework of logical curriculum development and current practice in quality assurance and enhancement. Throughout, the ideas and comments are related to the practice of teaching classics in university. (Contains 1 figure and 3 notes.)
Classical electromagnetic radiation
Heald, Mark A
2012-01-01
Newly corrected, this highly acclaimed text is suitable for advanced physics courses. The author presents a very accessible macroscopic view of classical electromagnetics that emphasizes integrating electromagnetic theory with physical optics. The survey follows the historical development of physics, culminating in the use of four-vector relativity to fully integrate electricity with magnetism.
Classical solutions in supergravity
International Nuclear Information System (INIS)
Baaklini, N.S.; Ferrara, S.; Nieuwenhuizen Van, P.
1977-06-01
Classical solutions of supergravity are obtained by making finite global supersymmetry rotation on known solutions of the field equations of the bosonic sector. The Schwarzschild and the Reissner-Nordstoem solutions of general relativity are extended to various supergravity systems and the modification to the perihelion precession of planets is discussed
Huddleston, Gregory H.
1993-01-01
Describes one teacher's methods for introducing to secondary English students the concepts of Classicism and Romanticism in relation to pictures of gardens, architecture, music, and literary works. Outlines how the unit leads to a writing assignment based on collected responses over time. (HB)
Classical Mythology. Fourth Edition.
Morford, Mark P. O.; Lenardon, Robert J.
Designed for students with little or no background in classical literature, this book introduces the Greek and Roman myths of creation, myths of the gods, Greek sagas and local legends, and presents contemporary theories about the myths. Drawing on Homer, Hesiod, Pindar, Vergil, and others, the book provides many translations and paraphrases of…
Tighe, Mary Ann; Avinger, Charles
1994-01-01
Describes young adult novels that may prove to be classics of the genre. Discusses "The "Chocolate War" by Robert Cormier, "The Outsiders" by S. E. Hinton, "The Witch of Blackbird Pond" by Elizabeth George Speare, and "On Fortune's Wheel" by Cynthia Voight. (HB)
Why Study Classical Languages?
Lieberman, Samuel
This speech emphasizes the significance of living literatures and living cultures which owe a direct debt to the Romans and the Greeks from whom they can trace their origins. After commenting on typical rejoinders to the question "Why study classical languages?" and poking fun at those who advance jaded, esoteric responses, the author dispels the…
Ngada, Narcisse
2015-06-15
The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for particle accelerators. Starting with the definition and basic principles of simulation, two simulation types, as well as their leading tools, are presented: analog and numerical simulations. Some practical applications of each simulation type are also considered. The final conclusion then summarizes the main important items to keep in mind before opting for a simulation tool or before performing a simulation.
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:
Franklin, Joel
2017-01-01
Classical field theory, which concerns the generation and interaction of fields, is a logical precursor to quantum field theory, and can be used to describe phenomena such as gravity and electromagnetism. Written for advanced undergraduates, and appropriate for graduate level classes, this book provides a comprehensive introduction to field theories, with a focus on their relativistic structural elements. Such structural notions enable a deeper understanding of Maxwell's equations, which lie at the heart of electromagnetism, and can also be applied to modern variants such as Chern–Simons and Born–Infeld. The structure of field theories and their physical predictions are illustrated with compelling examples, making this book perfect as a text in a dedicated field theory course, for self-study, or as a reference for those interested in classical field theory, advanced electromagnetism, or general relativity. Demonstrating a modern approach to model building, this text is also ideal for students of theoretic...
Directory of Open Access Journals (Sweden)
Adriana Coutinho de Azevedo Guimarães
2008-06-01
Full Text Available This study aimed to elucidate what injuries are most likely to occur due to classical ballet practice. The research used national and international bibliography. The bibliography analysis indicated that technical and esthetical demands lead to a practice of non-anatomical movements, causing the ballet dancer to suffer from a number of associated lesions. Most of the injuries are caused by technical mistakes and wrong training. Troubles in children are usually due to trying to force external rotation at hip level and to undue use of point ballet slippers. The commonest lesions are in feet and ankles, followed by knees and hips. The rarest ones are in the upper limbs. These injuries are caused by exercise excess, by repetitions always in the same side and by wrong and early use of point slippers. The study reached the conclusion that incorrect application of classical ballet technique predisposes the dancers to characteristic injuries.
Classical Diophantine equations
1993-01-01
The author had initiated a revision and translation of "Classical Diophantine Equations" prior to his death. Given the rapid advances in transcendence theory and diophantine approximation over recent years, one might fear that the present work, originally published in Russian in 1982, is mostly superseded. That is not so. A certain amount of updating had been prepared by the author himself before his untimely death. Some further revision was prepared by close colleagues. The first seven chapters provide a detailed, virtually exhaustive, discussion of the theory of lower bounds for linear forms in the logarithms of algebraic numbers and its applications to obtaining upper bounds for solutions to the eponymous classical diophantine equations. The detail may seem stark--- the author fears that the reader may react much as does the tourist on first seeing the centre Pompidou; notwithstanding that, Sprind zuk maintainsa pleasant and chatty approach, full of wise and interesting remarks. His emphases well warrant, ...
Classical and statistical thermodynamics
Rizk, Hanna A
2016-01-01
This is a text book of thermodynamics for the student who seeks thorough training in science or engineering. Systematic and thorough treatment of the fundamental principles rather than presenting the large mass of facts has been stressed. The book includes some of the historical and humanistic background of thermodynamics, but without affecting the continuity of the analytical treatment. For a clearer and more profound understanding of thermodynamics this book is highly recommended. In this respect, the author believes that a sound grounding in classical thermodynamics is an essential prerequisite for the understanding of statistical thermodynamics. Such a book comprising the two wide branches of thermodynamics is in fact unprecedented. Being a written work dealing systematically with the two main branches of thermodynamics, namely classical thermodynamics and statistical thermodynamics, together with some important indexes under only one cover, this treatise is so eminently useful.
Invitation to classical analysis
Duren, Peter
2012-01-01
This book gives a rigorous treatment of selected topics in classical analysis, with many applications and examples. The exposition is at the undergraduate level, building on basic principles of advanced calculus without appeal to more sophisticated techniques of complex analysis and Lebesgue integration. Among the topics covered are Fourier series and integrals, approximation theory, Stirling's formula, the gamma function, Bernoulli numbers and polynomials, the Riemann zeta function, Tauberian theorems, elliptic integrals, ramifications of the Cantor set, and a theoretical discussion of differ
Strong, John
1958-01-01
An intermediate course in optics, this volume explores both experimental and theoretical concepts, offering practical knowledge of geometrical optics that will enhance students' comprehension of any relevant applied science. Its exposition of the concepts of classical optics is presented with a minimum of mathematical detail but presumes some knowledge of calculus, vectors, and complex numbers.Subjects include light as wave motion; superposition of wave motions; electromagnetic waves; interaction of light and matter; velocities and scattering of light; polarized light and dielectric boundarie
Generalized classical mechanics
International Nuclear Information System (INIS)
De Leon, M.; Rodrigues, P.R.
1985-01-01
The geometrical study of Classical Mechanics shows that the Hamiltonian (respectively, Lagrangian) formalism may be characterized by intrinsical structures canonically defined on the cotangent (respectively, tangent) bundle of a differentiable manifold. A generalized formalism for higher order Lagrangians is developed. Then the Hamiltonian form of the theory is developed. Finally, the Poisson brackets are defined and the conditions under which a mapping is a canonical transformation are studied. The Hamilton-Jacobi equation for this type of mechanics is established. (Auth.)
Classical Weyl transverse gravity
Energy Technology Data Exchange (ETDEWEB)
Oda, Ichiro [University of the Ryukyus, Department of Physics, Faculty of Science, Nishihara, Okinawa (Japan)
2017-05-15
We study various classical aspects of the Weyl transverse (WTDiff) gravity in a general space-time dimension. First of all, we clarify a classical equivalence among three kinds of gravitational theories, those are, the conformally invariant scalar tensor gravity, Einstein's general relativity and the WTDiff gravity via the gauge-fixing procedure. Secondly, we show that in the WTDiff gravity the cosmological constant is a mere integration constant as in unimodular gravity, but it does not receive any radiative corrections unlike the unimodular gravity. A key point in this proof is to construct a covariantly conserved energy-momentum tensor, which is achieved on the basis of this equivalence relation. Thirdly, we demonstrate that the Noether current for the Weyl transformation is identically vanishing, thereby implying that the Weyl symmetry existing in both the conformally invariant scalar tensor gravity and the WTDiff gravity is a ''fake'' symmetry. We find it possible to extend this proof to all matter fields, i.e. the Weyl-invariant scalar, vector and spinor fields. Fourthly, it is explicitly shown that in the WTDiff gravity the Schwarzschild black hole metric and a charged black hole one are classical solutions to the equations of motion only when they are expressed in the Cartesian coordinate system. Finally, we consider the Friedmann-Lemaitre-Robertson-Walker (FLRW) cosmology and provide some exact solutions. (orig.)
Classical algebraic chromodynamics
International Nuclear Information System (INIS)
Adler, S.L.
1978-01-01
I develop an extension of the usual equations of SU(n) chromodynamics which permits the consistent introduction of classical, noncommuting quark source charges. The extension involves adding a singlet gluon, giving a U(n) -based theory with outer product P/sup a/(u,v) = (1/2)(d/sup a/bc + if/sup a/bc)(u/sup b/v/sup c/ - v/sup b/u/sup c/) which obeys the Jacobi identity, inner product S (u,v) = (1/2)(u/sup a/v/sup a/ + v/sup a/u/sup a/), and with the n 2 gluon fields elevated to algebraic fields over the quark color charge C* algebra. I show that provided the color charge algebra satisfies the condition S (P (u,v),w) = S (u,P (v,w)) for all elements u,v,w of the algebra, all the standard derivations of Lagrangian chromodynamics continue to hold in the algebraic chromodynamics case. I analyze in detail the color charge algebra in the two-particle (qq, qq-bar, q-barq-bar) case and show that the above consistency condition is satisfied for the following unique (and, interestingly, asymmetric) choice of quark and antiquark charges: Q/sup a//sub q/ = xi/sup a/, Q/sup a//sub q/ = xi-bar/sup a/ + delta/sup a/0(n/2)/sup 3/2/1, with xi/sup a/xi/sup b/ = (1/2)(d/sup a/bc + if/sup a/bc) xi/sup c/, xi-bar/sup a/xi-bar/sup b/ = -(1/2)(d/sup a/bc - if/sup a/bc) xi-bar/sup c/. The algebraic structure of the two-particle U(n) force problem, when expressed on an appropriately diagonalized basis, leads for all n to a classical dynamics problem involving an ordinary SU(2) Yang-Mills field with uniquely specified classical source charges which are nonparallel in the color-singlet state. An explicit calculation shows that local algebraic U(n) gauge transformations lead only to a rigid global rotation of axes in the overlying classical SU(2) problem, which implies that the relative orientations of the classical source charges have physical significance
Czech Academy of Sciences Publication Activity Database
Moučka, F.; Nezbeda, Ivo; Smith, W.R.
2016-01-01
Roč. 11, č. 4 (2016), s. 1756-1764 ISSN 1549-9618 Grant - others:NSERC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : monte-carlo simulations * molecular-dynamic simulations * free-energy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.245, year: 2016
Directory of Open Access Journals (Sweden)
Laurent Chusseau
2013-02-01
Full Text Available We show that the thermodynamics of ideal gases may be derived solely from the Democritean concept of corpuscles moving in vacuum plus a principle of simplicity, namely that these laws are independent of the laws of motion, aside from the law of energy conservation. Only a single corpuscle in contact with a heat bath submitted to a z and t-invariant force is considered. Most of the end results are known but the method appears to be novel. The mathematics being elementary, the present paper should facilitate the understanding of the ideal gas law and of classical thermodynamics even though not-usually-taught concepts are being introduced.
Institute of Scientific and Technical Information of China (English)
2002-01-01
FIVE years ago, an ancient Chinese air was beamed to outer space as a PR exercise. To humankind, music is a universal language, so the tune seemed an ideal medium for communication with extraterrestrial intelligence. So far there has been no response, but it is believed that the tune will play for a billion years, and eventually be heard and understood. The melody is called High Mountain and Flowing Stream, and it is played on the guqin, a seven-stringed classical musical instrument similar to the zither.
Jinzenji, Masao
2018-01-01
This book furnishes a brief introduction to classical mirror symmetry, a term that denotes the process of computing Gromov–Witten invariants of a Calabi–Yau threefold by using the Picard–Fuchs differential equation of period integrals of its mirror Calabi–Yau threefold. The book concentrates on the best-known example, the quintic hypersurface in 4-dimensional projective space, and its mirror manifold. First, there is a brief review of the process of discovery of mirror symmetry and the striking result proposed in the celebrated paper by Candelas and his collaborators. Next, some elementary results of complex manifolds and Chern classes needed for study of mirror symmetry are explained. Then the topological sigma models, the A-model and the B-model, are introduced. The classical mirror symmetry hypothesis is explained as the equivalence between the correlation function of the A-model of a quintic hyper-surface and that of the B-model of its mirror manifold. On the B-model side, the process of construct...
Friedmann-Bette, B
2008-08-01
For more than 40 years, the effects of classical altitude training on sea-level performance have been the subject of many scientific investigations in individual endurance sports. To our knowledge, no studies have been performed in team sports like football. Two well-controlled studies showed that living and training at an altitude of >or=1800-2700 m for 3-4 weeks is superior to equivalent training at sea level in well-trained athletes. Most of the controlled studies with elite athletes did not reveal such an effect. However, the results of some uncontrolled studies indicate that sea-level performance might be enhanced after altitude training also in elite athletes. Whether hypoxia provides an additional stimulus for muscular adaptation, when training is performed with equal intensity compared with sea-level training is not known. There is some evidence for an augmentation of total hemoglobin mass after classical altitude training with duration >or=3 weeks at an altitude >or=2000 m due to altitude acclimatization. Considerable individual variation is observed in the erythropoietic response to hypoxia and in the hypoxia-induced reduction of aerobic performance capacity during training at altitude, both of which are thought to contribute to inter-individual variation in the improvement of sea-level performance after altitude training.
International Nuclear Information System (INIS)
Barra, F.; Gaspard, P.
2001-01-01
We consider the classical evolution of a particle on a graph by using a time-continuous Frobenius-Perron operator that generalizes previous propositions. In this way, the relaxation rates as well as the chaotic properties can be defined for the time-continuous classical dynamics on graphs. These properties are given as the zeros of some periodic-orbit zeta functions. We consider in detail the case of infinite periodic graphs where the particle undergoes a diffusion process. The infinite spatial extension is taken into account by Fourier transforms that decompose the observables and probability densities into sectors corresponding to different values of the wave number. The hydrodynamic modes of diffusion are studied by an eigenvalue problem of a Frobenius-Perron operator corresponding to a given sector. The diffusion coefficient is obtained from the hydrodynamic modes of diffusion and has the Green-Kubo form. Moreover, we study finite but large open graphs that converge to the infinite periodic graph when their size goes to infinity. The lifetime of the particle on the open graph is shown to correspond to the lifetime of a system that undergoes a diffusion process before it escapes
Classical Trajectories and Quantum Spectra
Mielnik, Bogdan; Reyes, Marco A.
1996-01-01
A classical model of the Schrodinger's wave packet is considered. The problem of finding the energy levels corresponds to a classical manipulation game. It leads to an approximate but non-perturbative method of finding the eigenvalues, exploring the bifurcations of classical trajectories. The role of squeezing turns out decisive in the generation of the discrete spectra.
Directory of Open Access Journals (Sweden)
José Maria Pires
2012-01-01
Full Text Available A 1µs Molecular Dynamic simulation was performed with a realistic model system of Sodium Dodecyl Sulfate (SDS micelles in aqueous solution, comprising of 360 DS-, 360 Na+ and 90000 water particles. After 300 ns three different micellar shapes and sizes 41, 68 and 95 monomers, were observed. The process led to stabilization in the total number of SDS clusters and an increase in the micellar radius to 2.23 nm, in agreement with experimental results. An important conclusion, is be aware that simulations employed in one aggregate, should be considered as a constraint. Size and shape distribution must be analyzed.
Classical and quantum cosmology
Calcagni, Gianluca
2017-01-01
This comprehensive textbook is devoted to classical and quantum cosmology, with particular emphasis on modern approaches to quantum gravity and string theory and on their observational imprint. It covers major challenges in theoretical physics such as the big bang and the cosmological constant problem. An extensive review of standard cosmology, the cosmic microwave background, inflation and dark energy sets the scene for the phenomenological application of all the main quantum-gravity and string-theory models of cosmology. Born of the author's teaching experience and commitment to bridging the gap between cosmologists and theoreticians working beyond the established laws of particle physics and general relativity, this is a unique text where quantum-gravity approaches and string theory are treated on an equal footing. As well as introducing cosmology to undergraduate and graduate students with its pedagogical presentation and the help of 45 solved exercises, this book, which includes an ambitious bibliography...
International Nuclear Information System (INIS)
Sbisà, Fulvio
2015-01-01
The aim of these notes is to provide a self-contained review of why it is generically a problem when a solution of a theory possesses ghost fields among the perturbation modes. We define what a ghost field is and we show that its presence is associated with a classical instability whenever the ghost field interacts with standard fields. We then show that the instability is more severe at quantum level, and that perturbative ghosts can exist only in low energy effective theories. However, if we do not consider very ad hoc choices, compatibility with observational constraints implies that low energy effective ghosts can exist only at the price of giving up Lorentz invariance or locality above the cut-off, in which case the cut-off has to be much lower that the energy scales we currently probe in particle colliders. We also comment on the possible role of extra degrees of freedom which break Lorentz invariance spontaneously. (paper)
Classical mechanics with Mathematica
Romano, Antonio
2018-01-01
This textbook takes a broad yet thorough approach to mechanics, aimed at bridging the gap between classical analytic and modern differential geometric approaches to the subject. Developed by the authors from over 30 years of teaching experience, the presentation is designed to give students an overview of the many different models used through the history of the field—from Newton to Hamilton—while also painting a clear picture of the most modern developments. The text is organized into two parts. The first focuses on developing the mathematical framework of linear algebra and differential geometry necessary for the remainder of the book. Topics covered include tensor algebra, Euclidean and symplectic vector spaces, differential manifolds, and absolute differential calculus. The second part of the book applies these topics to kinematics, rigid body dynamics, Lagrangian and Hamiltonian dynamics, Hamilton–Jacobi theory, completely integrable systems, statistical mechanics of equilibrium, and impulsive dyna...
Mechanical Systems, Classical Models
Teodorescu, Petre P
2009-01-01
This third volume completes the Work Mechanical Systems, Classical Models. The first two volumes dealt with particle dynamics and with discrete and continuous mechanical systems. The present volume studies analytical mechanics. Topics like Lagrangian and Hamiltonian mechanics, the Hamilton-Jacobi method, and a study of systems with separate variables are thoroughly discussed. Also included are variational principles and canonical transformations, integral invariants and exterior differential calculus, and particular attention is given to non-holonomic mechanical systems. The author explains in detail all important aspects of the science of mechanics, regarded as a natural science, and shows how they are useful in understanding important natural phenomena and solving problems of interest in applied and engineering sciences. Professor Teodorescu has spent more than fifty years as a Professor of Mechanics at the University of Bucharest and this book relies on the extensive literature on the subject as well as th...
Quantum models of classical systems
International Nuclear Information System (INIS)
Hájíček, P
2015-01-01
Quantum statistical methods that are commonly used for the derivation of classical thermodynamic properties are extended to classical mechanical properties. The usual assumption that every real motion of a classical mechanical system is represented by a sharp trajectory is not testable and is replaced by a class of fuzzy models, the so-called maximum entropy (ME) packets. The fuzzier are the compared classical and quantum ME packets, the better seems to be the match between their dynamical trajectories. Classical and quantum models of a stiff rod will be constructed to illustrate the resulting unified quantum theory of thermodynamic and mechanical properties. (paper)
Directory of Open Access Journals (Sweden)
Maryann Wilson
2013-01-01
Full Text Available BACKGROUND: The impact of a scientific article is proportional to the citations it has received. In this study, we set out to identify the most cited works in epileptology in order to evaluate research trends in this field. METHODS: According to the Web of Science database, articles with more than 400 citations qualify as "citation classics". We conducted a literature search on the ISI Web of Science bibliometric database for scientific articles relevant to epilepsy. RESULTS: We retrieved 67 highly cited articles (400 or more citations, which were published in 31 journals: 17 clinical studies, 42 laboratory studies, 5 reviews and 3 classification articles. Clinical studies consisted of epidemiological analyses (n=3, studies on the clinical phenomenology of epilepsy (n=5 – including behavioral and prognostic aspects – and articles focusing on pharmacological (n=6 and non-pharmacological (n=3 treatment. The laboratory studies dealt with genetics (n=6, animal models (n=27, and neurobiology (n=9 – including both neurophysiology and neuropathology studies. The majority (61% of citation classics on epilepsy were published after 1986, possibly reflecting the expansion of research interest in laboratory studies driven by the development of new methodologies, specifically in the fields of genetics and animal models. Consequently, clinical studies were highly cited both before and after the mid 80s, whilst laboratory researches became widely cited after 1990. CONCLUSIONS: Our study indicates that the main drivers of scientific impact in the field of epileptology have increasingly become genetic and neurobiological studies, along with research on animal models of epilepsy. These articles are able to gain the highest numbers of citations in the time span of a few years and suggest potential directions for future research.
Toluene model for molecular dynamics simulations in the ranges 298
Fioroni, M.; Vogt, D.
2004-01-01
An all-atom model for toluene is presented in the framework of classical molecular dynamics (MD). The model has been parametrized under the GROMOS96 force field to reproduce the physicochemical properties of the neat liquid. Four new atom types have been introduced, distinguishing between carbons
Czech Academy of Sciences Publication Activity Database
Moučka, F.; Nezbeda, Ivo; Smith, W. R.
2013-01-01
Roč. 138, č. 15 (2013), s. 154102 ISSN 0021-9606 Grant - others:GA MŠMT(CZ) LH12019; GA ČR(CZ) GAP208/12/0105; NSERCC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : free-energy * computer -simulation * water Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.122, year: 2013
Czech Academy of Sciences Publication Activity Database
Zgarbová, M.; Jurečka, P.; Banáš, P.; Havrila, Marek; Šponer, Jiří; Otyepka, M.
2017-01-01
Roč. 121, č. 11 (2017), s. 2420-2433 ISSN 1520-6106 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * sugar-phosphate backbone * free-energy landscape * ribosomal-rna Subject RIV: BO - Biophysics OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016
Choi, Eunsong
Computer simulations are an integral part of research in modern condensed matter physics; they serve as a direct bridge between theory and experiment by systemactically applying a microscopic model to a collection of particles that effectively imitate a macroscopic system. In this thesis, we study two very differnt condensed systems, namely complex fluids and frustrated magnets, primarily by simulating classical dynamics of each system. In the first part of the thesis, we focus on ionic liquids (ILs) and polymers--the two complementary classes of materials that can be combined to provide various unique properties. The properties of polymers/ILs systems, such as conductivity, viscosity, and miscibility, can be fine tuned by choosing an appropriate combination of cations, anions, and polymers. However, designing a system that meets a specific need requires a concrete understanding of physics and chemistry that dictates a complex interplay between polymers and ionic liquids. In this regard, molecular dynamics (MD) simulation is an efficient tool that provides a molecular level picture of such complex systems. We study the behavior of Poly (ethylene oxide) (PEO) and the imidazolium based ionic liquids, using MD simulations and statistical mechanics. We also discuss our efforts to develop reliable and efficient classical force-fields for PEO and the ionic liquids. The second part is devoted to studies on geometrically frustrated magnets. In particular, a microscopic model, which gives rise to an incommensurate spiral magnetic ordering observed in a pyrochlore antiferromagnet is investigated. The validation of the model is made via a comparison of the spin-wave spectra with the neutron scattering data. Since the standard Holstein-Primakoff method is difficult to employ in such a complex ground state structure with a large unit cell, we carry out classical spin dynamics simulations to compute spin-wave spectra directly from the Fourier transform of spin trajectories. We
Construction of classical and non-classical coherent photon states
International Nuclear Information System (INIS)
Honegger, Reinhard; Rieckers, Alfred
2001-01-01
It is well known that the diagonal matrix elements of all-order coherent states for the quantized electromagnetic field have to constitute a Poisson distribution with respect to the photon number. The present work gives first the summary of a constructive scheme, developed previously, which determines in terms of an auxiliary Hilbert space all possible off-diagonal elements for the all-order coherent density operators in Fock space and which identifies all extremal coherent states. In terms of this formalism it is then demonstrated that each pure classical coherent state is a uniformly phase locked (quantum) coherent superposition of number states. In a mixed classical coherent state the exponential of the locked phase is shown to be replaced by a rather arbitrary unitary operator in the auxiliary Hilbert space. On the other hand classes for density operators--and for their normally ordered characteristic functions--of non-classical coherent states are obtained, especially by rather weak perturbations of classical coherent states. These illustrate various forms of breaking the classical uniform phase locking and exhibit rather peculiar properties, such as asymmetric fluctuations for the quadrature phase operators. Several criteria for non-classicality are put forward and applied to the elaborated non-classical coherent states, providing counterexamples against too simple arguments for classicality. It is concluded that classicality is only a stable concept for coherent states with macroscopic intensity
Crowder, Martin J
2001-01-01
If something can fail, it can often fail in one of several ways and sometimes in more than one way at a time. There is always some cause of failure, and almost always, more than one possible cause. In one sense, then, survival analysis is a lost cause. The methods of Competing Risks have often been neglected in the survival analysis literature. Written by a leading statistician, Classical Competing Risks thoroughly examines the probability framework and statistical analysis of data of Competing Risks. The author explores both the theory of the subject and the practicalities of fitting the models to data. In a coherent, self-contained, and sequential account, the treatment moves from the bare bones of the Competing Risks setup and the associated likelihood functions through survival analysis using hazard functions. It examines discrete failure times and the difficulties of identifiability, and concludes with an introduction to the counting-process approach and the associated martingale theory.With a dearth of ...
Grafakos, Loukas
2014-01-01
The main goal of this text is to present the theoretical foundation of the field of Fourier analysis on Euclidean spaces. It covers classical topics such as interpolation, Fourier series, the Fourier transform, maximal functions, singular integrals, and Littlewood–Paley theory. The primary readership is intended to be graduate students in mathematics with the prerequisite including satisfactory completion of courses in real and complex variables. The coverage of topics and exposition style are designed to leave no gaps in understanding and stimulate further study. This third edition includes new Sections 3.5, 4.4, 4.5 as well as a new chapter on “Weighted Inequalities,” which has been moved from GTM 250, 2nd Edition. Appendices I and B.9 are also new to this edition. Countless corrections and improvements have been made to the material from the second edition. Additions and improvements include: more examples and applications, new and more relevant hints for the existing exercises, new exercises, and...
Classical tokamak transport theory
International Nuclear Information System (INIS)
Nocentini, Aldo
1982-01-01
A qualitative treatment of the classical transport theory of a magnetically confined, toroidal, axisymmetric, two-species plasma is presented. The 'weakly collisional' ('banana' and 'plateau') and 'collision dominated' ('Pfirsch-Schlueter' and 'highly collisional') regimes, as well as the Ware effect are discussed. The method used to evaluate the diffusion coffieicnts of particles and heat in the weakly collisional regime is based on stochastic argument, that requires an analysis of the characteristic collision frequencies and lengths for particles moving in a tokamak-like magnetic field. The same method is used to evaluate the Ware effect. In the collision dominated regime on the other hand, the particle and heat fluxes across the magnetic field lines are dominated by macroscopic effects so that, although it is possible to present them as diffusion (in fact, the fluxes turn out to be proportional to the density and temperature gradients), a macroscopic treatment is more appropriate. Hence, fluid equations are used to inveatigate the collision dominated regime, to which particular attention is devoted, having been shown relatively recently that it is more complicated than the usual Pfirsch-Schlueter regime. The whole analysis presented here is qualitative, aiming to point out the relevant physical mechanisms involved in the various regimes more than to develop a rigorous mathematical derivation of the diffusion coefficients, for which appropriate references are given. (author)
Sullivan, Woodruff Turner
1982-01-01
Radio techniques were the nrst to lead astronomy away from the quiescent and limited Universe revealed by traditional observations at optical wave lengths. In the earliest days of radio astronomy, a handful of radio physicists and engineers made one startling discovery after another as they opened up the radio sky. With this collection of classic papers and the extensive intro ductory material, the reader can experience these exciting discoveries, as well as understand the developing techniques and follow the motivations which prompted the various lines of inquiry. For instance he or she will follow in detail the several attempts to detect radio waves from the sun at the turn of the century; the unravelling by Jansky of a "steady hiss type static"; the incredible story of Reber who built a 9 meter dish in his backyard in 1937 and then mapped the Milky Way; the vital discoveries by Hey and colleagues of radio bursts from the Sun and of a discrete source in the constellation of Cygnus; the development of re...
Ordering in classical Coulombic systems
International Nuclear Information System (INIS)
Schiffer, J. P.
1998-01-01
The author discusses the properties of classical Coulombic matter at low temperatures. It has been well known for some time [1,2] that infinite Coulombic matter will crystallize in body-centered cubic form when the quantity Λ (the dimensionless ratio of the average two-particle Coulomb energy to the kinetic energy per particle) is larger than approximately175. But the systems of such particles that have been produced in the laboratory in ion traps, or ion beams, are finite with surfaces defined by the boundary conditions that have to be satisfied. This results in ion clouds with sharply defined curved surfaces, and interior structures that show up as a set of concentric layers that are parallel to the outer surface. The ordering does not appear to be cubic, but the charges on each shell exhibit a ''hexatic'' pattern of equilateral triangles that is the characteristic of liquid crystals. The curvature of the surfaces prevents the structures on successive shells from interlocking in any simple fashion. This class of structures was first found in simulations [3] and later in experiments [4
Ellaby, Tom; Aarons, Jolyon; Varambhia, Aakash; Jones, Lewys; Nellist, Peter; Ozkaya, Dogan; Sarwar, Misbah; Thompsett, David; Skylaris, Chris-Kriton
2018-04-01
Platinum nanoparticles find significant use as catalysts in industrial applications such as fuel cells. Research into their design has focussed heavily on nanoparticle size and shape as they greatly influence activity. Using high throughput, high precision electron microscopy, the structures of commercially available Pt catalysts have been determined, and we have used classical and quantum atomistic simulations to examine and compare them with geometric cuboctahedral and truncated octahedral structures. A simulated annealing procedure was used both to explore the potential energy surface at different temperatures, and also to assess the effect on catalytic activity that annealing would have on nanoparticles with different geometries and sizes. The differences in response to annealing between the real and geometric nanoparticles are discussed in terms of thermal stability, coordination number and the proportion of optimal binding sites on the surface of the nanoparticles. We find that annealing both experimental and geometric nanoparticles results in structures that appear similar in shape and predicted activity, using oxygen adsorption as a measure. Annealing is predicted to increase the catalytic activity in all cases except the truncated octahedra, where it has the opposite effect. As our simulations have been performed with a classical force field, we also assess its suitability to describe the potential energy of such nanoparticles by comparing with large scale density functional theory calculations.
Quantum symmetries of classical spaces
Bhowmick, Jyotishman; Goswami, Debashish; Roy, Subrata Shyam
2009-01-01
We give a general scheme for constructing faithful actions of genuine (noncommutative as $C^*$ algebra) compact quantum groups on classical topological spaces. Using this, we show that: (i) a compact connected classical space can have a faithful action by a genuine compact quantum group, and (ii) there exists a spectral triple on a classical connected compact space for which the quantum group of orientation and volume preserving isometries (in the sense of \\cite{qorient}) is a genuine quantum...
Dynamics of unitarization by classicalization
International Nuclear Information System (INIS)
Dvali, Gia; Pirtskhalava, David
2011-01-01
We study dynamics of the classicalization phenomenon suggested in G. Dvali et al. , according to which a class of non-renormalizable theories self-unitarizes at very high-energies via creation of classical configurations (classicalons). We study this phenomenon in an explicit model of derivatively-self-coupled scalar that serves as a prototype for a Nambu-Goldstone-Stueckelberg field. We prepare the initial state in form of a collapsing wave-packet of a small occupation number but of very high energy, and observe that the classical configuration indeed develops. Our results confirm the previous estimates, showing that because of self-sourcing the wave-packet forms a classicalon configuration with radius that increases with center of mass energy. Thus, classicalization takes place before the waves get any chance of probing short-distances. The self-sourcing by energy is the crucial point, which makes classicalization phenomenon different from the ordinary dispersion of the wave-packets in other interacting theories. Thanks to this, unlike solitons or other non-perturbative objects, the production of classicalons is not only unsuppressed, but in fact dominates the high-energy scattering. In order to make the difference between classicalizing and non-classicalizing theories clear, we use a language in which the scattering cross section in a generic theory can be universally understood as a geometric cross section set by a classical radius down to which waves can propagate freely, before being scattered. We then show, that in non-classicalizing examples this radius shrinks with increasing energy and becomes microscopic, whereas in classicalizing theories expands and becomes macroscopic. We study analogous scattering in a Galileon system and discover that classicalization also takes place there, although somewhat differently. We thus observe, that classicalization is source-sensitive and that Goldstones pass the first test.
The classic: Bone morphogenetic protein.
Urist, Marshall R; Strates, Basil S
2009-12-01
This Classic Article is a reprint of the original work by Marshall R. Urist and Basil S. Strates, Bone Morphogenetic Protein. An accompanying biographical sketch of Marshall R. Urist, MD is available at DOI 10.1007/s11999-009-1067-4; a second Classic Article is available at DOI 10.1007/s11999-009-1069-2; and a third Classic Article is available at DOI 10.1007/s11999-009-1070-9. The Classic Article is copyright 1971 by Sage Publications Inc. Journals and is reprinted with permission from Urist MR, Strates BS. Bone morphogenetic protein. J Dent Res. 1971;50:1392-1406.
Cai, Kaicong; Zheng, Xuan; Du, Fenfen
2017-08-01
The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.
Energy Technology Data Exchange (ETDEWEB)
Unger, E.; Beck, M.; Lipski, R.J.; Dreybrodt, W.; Medforth, C.J.; Smith, K.M.; Schweitzer-Stenner, R.
1999-11-11
The authors have developed a novel method for molecular mechanics calculations and normal-mode analysis. It is based on symmetry of local units that constitutes the given molecule. Compared with general valence force field calculations, the number of free parameters is reduced by 40--80% in the procedure. It was found to reproduce very well the vibrational frequencies and mode compositions of aromatic compounds and porphyrins, as shown by comparison with DFT calculations. A slightly altered force field obtained from Ni(II) porphin was then used to calculate the structure and the normal modes of several meso-substituted Ni(II) porphyrins which are known to be subject to significant ruffling and/or saddling distortions. This method satisfactorily reproduces their nonplanar structure and Raman band frequencies in the natural abundance and isotopic derivative spectra. The polarization properties of bands from out-of-plane modes are in accordance with the predicted nonplanar distortions. Moreover, some of the modes below 800 cm{sup {minus}1} which appear intense in the Raman spectra contain considerable contributions from both in-plane and out-of-plane vibrations, so that the conventional mode assignments become questionable. The authors also demonstrate that the intensity and polarization of some low-frequency Raman bands can be used as a (quantitative) marker to elucidate type and magnitude of out-of-plane distortions. These were recently shown to affect heme groups of hemoglobin, myoglobin, and, in particular, of cytochrome c.
Choi, Jong-Ha; Niketić, Svetozar R; Djordjević, Ivana; Clegg, William; Harrington, Ross W
2012-05-01
The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N'-diacetate; acac = acetylacetonato) has been determined by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P2(1)/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) Å, β =101.201(9)° and Z = 4. The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) Å while the angles O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N-H···O hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF), capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated on selected chromium(III) complexes with similar ligands.
Eberhardt, Oliver; Wallmersperger, Thomas
2018-03-01
The outstanding properties of carbon nanotubes (CNTs) keep attracting the attention of researchers from different fields. CNTs are promising candidates for applications e.g. in lightweight construction but also in electronics, medicine and many more. The basis for the realization of the manifold applications is a detailed knowledge of the material properties of the carbon nanotubes. In particular for applications in lightweight constructions or in composites, the knowledge of the mechanical behavior of the CNTs is of vital interest. Hence, a lot of effort is put into the experimental and theoretical determination of the mechanical material properties of CNTs. Due to their small size, special techniques have to be applied. In this research, a modified molecular structural mechanics model for the numerical determination of the mechanical behavior of carbon nanotubes is presented. It uses an advanced approach for the geometrical representation of the CNT structure while the covalent bonds in the CNTs are represented by beam elements. Furthermore, the model is specifically designed to overcome major drawbacks in existing molecular structural mechanics models. This includes energetic consistency with the underlying chemical force field. The model is developed further to enable the application of a more advanced chemical force field representation. The developed model is able to predict, inter alia, the lateral and radial stiffness properties of the CNTs. The results for the lateral stiffness are given and discussed in order to emphasize the progress made with the presented approach.
Innovation: the classic traps.
Kanter, Rosabeth Moss
2006-11-01
Never a fad, but always in or out of fashion, innovation gets rediscovered as a growth enabler every half dozen years. Too often, though, grand declarations about innovation are followed by mediocre execution that produces anemic results, and innovation groups are quietly disbanded in cost-cutting drives. Each managerial generation embarks on the same enthusiastic quest for the next new thing. And each generation faces the same vexing challenges- most of which stem from the tensions between protecting existing revenue streams critical to current success and supporting new concepts that may be crucial to future success. In this article, Harvard Business School professor Rosabeth Moss Kanter reflects on the four major waves of innovation enthusiasm she's observed over the past 25 years. She describes the classic mistakes companies make in innovation strategy, process, structure, and skills assessment, illustrating her points with a plethora of real-world examples--including AT&T Worldnet, Timberland, and Ocean Spray. A typical strategic blunder is when managers set their hurdles too high or limit the scope of their innovation efforts. Quaker Oats, for instance, was so busy in the 1990s making minor tweaks to its product formulas that it missed larger opportunities in distribution. A common process mistake is when managers strangle innovation efforts with the same rigid planning, budgeting, and reviewing approaches they use in their existing businesses--thereby discouraging people from adapting as circumstances warrant. Companies must be careful how they structure fledgling entities alongside existing ones, Kanter says, to avoid a clash of cultures and agendas--which Arrow Electronics experienced in its attempts to create an online venture. Finally, companies commonly undervalue and underinvest in the human side of innovation--for instance, promoting individuals out of innovation teams long before their efforts can pay off. Kanter offers practical advice for avoiding
Quantum scattering from classical field theory
International Nuclear Information System (INIS)
Gould, T.M.; Poppitz, E.R.
1995-01-01
We show that scattering amplitudes between initial wave packet states and certain coherent final states can be computed in a systematic weak coupling expansion about classical solutions satisfying initial-value conditions. The initial-value conditions are such as to make the solution of the classical field equations amenable to numerical methods. We propose a practical procedure for computing classical solutions which contribute to high energy two-particle scattering amplitudes. We consider in this regard the implications of a recent numerical simulation in classical SU(2) Yang-Mills theory for multiparticle scattering in quantum gauge theories and speculate on its generalization to electroweak theory. We also generalize our results to the case of complex trajectories and discuss the prospects for finding a solution to the resulting complex boundary value problem, which would allow the application of our method to any wave packet to coherent state transition. Finally, we discuss the relevance of these results to the issues of baryon number violation and multiparticle scattering at high energies. ((orig.))
DEFF Research Database (Denmark)
Gould, Derek A; Chalmers, Nicholas; Johnson, Sheena J
2012-01-01
Recognition of the many limitations of traditional apprenticeship training is driving new approaches to learning medical procedural skills. Among simulation technologies and methods available today, computer-based systems are topical and bring the benefits of automated, repeatable, and reliable p...... performance assessments. Human factors research is central to simulator model development that is relevant to real-world imaging-guided interventional tasks and to the credentialing programs in which it would be used....
A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein
Directory of Open Access Journals (Sweden)
Mingyuan Xu
2018-05-01
Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.
Markthaler, Daniel; Zeman, Johannes; Baz, Jörg; Smiatek, Jens; Hansen, Niels
2017-11-30
Five molecular models for trimethylamine N-oxide (TMAO) to be used in conjunction with compatible models for liquid water are evaluated by comparison of molecular dynamics (MD) simulation results to experimental data as functions of TMAO molality. The experimental data comprise thermodynamic properties (density, apparent molar volume, and partial molar volume at infinite dilution), transport properties (self-diffusion and shear viscosity), structural properties (radial distribution functions and degree of hydrogen bonding), and dielectric properties (dielectric spectra and static permittivity). The thermodynamic and transport properties turned out to be useful in TMAO model discrimination while the influence of the water model and the TMAO-water interaction are effectively probed through the calculation of dielectric spectra.
Czech Academy of Sciences Publication Activity Database
Mlýnský, V.; Kuehrova, P.; Zgarbová, M.; Jurečka, P.; Walter, Nils G.; Otyepka, M.; Šponer, Jiří; Banáš, Pavel
2015-01-01
Roč. 119, č. 11 (2015), s. 4220-4229 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : ACID- BASE CATALYSIS * NUCLEIC-ACIDS * RNA CATALYSIS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015
Classic romance in electronic arrangement
Directory of Open Access Journals (Sweden)
Kizin M.M.
2017-03-01
Full Text Available this article analyses the transformation of the performing arts of classical romance in the terms of electronic sound and performance via electronic sounds arrangements. The author focuses on the problem of synthesis of electronic sound arrangements and classical romance, offering to acquire the skills of the creative process in constantly changing conditions of live performances.
Classical higher-order processes
DEFF Research Database (Denmark)
Montesi, Fabrizio
2017-01-01
Classical Processes (CP) is a calculus where the proof theory of classical linear logic types processes à la Π-calculus, building on a Curry-Howard correspondence between session types and linear propositions. We contribute to this research line by extending CP with process mobility, inspired by ...
COMPETITION: CLASSICAL VERSUS NEOCLASSICAL VIEW
Mihaela Cornelia Sandu
2013-01-01
Competition is an important element from economical theory. Over time it has experienced several definitions and classifications much of them being contradictory. In this paper I will make a parallel between classical and neoclassical point of view according to competition. Keywords. Competition; neoclassical theory; classical theory; monopolistic; perfect competition.
Classical models for Regge trajectories
International Nuclear Information System (INIS)
Biedenharn, L.C.; Van Dam, H.; Marmo, G.; Morandi, G.; Mukunda, N.; Samuel, J.; Sudarshan, E.C.G.
1987-01-01
Two classical models for particles with internal structure and which describe Regge trajectories are developed. The remarkable geometric and other properties of the two internal spaces are highlighted. It is shown that the conditions of positive time-like four-velocity and energy momentum for the classical system imply strong and physically reasonable conditions on the Regge mass-spin relationship
Sum rules in classical scattering
International Nuclear Information System (INIS)
Bolle, D.; Osborn, T.A.
1981-01-01
This paper derives sum rules associated with the classical scattering of two particles. These sum rules are the analogs of Levinson's theorem in quantum mechanics which provides a relationship between the number of bound-state wavefunctions and the energy integral of the time delay of the scattering process. The associated classical relation is an identity involving classical time delay and an integral over the classical bound-state density. We show that equalities between the Nth-order energy moment of the classical time delay and the Nth-order energy moment of the classical bound-state density hold in both a local and a global form. Local sum rules involve the time delay defined on a finite but otherwise arbitrary coordinate space volume S and the bound-state density associated with this same region. Global sum rules are those that obtain when S is the whole coordinate space. Both the local and global sum rules are derived for potentials of arbitrary shape and for scattering in any space dimension. Finally the set of classical sum rules, together with the known quantum mechanical analogs, are shown to provide a unified method of obtaining the high-temperature expansion of the classical, respectively the quantum-mechanical, virial coefficients
'Leonard pairs' in classical mechanics
International Nuclear Information System (INIS)
Zhedanov, Alexei; Korovnichenko, Alyona
2002-01-01
Leonard pairs (LP) are matrices with the property of mutual tri-diagonality. We introduce and study a classical analogue of LP. We show that corresponding classical 'Leonard' dynamical variables satisfy non-linear relations of the AW-type with respect to Poisson brackets. (author)
Quantum mechanics from classical statistics
International Nuclear Information System (INIS)
Wetterich, C.
2010-01-01
Quantum mechanics can emerge from classical statistics. A typical quantum system describes an isolated subsystem of a classical statistical ensemble with infinitely many classical states. The state of this subsystem can be characterized by only a few probabilistic observables. Their expectation values define a density matrix if they obey a 'purity constraint'. Then all the usual laws of quantum mechanics follow, including Heisenberg's uncertainty relation, entanglement and a violation of Bell's inequalities. No concepts beyond classical statistics are needed for quantum physics - the differences are only apparent and result from the particularities of those classical statistical systems which admit a quantum mechanical description. Born's rule for quantum mechanical probabilities follows from the probability concept for a classical statistical ensemble. In particular, we show how the non-commuting properties of quantum operators are associated to the use of conditional probabilities within the classical system, and how a unitary time evolution reflects the isolation of the subsystem. As an illustration, we discuss a classical statistical implementation of a quantum computer.
Classicalization of Gravitons and Goldstones
Dvali, Gia; Kehagias, Alex
2011-01-01
We establish a close parallel between classicalization of gravitons and derivatively-coupled Nambu-Goldstone-type scalars. We show, that black hole formation in high energy scattering process represents classicalization with the classicalization radius given by Schwarzschild radius of center of mass energy, and with the precursor of black hole entropy being given by number of soft quanta composing this classical configuration. Such an entropy-equivalent is defined for scalar classicalons also and is responsible for exponential suppression of their decay into small number of final particles. This parallel works in both ways. For optimists that are willing to hypothesize that gravity may indeed self-unitarize at high energies via black hole formation, it illustrates that the Goldstones may not be much different in this respect, and they classicalize essentially by similar dynamics as gravitons. In the other direction, it may serve as an useful de-mystifier of via-black-hole-unitarization process and of the role...
Classical dynamics a modern perspective
Sudarshan, Ennackal Chandy George
2016-01-01
Classical dynamics is traditionally treated as an early stage in the development of physics, a stage that has long been superseded by more ambitious theories. Here, in this book, classical dynamics is treated as a subject on its own as well as a research frontier. Incorporating insights gained over the past several decades, the essential principles of classical dynamics are presented, while demonstrating that a number of key results originally considered only in the context of quantum theory and particle physics, have their foundations in classical dynamics.Graduate students in physics and practicing physicists will welcome the present approach to classical dynamics that encompasses systems of particles, free and interacting fields, and coupled systems. Lie groups and Lie algebras are incorporated at a basic level and are used in describing space-time symmetry groups. There is an extensive discussion on constrained systems, Dirac brackets and their geometrical interpretation. The Lie-algebraic description of ...
Kutzner, Florian; Vogel, Tobias; Freytag, Peter; Fiedler, Klaus
2011-01-01
In the present research, we argue for the robustness of illusory correlations (ICs, Hamilton & Gifford, 1976) regarding two boundary conditions suggested in previous research. First, we argue that ICs are maintained under extended experience. Using simulations, we derive conflicting predictions. Whereas noise-based accounts predict ICs to be maintained (Fielder, 2000; Smith, 1991), a prominent account based on discrepancy-reducing feedback learning predicts ICs to disappear (Van Rooy et al., 2003). An experiment involving 320 observations with majority and minority members supports the claim that ICs are maintained. Second, we show that actively using the stereotype to make predictions that are met with reward and punishment does not eliminate the bias. In addition, participants' operant reactions afford a novel online measure of ICs. In sum, our findings highlight the robustness of ICs that can be explained as a result of unbiased but noisy learning.
Ross, Sheldon
2006-01-01
Ross's Simulation, Fourth Edition introduces aspiring and practicing actuaries, engineers, computer scientists and others to the practical aspects of constructing computerized simulation studies to analyze and interpret real phenomena. Readers learn to apply results of these analyses to problems in a wide variety of fields to obtain effective, accurate solutions and make predictions about future outcomes. This text explains how a computer can be used to generate random numbers, and how to use these random numbers to generate the behavior of a stochastic model over time. It presents the statist
Vortex rings in classical and quantum systems
International Nuclear Information System (INIS)
Barenghi, C F; Donnelly, R J
2009-01-01
The study of vortex rings has been pursued for decades and is a particularly difficult subject. However, the discovery of quantized vortex rings in superfluid helium has greatly increased interest in vortex rings with very thin cores. While rapid progress has been made in the simulation of quantized vortex rings, there has not been comparable progress in laboratory studies of vortex rings in a viscous fluid such as water. This article overviews the history and current frontiers of classical and quantum vortex rings. After introducing the classical results, this review discusses thin-cored vortex rings in superfluid helium in section 2, and recent progress in understanding vortex rings of very thin cores propagating in water in section 3. (invited paper)
Simultaneous classical communication and quantum key distribution using continuous variables*
Qi, Bing
2016-10-01
Presently, classical optical communication systems employing strong laser pulses and quantum key distribution (QKD) systems working at single-photon levels are very different communication modalities. Dedicated devices are commonly required to implement QKD. In this paper, we propose a scheme which allows classical communication and QKD to be implemented simultaneously using the same communication infrastructure. More specially, we propose a coherent communication scheme where both the bits for classical communication and the Gaussian distributed random numbers for QKD are encoded on the same weak coherent pulse and decoded by the same coherent receiver. Simulation results based on practical system parameters show that both deterministic classical communication with a bit error rate of 10-9 and secure key distribution could be achieved over tens of kilometers of single-mode fibers. It is conceivable that in the future coherent optical communication network, QKD will be operated in the background of classical communication at a minimal cost.
DEFF Research Database (Denmark)
Bieniasz, Leslaw K.; Østerby, Ole; Britz, Dieter
1995-01-01
The stepwise numerical stability of the classic explicit, fully implicit and Crank-Nicolson finite difference discretizations of example diffusional initial boundary value problems from electrochemical kinetics has been investigated using the matrix method of stability analysis. Special attention...... has been paid to the effect of the discretization of the mixed, linear boundary condition with time-dependent coefficients on stability, assuming the two-point forward-difference approximations for the gradient at the left boundary (electrode). Under accepted assumptions one obtains the usual...... stability criteria for the classic explicit and fully implicit methods. The Crank-Nicolson method turns out to be only conditionally stable in contrast to the current thought regarding this method....
Hybrid Quantum-Classical Approach to Quantum Optimal Control.
Li, Jun; Yang, Xiaodong; Peng, Xinhua; Sun, Chang-Pu
2017-04-14
A central challenge in quantum computing is to identify more computational problems for which utilization of quantum resources can offer significant speedup. Here, we propose a hybrid quantum-classical scheme to tackle the quantum optimal control problem. We show that the most computationally demanding part of gradient-based algorithms, namely, computing the fitness function and its gradient for a control input, can be accomplished by the process of evolution and measurement on a quantum simulator. By posing queries to and receiving answers from the quantum simulator, classical computing devices update the control parameters until an optimal control solution is found. To demonstrate the quantum-classical scheme in experiment, we use a seven-qubit nuclear magnetic resonance system, on which we have succeeded in optimizing state preparation without involving classical computation of the large Hilbert space evolution.
Loire Classics: Reviving Classicism in some Loire Poets
Directory of Open Access Journals (Sweden)
Wim Verbaal
2017-06-01
Full Text Available The term 'Loire poets' has come to refer to a rather undefinable group of poets that in the second half of the eleventh century distinguishes itself through its refined poetics. They are often characterized as medieval humanists thanks to their renewed interest in the classics. Sometimes their movement is labelled a 'classicist' one. But what does this 'classicism' mean? Is it even permitted to speak of medieval 'classicisms'? This contribution approaches the question of whether we can apply this modern label to pre-modern phenomena. Moreover, it explores the changes in attitude towards the classics that sets the Loire poets off from their predecessors and contemporaries. The article focuses on poems by Hildebert of Lavardin, Baudri of Bourgueil, Marbod of Rennes, and Geoffrey of Reims. They are compared with some contemporary poets, such as Reginald of Canterbury and Sigebert of Gembloux.
Steffen, Julien; Hartke, Bernd
2017-10-28
Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.
The Wigner representation of classical mechanics, quantization and classical limit
International Nuclear Information System (INIS)
Bolivar, A.O.
2001-08-01
Starting from the Liouvillian formulation of classical physics it is possible by means of a Fourier transform to introduce the Wigner representation and to derive an operator structure to classical mechanisms. The importance of this new representation lies on the fact that it turns out to be suitable route to establish a general method of quantization directly from the equations of motion without alluding to the existence of Hamiltonian and Lagrangian functions. Following this approach we quantize only the motion of a Browian particle with non-linear friction in the Markovian approximation - the thermal bath may be quantum or classical -, thus when the bath is classically described we obtain a master equation which reduces to Caldeira-Legget equation for the linear friction case, and when the reservoir is quantum we get an equation reducing to the one found by Caldeira et al. By neglecting the environmental influence we show that the system can be approximately described by equations of motion in terms of wave function, such as the Schrodinger-Langevin equation and equations of the Caldirola-Kanai type. Finally to make the present study self-consistent we evaluate the classical limit of these dynamical equations employing a new classical limiting method h/2π → 0. (author)
The Wigner representation of classical mechanics, quantization and classical limit
Energy Technology Data Exchange (ETDEWEB)
Bolivar, A.O. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)
2001-08-01
Starting from the Liouvillian formulation of classical physics it is possible by means of a Fourier transform to introduce the Wigner representation and to derive an operator structure to classical mechanisms. The importance of this new representation lies on the fact that it turns out to be suitable route to establish a general method of quantization directly from the equations of motion without alluding to the existence of Hamiltonian and Lagrangian functions. Following this approach we quantize only the motion of a Browian particle with non-linear friction in the Markovian approximation - the thermal bath may be quantum or classical -, thus when the bath is classically described we obtain a master equation which reduces to Caldeira-Legget equation for the linear friction case, and when the reservoir is quantum we get an equation reducing to the one found by Caldeira et al. By neglecting the environmental influence we show that the system can be approximately described by equations of motion in terms of wave function, such as the Schrodinger-Langevin equation and equations of the Caldirola-Kanai type. Finally to make the present study self-consistent we evaluate the classical limit of these dynamical equations employing a new classical limiting method h/2{pi} {yields} 0. (author)
Mathematical methods of classical physics
Cortés, Vicente
2017-01-01
This short primer, geared towards students with a strong interest in mathematically rigorous approaches, introduces the essentials of classical physics, briefly points out its place in the history of physics and its relation to modern physics, and explains what benefits can be gained from a mathematical perspective. As a starting point, Newtonian mechanics is introduced and its limitations are discussed. This leads to and motivates the study of different formulations of classical mechanics, such as Lagrangian and Hamiltonian mechanics, which are the subjects of later chapters. In the second part, a chapter on classical field theories introduces more advanced material. Numerous exercises are collected in the appendix.
Classicality of quantum information processing
International Nuclear Information System (INIS)
Poulin, David
2002-01-01
The ultimate goal of the classicality program is to quantify the amount of quantumness of certain processes. Here, classicality is studied for a restricted type of process: quantum information processing (QIP). Under special conditions, one can force some qubits of a quantum computer into a classical state without affecting the outcome of the computation. The minimal set of conditions is described and its structure is studied. Some implications of this formalism are the increase of noise robustness, a proof of the quantumness of mixed state quantum computing, and a step forward in understanding the very foundation of QIP